9FKS | pdb_00009fks

Respiratory supercomplex CIII2-CIV2 from alphaproteobacterium

PDB DOI: https://doi.org/10.2210/pdb9FKS/pdb
EM Map EMD-50526: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Paracoccus denitrificans PD1222
Mutation(s): No

Deposited: 2024-06-04 Released: 2025-12-17
Deposition Author(s): Yaikhomba, M., Hirst, J., Croll, T.I., Spikes, T.E., Agip, A.N.A.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.31 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Minimal supercomplexes in alphaproteobacteria reveal conserved structural mechanisms for efficient respiration

Yaikhomba, M., Hirst, J., Croll, T.I., Spikes, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 583.83 kDa
Atom Count: 34,791
Modeled Residue Count: 4,019
Deposited Residue Count: 4,914
Unique protein chains: 8

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	A [auth a], D [auth d]	440	Paracoccus denitrificans PD1222	Mutation(s): 0
UniProt
Find proteins for A1B4F3 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B4F3 Go to UniProtKB: A1B4F3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1B4F3
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1	B [auth b], E [auth e]	450	Paracoccus denitrificans PD1222	Mutation(s): 0
UniProt
Find proteins for A1B4F4 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B4F4 Go to UniProtKB: A1B4F4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1B4F4
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome c reductase iron-sulfur subunit	C [auth c], F [auth f]	195	Paracoccus denitrificans PD1222	Mutation(s): 0 EC: 7.1.1.8
UniProt
Find proteins for A1B4F2 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B4F2 Go to UniProtKB: A1B4F2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1B4F2
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	G [auth g], K [auth k]	558	Paracoccus denitrificans PD1222	Mutation(s): 0 EC: 7.1.1.9
UniProt
Find proteins for A1B3D7 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B3D7 Go to UniProtKB: A1B3D7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1B3D7
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	H [auth h], L [auth l]	298	Paracoccus denitrificans PD1222	Mutation(s): 0 EC: 7.1.1.9
UniProt
Find proteins for A1BA41 (Paracoccus denitrificans (strain Pd 1222)) Explore A1BA41 Go to UniProtKB: A1BA41
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1BA41
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
cytochrome-c oxidase	I [auth i], M [auth m]	274	Paracoccus denitrificans PD1222	Mutation(s): 0 EC: 7.1.1.9
UniProt
Find proteins for A1BA37 (Paracoccus denitrificans (strain Pd 1222)) Explore A1BA37 Go to UniProtKB: A1BA37
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1BA37
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Aa3 type cytochrome c oxidase subunit IV	J [auth j], N [auth n]	66	Paracoccus denitrificans PD1222	Mutation(s): 0
UniProt
Find proteins for A1AZ52 (Paracoccus denitrificans (strain Pd 1222)) Explore A1AZ52 Go to UniProtKB: A1AZ52
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1AZ52
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c, class I	O [auth o], P [auth p]	176	Paracoccus denitrificans PD1222	Mutation(s): 0
UniProt
Find proteins for A1B311 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B311 Go to UniProtKB: A1B311
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1B311
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 15 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain EA [auth d] MOL2 format, chain EA [auth d] mmCIF format, chain EA [auth d]	EA [auth d]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain EA [auth d] Interactions & Density Focus chain EA [auth d]
U10 (Subject of Investigation/LOI) Query on U10 Download Ideal Coordinates CCD File SDF format, chain JA [auth d] SDF format, chain LA [auth d] SDF format, chain R [auth a] SDF format, chain V [auth a] MOL2 format, chain JA [auth d] MOL2 format, chain LA [auth d] MOL2 format, chain R [auth a] MOL2 format, chain V [auth a] mmCIF format, chain JA [auth d] mmCIF format, chain LA [auth d] mmCIF format, chain R [auth a] mmCIF format, chain V [auth a]	JA [auth d], LA [auth d], R [auth a], V [auth a]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain JA [auth d] Focus chain LA [auth d] Focus chain R [auth a] Focus chain V [auth a] Interactions & Density Focus chain JA [auth d] Focus chain LA [auth d] Focus chain R [auth a] Focus chain V [auth a]
HEA (Subject of Investigation/LOI) Query on HEA Download Ideal Coordinates CCD File SDF format, chain XA [auth g] SDF format, chain ZA [auth g] SDF format, chain SB [auth k] SDF format, chain NB [auth k] MOL2 format, chain XA [auth g] MOL2 format, chain ZA [auth g] MOL2 format, chain SB [auth k] MOL2 format, chain NB [auth k] mmCIF format, chain XA [auth g] mmCIF format, chain ZA [auth g] mmCIF format, chain SB [auth k] mmCIF format, chain NB [auth k]	NB [auth k], SB [auth k], XA [auth g], ZA [auth g]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain NB [auth k] Focus chain SB [auth k] Focus chain XA [auth g] Focus chain ZA [auth g] Interactions & Density Focus chain NB [auth k] Focus chain SB [auth k] Focus chain XA [auth g] Focus chain ZA [auth g]
PC1 Query on PC1 Download Ideal Coordinates CCD File SDF format, chain CC [auth m] SDF format, chain FB [auth i] SDF format, chain FC [auth m] SDF format, chain GA [auth d] SDF format, chain JB [auth i] SDF format, chain KC [auth n] SDF format, chain LC [auth o] SDF format, chain MB [auth j] SDF format, chain Q [auth a] SDF format, chain W [auth b] SDF format, chain YB [auth m] SDF format, chain S [auth a] MOL2 format, chain CC [auth m] MOL2 format, chain FB [auth i] MOL2 format, chain FC [auth m] MOL2 format, chain GA [auth d] MOL2 format, chain JB [auth i] MOL2 format, chain KC [auth n] MOL2 format, chain LC [auth o] MOL2 format, chain MB [auth j] MOL2 format, chain Q [auth a] MOL2 format, chain W [auth b] MOL2 format, chain YB [auth m] MOL2 format, chain S [auth a] mmCIF format, chain CC [auth m] mmCIF format, chain FB [auth i] mmCIF format, chain FC [auth m] mmCIF format, chain GA [auth d] mmCIF format, chain JB [auth i] mmCIF format, chain KC [auth n] mmCIF format, chain LC [auth o] mmCIF format, chain MB [auth j] mmCIF format, chain Q [auth a] mmCIF format, chain W [auth b] mmCIF format, chain YB [auth m] mmCIF format, chain S [auth a]	CC [auth m] FB [auth i] FC [auth m] GA [auth d] JB [auth i] CC [auth m], FB [auth i], FC [auth m], GA [auth d], JB [auth i], KC [auth n], LC [auth o], MB [auth j], Q [auth a], S [auth a], W [auth b], YB [auth m]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain CC [auth m] Focus chain FB [auth i] Focus chain FC [auth m] Focus chain GA [auth d] Focus chain JB [auth i] Focus chain KC [auth n] Focus chain LC [auth o] Focus chain MB [auth j] Focus chain Q [auth a] Focus chain S [auth a] Focus chain W [auth b] Focus chain YB [auth m] Interactions & Density Focus chain CC [auth m] Focus chain FB [auth i] Focus chain FC [auth m] Focus chain GA [auth d] Focus chain JB [auth i] Focus chain KC [auth n] Focus chain LC [auth o] Focus chain MB [auth j] Focus chain Q [auth a] Focus chain S [auth a] Focus chain W [auth b] Focus chain YB [auth m]
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain AC [auth m] SDF format, chain BB [auth g] SDF format, chain BC [auth m] SDF format, chain DC [auth m] SDF format, chain HB [auth i] SDF format, chain JC [auth n] SDF format, chain KB [auth i] SDF format, chain LB [auth i] SDF format, chain NA [auth e] SDF format, chain QA [auth e] SDF format, chain UB [auth k] SDF format, chain Z [auth c] SDF format, chain IC [auth m] MOL2 format, chain AC [auth m] MOL2 format, chain BB [auth g] MOL2 format, chain BC [auth m] MOL2 format, chain DC [auth m] MOL2 format, chain HB [auth i] MOL2 format, chain JC [auth n] MOL2 format, chain KB [auth i] MOL2 format, chain LB [auth i] MOL2 format, chain NA [auth e] MOL2 format, chain QA [auth e] MOL2 format, chain UB [auth k] MOL2 format, chain Z [auth c] MOL2 format, chain IC [auth m] mmCIF format, chain AC [auth m] mmCIF format, chain BB [auth g] mmCIF format, chain BC [auth m] mmCIF format, chain DC [auth m] mmCIF format, chain HB [auth i] mmCIF format, chain JC [auth n] mmCIF format, chain KB [auth i] mmCIF format, chain LB [auth i] mmCIF format, chain NA [auth e] mmCIF format, chain QA [auth e] mmCIF format, chain UB [auth k] mmCIF format, chain Z [auth c] mmCIF format, chain IC [auth m]	AC [auth m] BB [auth g] BC [auth m] DC [auth m] HB [auth i] AC [auth m], BB [auth g], BC [auth m], DC [auth m], HB [auth i], IC [auth m], JC [auth n], KB [auth i], LB [auth i], NA [auth e], QA [auth e], UB [auth k], Z [auth c]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain AC [auth m] Focus chain BB [auth g] Focus chain BC [auth m] Focus chain DC [auth m] Focus chain HB [auth i] Focus chain IC [auth m] Focus chain JC [auth n] Focus chain KB [auth i] Focus chain LB [auth i] Focus chain NA [auth e] Focus chain QA [auth e] Focus chain UB [auth k] Focus chain Z [auth c] Interactions & Density Focus chain AC [auth m] Focus chain BB [auth g] Focus chain BC [auth m] Focus chain DC [auth m] Focus chain HB [auth i] Focus chain IC [auth m] Focus chain JC [auth n] Focus chain KB [auth i] Focus chain LB [auth i] Focus chain NA [auth e] Focus chain QA [auth e] Focus chain UB [auth k] Focus chain Z [auth c]
3PH (Subject of Investigation/LOI) Query on 3PH Download Ideal Coordinates CCD File SDF format, chain DA [auth c] SDF format, chain GB [auth i] SDF format, chain KA [auth d] SDF format, chain MC [auth p] SDF format, chain OB [auth k] SDF format, chain VA [auth g] SDF format, chain WB [auth m] SDF format, chain XB [auth m] SDF format, chain ZB [auth m] SDF format, chain UA [auth f] MOL2 format, chain DA [auth c] MOL2 format, chain GB [auth i] MOL2 format, chain KA [auth d] MOL2 format, chain MC [auth p] MOL2 format, chain OB [auth k] MOL2 format, chain VA [auth g] MOL2 format, chain WB [auth m] MOL2 format, chain XB [auth m] MOL2 format, chain ZB [auth m] MOL2 format, chain UA [auth f] mmCIF format, chain DA [auth c] mmCIF format, chain GB [auth i] mmCIF format, chain KA [auth d] mmCIF format, chain MC [auth p] mmCIF format, chain OB [auth k] mmCIF format, chain VA [auth g] mmCIF format, chain WB [auth m] mmCIF format, chain XB [auth m] mmCIF format, chain ZB [auth m] mmCIF format, chain UA [auth f]	DA [auth c] GB [auth i] KA [auth d] MC [auth p] OB [auth k] DA [auth c], GB [auth i], KA [auth d], MC [auth p], OB [auth k], UA [auth f], VA [auth g], WB [auth m], XB [auth m], ZB [auth m]	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE C₃₉ H₇₇ O₈ P YFWHNAWEOZTIPI-DIPNUNPCSA-N		Interactions Focus chain DA [auth c] Focus chain GB [auth i] Focus chain KA [auth d] Focus chain MC [auth p] Focus chain OB [auth k] Focus chain UA [auth f] Focus chain VA [auth g] Focus chain WB [auth m] Focus chain XB [auth m] Focus chain ZB [auth m] Interactions & Density Focus chain DA [auth c] Focus chain GB [auth i] Focus chain KA [auth d] Focus chain MC [auth p] Focus chain OB [auth k] Focus chain UA [auth f] Focus chain VA [auth g] Focus chain WB [auth m] Focus chain XB [auth m] Focus chain ZB [auth m]
HEC (Subject of Investigation/LOI) Query on HEC Download Ideal Coordinates CCD File SDF format, chain PA [auth e] SDF format, chain Y [auth b] MOL2 format, chain PA [auth e] MOL2 format, chain Y [auth b] mmCIF format, chain PA [auth e] mmCIF format, chain Y [auth b]	PA [auth e], Y [auth b]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain PA [auth e] Focus chain Y [auth b] Interactions & Density Focus chain PA [auth e] Focus chain Y [auth b]
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain IA [auth d] SDF format, chain U [auth a] SDF format, chain T [auth a] SDF format, chain HA [auth d] MOL2 format, chain IA [auth d] MOL2 format, chain U [auth a] MOL2 format, chain T [auth a] MOL2 format, chain HA [auth d] mmCIF format, chain IA [auth d] mmCIF format, chain U [auth a] mmCIF format, chain T [auth a] mmCIF format, chain HA [auth d]	HA [auth d], IA [auth d], T [auth a], U [auth a]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain HA [auth d] Focus chain IA [auth d] Focus chain T [auth a] Focus chain U [auth a] Interactions & Density Focus chain HA [auth d] Focus chain IA [auth d] Focus chain T [auth a] Focus chain U [auth a]
DU0 Query on DU0 Download Ideal Coordinates CCD File SDF format, chain AA [auth c] SDF format, chain BA [auth c] SDF format, chain EB [auth i] SDF format, chain FA [auth d] SDF format, chain HC [auth m] SDF format, chain MA [auth d] SDF format, chain RA [auth f] SDF format, chain RB [auth k] SDF format, chain TA [auth f] SDF format, chain GC [auth m] SDF format, chain DB [auth i] MOL2 format, chain AA [auth c] MOL2 format, chain BA [auth c] MOL2 format, chain EB [auth i] MOL2 format, chain FA [auth d] MOL2 format, chain HC [auth m] MOL2 format, chain MA [auth d] MOL2 format, chain RA [auth f] MOL2 format, chain RB [auth k] MOL2 format, chain TA [auth f] MOL2 format, chain GC [auth m] MOL2 format, chain DB [auth i] mmCIF format, chain AA [auth c] mmCIF format, chain BA [auth c] mmCIF format, chain EB [auth i] mmCIF format, chain FA [auth d] mmCIF format, chain HC [auth m] mmCIF format, chain MA [auth d] mmCIF format, chain RA [auth f] mmCIF format, chain RB [auth k] mmCIF format, chain TA [auth f] mmCIF format, chain GC [auth m] mmCIF format, chain DB [auth i]	AA [auth c] BA [auth c] DB [auth i] EB [auth i] FA [auth d] AA [auth c], BA [auth c], DB [auth i], EB [auth i], FA [auth d], GC [auth m], HC [auth m], MA [auth d], RA [auth f], RB [auth k], TA [auth f]	2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol C₃₂ H₅₂ O₅ GFDJQXOBWHMOSQ-LEZUHYJESA-N		Interactions Focus chain AA [auth c] Focus chain BA [auth c] Focus chain DB [auth i] Focus chain EB [auth i] Focus chain FA [auth d] Focus chain GC [auth m] Focus chain HC [auth m] Focus chain MA [auth d] Focus chain RA [auth f] Focus chain RB [auth k] Focus chain TA [auth f] Interactions & Density Focus chain AA [auth c] Focus chain BA [auth c] Focus chain DB [auth i] Focus chain EB [auth i] Focus chain FA [auth d] Focus chain GC [auth m] Focus chain HC [auth m] Focus chain MA [auth d] Focus chain RA [auth f] Focus chain RB [auth k] Focus chain TA [auth f]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain CA [auth c] SDF format, chain SA [auth f] MOL2 format, chain CA [auth c] MOL2 format, chain SA [auth f] mmCIF format, chain CA [auth c] mmCIF format, chain SA [auth f]	CA [auth c], SA [auth f]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain CA [auth c] Focus chain SA [auth f] Interactions & Density Focus chain CA [auth c] Focus chain SA [auth f]
CUA Query on CUA Download Ideal Coordinates CCD File SDF format, chain VB [auth l] SDF format, chain CB [auth h] MOL2 format, chain VB [auth l] MOL2 format, chain CB [auth h] mmCIF format, chain VB [auth l] mmCIF format, chain CB [auth h]	CB [auth h], VB [auth l]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain CB [auth h] Focus chain VB [auth l] Interactions & Density Focus chain CB [auth h] Focus chain VB [auth l]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain EC [auth m] SDF format, chain IB [auth i] MOL2 format, chain EC [auth m] MOL2 format, chain IB [auth i] mmCIF format, chain EC [auth m] mmCIF format, chain IB [auth i]	EC [auth m], IB [auth i]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain EC [auth m] Focus chain IB [auth i] Interactions & Density Focus chain EC [auth m] Focus chain IB [auth i]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain YA [auth g] SDF format, chain PB [auth k] MOL2 format, chain YA [auth g] MOL2 format, chain PB [auth k] mmCIF format, chain YA [auth g] mmCIF format, chain PB [auth k]	PB [auth k], YA [auth g]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain PB [auth k] Focus chain YA [auth g] Interactions & Density Focus chain PB [auth k] Focus chain YA [auth g]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain AB [auth g] SDF format, chain TB [auth k] MOL2 format, chain AB [auth g] MOL2 format, chain TB [auth k] mmCIF format, chain AB [auth g] mmCIF format, chain TB [auth k]	AB [auth g], TB [auth k]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AB [auth g] Focus chain TB [auth k] Interactions & Density Focus chain AB [auth g] Focus chain TB [auth k]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain OA [auth e] SDF format, chain QB [auth k] SDF format, chain X [auth b] SDF format, chain WA [auth g] MOL2 format, chain OA [auth e] MOL2 format, chain QB [auth k] MOL2 format, chain X [auth b] MOL2 format, chain WA [auth g] mmCIF format, chain OA [auth e] mmCIF format, chain QB [auth k] mmCIF format, chain X [auth b] mmCIF format, chain WA [auth g]	OA [auth e], QB [auth k], WA [auth g], X [auth b]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain OA [auth e] Focus chain QB [auth k] Focus chain WA [auth g] Focus chain X [auth b] Interactions & Density Focus chain OA [auth e] Focus chain QB [auth k] Focus chain WA [auth g] Focus chain X [auth b]