9FQ8 | pdb_00009fq8

Perkinsus marinus Respiratory complex CIV

PDB DOI: https://doi.org/10.2210/pdb9FQ8/pdb
EM Map EMD-50363: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Perkinsus marinus
Mutation(s): No

Deposited: 2024-06-14 Released: 2025-06-25
Deposition Author(s): Wu, F., Amunts, A.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of the II2-III2-IV2 mitochondrial supercomplex from the parasite Perkinsus marinus

Wu, F., Muhleip, A., Gruhl, T., Sheiner, L., Marechal, A., Amunts, A.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2024.05.25.595893

Macromolecule Content

Total Structure Weight: 451.68 kDa
Atom Count: 31,410
Modeled Residue Count: 3,569
Deposited Residue Count: 3,569
Unique protein chains: 26

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6B	A [auth 4A]	100	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5K7H0 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5K7H0 Go to UniProtKB: C5K7H0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C5K7H0
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase M14 carboxypeptidase A domain-containing protein	B [auth 4B]	93	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5KED7 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5KED7 Go to UniProtKB: C5KED7
Entity Groups
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UniProt Group	C5KED7
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 40	C [auth 4C]	75	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5L7H1 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5L7H1 Go to UniProtKB: C5L7H1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C5L7H1
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 34	D [auth 4D]	90	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LUF4 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LUF4 Go to UniProtKB: C5LUF4
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UniProt Group	C5LUF4
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Merozoite surface protein, putative	E [auth 4E]	152	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5L0U1 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5L0U1 Go to UniProtKB: C5L0U1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C5L0U1
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin, putative	F [auth 4F]	80	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5KBY9 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5KBY9 Go to UniProtKB: C5KBY9
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UniProt Group	C5KBY9
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 33	G [auth 4G]	100	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5KJE7 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5KJE7 Go to UniProtKB: C5KJE7
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UniProt Group	C5KJE7
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 30	H [auth 4H]	141	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5L104 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5L104 Go to UniProtKB: C5L104
Entity Groups
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UniProt Group	C5L104
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6C	I [auth 4I]	196	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LPW2 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LPW2 Go to UniProtKB: C5LPW2
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UniProt Group	C5LPW2
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 24	J [auth 4J]	186	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5L533 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5L533 Go to UniProtKB: C5L533
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UniProt Group	C5L533
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 37	K [auth 4K]	93	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5KST9 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5KST9 Go to UniProtKB: C5KST9
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UniProt Group	C5KST9
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7A	L [auth 4L]	122	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5KPD1 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5KPD1 Go to UniProtKB: C5KPD1
Entity Groups
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UniProt Group	C5KPD1
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 35	M [auth 4M]	99	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LDS7 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LDS7 Go to UniProtKB: C5LDS7
Entity Groups
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UniProt Group	C5LDS7
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase polypeptide II	N [auth 4N]	131	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5K5E4 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5K5E4 Go to UniProtKB: C5K5E4
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UniProt Group	C5K5E4
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
GINS subunit domain-containing protein	O [auth 4O]	47	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LG07 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LG07 Go to UniProtKB: C5LG07
Entity Groups
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UniProt Group	C5LG07
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome oxidase subunit II copper A binding domain-containing protein	P [auth 4P]	180	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LK31 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LK31 Go to UniProtKB: C5LK31
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UniProt Group	C5LK31
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	Q [auth 4Q]	459	Perkinsus marinus	Mutation(s): 0 EC: 7.1.1.9
UniProt
Find proteins for F8SRI9 (Perkinsus marinus ATCC 50439) Explore F8SRI9 Go to UniProtKB: F8SRI9
Entity Groups
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UniProt Group	F8SRI9
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 32	R [auth 4R]	103	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5KSX3 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5KSX3 Go to UniProtKB: C5KSX3
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UniProt Group	C5KSX3
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7C	S [auth 4S]	65	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5L3V7 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5L3V7 Go to UniProtKB: C5L3V7
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UniProt Group	C5L3V7
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase 13	T [auth 4T]	121	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5K4P8 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5K4P8 Go to UniProtKB: C5K4P8
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UniProt Group	C5K4P8
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid transporter transmembrane domain-containing protein	U [auth 4U]	91	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LG64 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LG64 Go to UniProtKB: C5LG64
Entity Groups
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UniProt Group	C5LG64
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Reference Sequence

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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Cg8 protein	V [auth 4V]	185	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LR54 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LR54 Go to UniProtKB: C5LR54
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UniProt Group	C5LR54
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Reference Sequence

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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 19	W [auth 4W]	141	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5L0W2 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5L0W2 Go to UniProtKB: C5L0W2
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UniProt Group	C5L0W2
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Reference Sequence

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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome Coxidase subunit, putative	X [auth 4X]	226	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LUB2 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LUB2 Go to UniProtKB: C5LUB2
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UniProt Group	C5LUB2
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Reference Sequence

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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 18	Y [auth 4Y]	107	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LUI5 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LUI5 Go to UniProtKB: C5LUI5
Entity Groups
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UniProt Group	C5LUI5
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 31	Z [auth 4Z]	186	Perkinsus marinus	Mutation(s): 0
UniProt
Find proteins for C5LYX8 (Perkinsus marinus (strain ATCC 50983 / TXsc)) Explore C5LYX8 Go to UniProtKB: C5LYX8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C5LYX8
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Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL (Subject of Investigation/LOI) Query on CDL Download Ideal Coordinates CCD File SDF format, chain BB [auth 4S] SDF format, chain DA [auth 4E] SDF format, chain EA [auth 4E] SDF format, chain EB [auth 4U] SDF format, chain GA [auth 4F] SDF format, chain GB [auth 4W] SDF format, chain IA [auth 4J] SDF format, chain JA [auth 4K] SDF format, chain KB [auth 4Z] SDF format, chain LA [auth 4L] SDF format, chain MA [auth 4M] SDF format, chain OA [auth 4O] SDF format, chain RA [auth 4Q] SDF format, chain SA [auth 4Q] MOL2 format, chain BB [auth 4S] MOL2 format, chain DA [auth 4E] MOL2 format, chain EA [auth 4E] MOL2 format, chain EB [auth 4U] MOL2 format, chain GA [auth 4F] MOL2 format, chain GB [auth 4W] MOL2 format, chain IA [auth 4J] MOL2 format, chain JA [auth 4K] MOL2 format, chain KB [auth 4Z] MOL2 format, chain LA [auth 4L] MOL2 format, chain MA [auth 4M] MOL2 format, chain OA [auth 4O] MOL2 format, chain RA [auth 4Q] MOL2 format, chain SA [auth 4Q] mmCIF format, chain BB [auth 4S] mmCIF format, chain DA [auth 4E] mmCIF format, chain EA [auth 4E] mmCIF format, chain EB [auth 4U] mmCIF format, chain GA [auth 4F] mmCIF format, chain GB [auth 4W] mmCIF format, chain IA [auth 4J] mmCIF format, chain JA [auth 4K] mmCIF format, chain KB [auth 4Z] mmCIF format, chain LA [auth 4L] mmCIF format, chain MA [auth 4M] mmCIF format, chain OA [auth 4O] mmCIF format, chain RA [auth 4Q] mmCIF format, chain SA [auth 4Q]	BB [auth 4S] DA [auth 4E] EA [auth 4E] EB [auth 4U] GA [auth 4F] BB [auth 4S], DA [auth 4E], EA [auth 4E], EB [auth 4U], GA [auth 4F], GB [auth 4W], IA [auth 4J], JA [auth 4K], KB [auth 4Z], LA [auth 4L], MA [auth 4M], OA [auth 4O], RA [auth 4Q], SA [auth 4Q]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain BB [auth 4S] Focus chain DA [auth 4E] Focus chain EA [auth 4E] Focus chain EB [auth 4U] Focus chain GA [auth 4F] Focus chain GB [auth 4W] Focus chain IA [auth 4J] Focus chain JA [auth 4K] Focus chain KB [auth 4Z] Focus chain LA [auth 4L] Focus chain MA [auth 4M] Focus chain OA [auth 4O] Focus chain RA [auth 4Q] Focus chain SA [auth 4Q] Interactions & Density Focus chain BB [auth 4S] Focus chain DA [auth 4E] Focus chain EA [auth 4E] Focus chain EB [auth 4U] Focus chain GA [auth 4F] Focus chain GB [auth 4W] Focus chain IA [auth 4J] Focus chain JA [auth 4K] Focus chain KB [auth 4Z] Focus chain LA [auth 4L] Focus chain MA [auth 4M] Focus chain OA [auth 4O] Focus chain RA [auth 4Q] Focus chain SA [auth 4Q]
HEA (Subject of Investigation/LOI) Query on HEA Download Ideal Coordinates CCD File SDF format, chain WA [auth 4Q] SDF format, chain XA [auth 4Q] MOL2 format, chain WA [auth 4Q] MOL2 format, chain XA [auth 4Q] mmCIF format, chain WA [auth 4Q] mmCIF format, chain XA [auth 4Q]	WA [auth 4Q], XA [auth 4Q]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain WA [auth 4Q] Focus chain XA [auth 4Q] Interactions & Density Focus chain WA [auth 4Q] Focus chain XA [auth 4Q]
PC1 (Subject of Investigation/LOI) Query on PC1 Download Ideal Coordinates CCD File SDF format, chain FA [auth 4F] MOL2 format, chain FA [auth 4F] mmCIF format, chain FA [auth 4F]	FA [auth 4F]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain FA [auth 4F] Interactions & Density Focus chain FA [auth 4F]
PEE (Subject of Investigation/LOI) Query on PEE Download Ideal Coordinates CCD File SDF format, chain AB [auth 4S] SDF format, chain BA [auth 4D] SDF format, chain CA [auth 4E] SDF format, chain FB [auth 4W] SDF format, chain HA [auth 4G] SDF format, chain JB [auth 4Z] SDF format, chain KA [auth 4L] SDF format, chain PA [auth 4Q] SDF format, chain QA [auth 4Q] SDF format, chain ZA [auth 4R] MOL2 format, chain AB [auth 4S] MOL2 format, chain BA [auth 4D] MOL2 format, chain CA [auth 4E] MOL2 format, chain FB [auth 4W] MOL2 format, chain HA [auth 4G] MOL2 format, chain JB [auth 4Z] MOL2 format, chain KA [auth 4L] MOL2 format, chain PA [auth 4Q] MOL2 format, chain QA [auth 4Q] MOL2 format, chain ZA [auth 4R] mmCIF format, chain AB [auth 4S] mmCIF format, chain BA [auth 4D] mmCIF format, chain CA [auth 4E] mmCIF format, chain FB [auth 4W] mmCIF format, chain HA [auth 4G] mmCIF format, chain JB [auth 4Z] mmCIF format, chain KA [auth 4L] mmCIF format, chain PA [auth 4Q] mmCIF format, chain QA [auth 4Q] mmCIF format, chain ZA [auth 4R]	AB [auth 4S] BA [auth 4D] CA [auth 4E] FB [auth 4W] HA [auth 4G] AB [auth 4S], BA [auth 4D], CA [auth 4E], FB [auth 4W], HA [auth 4G], JB [auth 4Z], KA [auth 4L], PA [auth 4Q], QA [auth 4Q], ZA [auth 4R]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain AB [auth 4S] Focus chain BA [auth 4D] Focus chain CA [auth 4E] Focus chain FB [auth 4W] Focus chain HA [auth 4G] Focus chain JB [auth 4Z] Focus chain KA [auth 4L] Focus chain PA [auth 4Q] Focus chain QA [auth 4Q] Focus chain ZA [auth 4R] Interactions & Density Focus chain AB [auth 4S] Focus chain BA [auth 4D] Focus chain CA [auth 4E] Focus chain FB [auth 4W] Focus chain HA [auth 4G] Focus chain JB [auth 4Z] Focus chain KA [auth 4L] Focus chain PA [auth 4Q] Focus chain QA [auth 4Q] Focus chain ZA [auth 4R]
LPP (Subject of Investigation/LOI) Query on LPP Download Ideal Coordinates CCD File SDF format, chain AA [auth 4C] SDF format, chain IB [auth 4Z] MOL2 format, chain AA [auth 4C] MOL2 format, chain IB [auth 4Z] mmCIF format, chain AA [auth 4C] mmCIF format, chain IB [auth 4Z]	AA [auth 4C], IB [auth 4Z]	2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE C₃₅ H₆₉ O₈ P PORPENFLTBBHSG-MGBGTMOVSA-N		Interactions Focus chain AA [auth 4C] Focus chain IB [auth 4Z] Interactions & Density Focus chain AA [auth 4C] Focus chain IB [auth 4Z]
CUA (Subject of Investigation/LOI) Query on CUA Download Ideal Coordinates CCD File SDF format, chain NA [auth 4N] MOL2 format, chain NA [auth 4N] mmCIF format, chain NA [auth 4N]	NA [auth 4N]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain NA [auth 4N] Interactions & Density Focus chain NA [auth 4N]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain CB [auth 4T] SDF format, chain DB [auth 4T] SDF format, chain HB [auth 4X] MOL2 format, chain CB [auth 4T] MOL2 format, chain DB [auth 4T] MOL2 format, chain HB [auth 4X] mmCIF format, chain CB [auth 4T] mmCIF format, chain DB [auth 4T] mmCIF format, chain HB [auth 4X]	CB [auth 4T], DB [auth 4T], HB [auth 4X]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CB [auth 4T] Focus chain DB [auth 4T] Focus chain HB [auth 4X] Interactions & Density Focus chain CB [auth 4T] Focus chain DB [auth 4T] Focus chain HB [auth 4X]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain UA [auth 4Q] MOL2 format, chain UA [auth 4Q] mmCIF format, chain UA [auth 4Q]	UA [auth 4Q]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain UA [auth 4Q] Interactions & Density Focus chain UA [auth 4Q]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain TA [auth 4Q] MOL2 format, chain TA [auth 4Q] mmCIF format, chain TA [auth 4Q]	TA [auth 4Q]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain TA [auth 4Q] Interactions & Density Focus chain TA [auth 4Q]
PER (Subject of Investigation/LOI) Query on PER Download Ideal Coordinates CCD File SDF format, chain YA [auth 4Q] MOL2 format, chain YA [auth 4Q] mmCIF format, chain YA [auth 4Q]	YA [auth 4Q]	PEROXIDE ION O₂ ANAIPYUSIMHBEL-UHFFFAOYSA-N		Interactions Focus chain YA [auth 4Q] Interactions & Density Focus chain YA [auth 4Q]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain VA [auth 4Q] MOL2 format, chain VA [auth 4Q] mmCIF format, chain VA [auth 4Q]	VA [auth 4Q]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain VA [auth 4Q] Interactions & Density Focus chain VA [auth 4Q]