9SW6 | pdb_00009sw6

Structure of the Mvh-Hdr-Fmd complex of Methanothermobacter marburgensis (composite structure)

PDB DOI: https://doi.org/10.2210/pdb9SW6/pdb
EM Map EMD-55299: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Methanothermobacter marburgensis
Mutation(s): No

Deposited: 2025-10-04 Released: 2026-04-29
Deposition Author(s): San Segundo-Acosta, P., Murphy, B.J.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Diversity of electron-bifurcating CO2-fixing supercomplexes in methanogens

San Segundo-Acosta, P., Nomura, S., Fernandes-Queiroz, J.P., Protasov, E., Kahnt, J., Kaneko, M., Hochberg, G., Shima, S., Murphy, B.J.

(2026) Science Advances

Macromolecule Content

Total Structure Weight: 698 kDa
Atom Count: 46,989
Modeled Residue Count: 6,015
Deposited Residue Count: 6,151
Unique protein chains: 12

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A	A	659	Methanothermobacter marburgensis	Mutation(s): 0 EC: 1.8.98.5
UniProt
Find proteins for Q50756 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore Q50756 Go to UniProtKB: Q50756
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q50756
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B	B	302	Methanothermobacter marburgensis	Mutation(s): 0 EC: 1.8.98.5
UniProt
Find proteins for Q50755 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore Q50755 Go to UniProtKB: Q50755
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q50755
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C	C	185	Methanothermobacter marburgensis	Mutation(s): 0 EC: 1.8.98.5
UniProt
Find proteins for Q50754 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore Q50754 Go to UniProtKB: Q50754
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q50754
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-non-reducing hydrogenase iron-sulfur subunit D	D	141	Methanothermobacter marburgensis	Mutation(s): 0 EC: 1.12.99
UniProt
Find proteins for P60238 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P60238 Go to UniProtKB: P60238
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60238
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-non-reducing hydrogenase subunit G	E	308	Methanothermobacter marburgensis	Mutation(s): 0 EC: 1.12.99
UniProt
Find proteins for P60239 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P60239 Go to UniProtKB: P60239
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60239
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten formylmethanofuran dehydrogenase, subunit F	F [auth H], N [auth h]	349	Methanothermobacter marburgensis	Mutation(s): 0 EC: 1.2.99.5
UniProt
Find proteins for D9PU51 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore D9PU51 Go to UniProtKB: D9PU51
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D9PU51
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten formylmethanofuran dehydrogenase, subunit A	G [auth I], J [auth i]	569	Methanothermobacter marburgensis	Mutation(s): 0 EC: 1.2.99.5
UniProt
Find proteins for D9PU54 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore D9PU54 Go to UniProtKB: D9PU54
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D9PU54
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
formylmethanofuran dehydrogenase subunit B	H [auth J], L [auth j]	436	Methanothermobacter marburgensis	Mutation(s): 0 EC: 1.2.7.12
UniProt
Find proteins for D9PXE7 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore D9PXE7 Go to UniProtKB: D9PXE7
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UniProt Group	D9PXE7
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten formylmethanofuran dehydrogenase, subunit G	I [auth L], K [auth l]	82	Methanothermobacter marburgensis	Mutation(s): 0 EC: 1.2.99.5
UniProt
Find proteins for D9PU52 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore D9PU52 Go to UniProtKB: D9PU52
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D9PU52
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdenum-containing formylmethanofuran dehydrogenase 1 subunit C	M [auth K], O [auth k]	400	Methanothermobacter marburgensis	Mutation(s): 0 EC: 1.2.7.12
UniProt
Find proteins for P61937 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P61937 Go to UniProtKB: P61937
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61937
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyferredoxin protein MvhB	P [auth G]	412	Methanothermobacter marburgensis	Mutation(s): 0
UniProt
Find proteins for P60232 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P60232 Go to UniProtKB: P60232
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60232
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
F420-non-reducing hydrogenase subunit A	Q [auth F]	472	Methanothermobacter marburgensis	Mutation(s): 0 EC: 1.12.99
UniProt
Find proteins for P60227 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P60227 Go to UniProtKB: P60227
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60227
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Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A] mmCIF format, chain U [auth A]	U [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]
MGD (Subject of Investigation/LOI) Query on MGD Download:Ideal Coordinates CCD File SDF format, chain TA [auth J] SDF format, chain SA [auth J] SDF format, chain EB [auth j] SDF format, chain DB [auth j] MOL2 format, chain TA [auth J] MOL2 format, chain SA [auth J] MOL2 format, chain EB [auth j] MOL2 format, chain DB [auth j] mmCIF format, chain TA [auth J] mmCIF format, chain SA [auth J] mmCIF format, chain EB [auth j] mmCIF format, chain DB [auth j]	DB [auth j], EB [auth j], SA [auth J], TA [auth J]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C₂₀ H₂₆ N₁₀ O₁₃ P₂ S₂ VQAGYJCYOLHZDH-ILXWUORBSA-N		Interactions Focus chain DB [auth j] Focus chain EB [auth j] Focus chain SA [auth J] Focus chain TA [auth J] Interactions & Density Focus chain DB [auth j] Focus chain EB [auth j] Focus chain SA [auth J] Focus chain TA [auth J]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain ZB [auth G] SDF format, chain YB [auth G] SDF format, chain XB [auth G] SDF format, chain XA [auth L] SDF format, chain X [auth A] SDF format, chain WB [auth G] SDF format, chain WA [auth L] SDF format, chain W [auth A] SDF format, chain VB [auth G] SDF format, chain V [auth A] SDF format, chain UB [auth G] SDF format, chain TB [auth G] SDF format, chain T [auth A] SDF format, chain SB [auth G] SDF format, chain S [auth A] SDF format, chain RB [auth G] SDF format, chain RA [auth J] SDF format, chain R [auth A] SDF format, chain QB [auth G] SDF format, chain PB [auth G] SDF format, chain OB [auth h] SDF format, chain OA [auth H] SDF format, chain NB [auth h] SDF format, chain NA [auth H] SDF format, chain MB [auth h] SDF format, chain MA [auth H] SDF format, chain LB [auth h] SDF format, chain LA [auth H] SDF format, chain KB [auth h] SDF format, chain KA [auth H] SDF format, chain JB [auth h] SDF format, chain JA [auth H] SDF format, chain IB [auth h] SDF format, chain IA [auth H] SDF format, chain HB [auth h] SDF format, chain HA [auth H] SDF format, chain GA [auth H] SDF format, chain FA [auth E] SDF format, chain EA [auth E] SDF format, chain DA [auth E] SDF format, chain CB [auth j] SDF format, chain BB [auth l] SDF format, chain BA [auth C] SDF format, chain AB [auth l] SDF format, chain AA [auth C] MOL2 format, chain ZB [auth G] MOL2 format, chain YB [auth G] MOL2 format, chain XB [auth G] MOL2 format, chain XA [auth L] MOL2 format, chain X [auth A] MOL2 format, chain WB [auth G] MOL2 format, chain WA [auth L] MOL2 format, chain W [auth A] MOL2 format, chain VB [auth G] MOL2 format, chain V [auth A] MOL2 format, chain UB [auth G] MOL2 format, chain TB [auth G] MOL2 format, chain T [auth A] MOL2 format, chain SB [auth G] MOL2 format, chain S [auth A] MOL2 format, chain RB [auth G] MOL2 format, chain RA [auth J] MOL2 format, chain R [auth A] MOL2 format, chain QB [auth G] MOL2 format, chain PB [auth G] MOL2 format, chain OB [auth h] MOL2 format, chain OA [auth H] MOL2 format, chain NB [auth h] MOL2 format, chain NA [auth H] MOL2 format, chain MB [auth h] MOL2 format, chain MA [auth H] MOL2 format, chain LB [auth h] MOL2 format, chain LA [auth H] MOL2 format, chain KB [auth h] MOL2 format, chain KA [auth H] MOL2 format, chain JB [auth h] MOL2 format, chain JA [auth H] MOL2 format, chain IB [auth h] MOL2 format, chain IA [auth H] MOL2 format, chain HB [auth h] MOL2 format, chain HA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain FA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain CB [auth j] MOL2 format, chain BB [auth l] MOL2 format, chain BA [auth C] MOL2 format, chain AB [auth l] MOL2 format, chain AA [auth C] mmCIF format, chain ZB [auth G] mmCIF format, chain YB [auth G] mmCIF format, chain XB [auth G] mmCIF format, chain XA [auth L] mmCIF format, chain X [auth A] mmCIF format, chain WB [auth G] mmCIF format, chain WA [auth L] mmCIF format, chain W [auth A] mmCIF format, chain VB [auth G] mmCIF format, chain V [auth A] mmCIF format, chain UB [auth G] mmCIF format, chain TB [auth G] mmCIF format, chain T [auth A] mmCIF format, chain SB [auth G] mmCIF format, chain S [auth A] mmCIF format, chain RB [auth G] mmCIF format, chain RA [auth J] mmCIF format, chain R [auth A] mmCIF format, chain QB [auth G] mmCIF format, chain PB [auth G] mmCIF format, chain OB [auth h] mmCIF format, chain OA [auth H] mmCIF format, chain NB [auth h] mmCIF format, chain NA [auth H] mmCIF format, chain MB [auth h] mmCIF format, chain MA [auth H] mmCIF format, chain LB [auth h] mmCIF format, chain LA [auth H] mmCIF format, chain KB [auth h] mmCIF format, chain KA [auth H] mmCIF format, chain JB [auth h] mmCIF format, chain JA [auth H] mmCIF format, chain IB [auth h] mmCIF format, chain IA [auth H] mmCIF format, chain HB [auth h] mmCIF format, chain HA [auth H] mmCIF format, chain GA [auth H] mmCIF format, chain FA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain CB [auth j] mmCIF format, chain BB [auth l] mmCIF format, chain BA [auth C] mmCIF format, chain AB [auth l] mmCIF format, chain AA [auth C]	AA [auth C] AB [auth l] BA [auth C] BB [auth l] CB [auth j] AA [auth C], AB [auth l], BA [auth C], BB [auth l], CB [auth j], DA [auth E], EA [auth E], FA [auth E], GA [auth H], HA [auth H], HB [auth h], IA [auth H], IB [auth h], JA [auth H], JB [auth h], KA [auth H], KB [auth h], LA [auth H], LB [auth h], MA [auth H], MB [auth h], NA [auth H], NB [auth h], OA [auth H], OB [auth h], PB [auth G], QB [auth G], R [auth A], RA [auth J], RB [auth G], S [auth A], SB [auth G], T [auth A], TB [auth G], UB [auth G], V [auth A], VB [auth G], W [auth A], WA [auth L], WB [auth G], X [auth A], XA [auth L], XB [auth G], YB [auth G], ZB [auth G]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth l] Focus chain BA [auth C] Focus chain BB [auth l] Focus chain CB [auth j] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain HB [auth h] Focus chain IA [auth H] Focus chain IB [auth h] Focus chain JA [auth H] Focus chain JB [auth h] Focus chain KA [auth H] Focus chain KB [auth h] Focus chain LA [auth H] Focus chain LB [auth h] Focus chain MA [auth H] Focus chain MB [auth h] Focus chain NA [auth H] Focus chain NB [auth h] Focus chain OA [auth H] Focus chain OB [auth h] Focus chain PB [auth G] Focus chain QB [auth G] Focus chain R [auth A] Focus chain RA [auth J] Focus chain RB [auth G] Focus chain S [auth A] Focus chain SB [auth G] Focus chain T [auth A] Focus chain TB [auth G] Focus chain UB [auth G] Focus chain V [auth A] Focus chain VB [auth G] Focus chain W [auth A] Focus chain WA [auth L] Focus chain WB [auth G] Focus chain X [auth A] Focus chain XA [auth L] Focus chain XB [auth G] Focus chain YB [auth G] Focus chain ZB [auth G] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth l] Focus chain BA [auth C] Focus chain BB [auth l] Focus chain CB [auth j] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain HB [auth h] Focus chain IA [auth H] Focus chain IB [auth h] Focus chain JA [auth H] Focus chain JB [auth h] Focus chain KA [auth H] Focus chain KB [auth h] Focus chain LA [auth H] Focus chain LB [auth h] Focus chain MA [auth H] Focus chain MB [auth h] Focus chain NA [auth H] Focus chain NB [auth h] Focus chain OA [auth H] Focus chain OB [auth h] Focus chain PB [auth G] Focus chain QB [auth G] Focus chain R [auth A] Focus chain RA [auth J] Focus chain RB [auth G] Focus chain S [auth A] Focus chain SB [auth G] Focus chain T [auth A] Focus chain TB [auth G] Focus chain UB [auth G] Focus chain V [auth A] Focus chain VB [auth G] Focus chain W [auth A] Focus chain WA [auth L] Focus chain WB [auth G] Focus chain X [auth A] Focus chain XA [auth L] Focus chain XB [auth G] Focus chain YB [auth G] Focus chain ZB [auth G]
9S8 (Subject of Investigation/LOI) Query on 9S8 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B]	Y [auth B], Z [auth B]	Non-cubane [4Fe-4S]-cluster Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain Y [auth B] Focus chain Z [auth B]
F3S (Subject of Investigation/LOI) Query on F3S Download:Ideal Coordinates CCD File SDF format, chain AC [auth G] MOL2 format, chain AC [auth G] mmCIF format, chain AC [auth G]	AC [auth G]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain AC [auth G] Interactions & Density Focus chain AC [auth G]
NFU (Subject of Investigation/LOI) Query on NFU Download:Ideal Coordinates CCD File SDF format, chain BC [auth F] MOL2 format, chain BC [auth F] mmCIF format, chain BC [auth F]	BC [auth F]	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) C₃ H Fe N₂ Ni O QCZROEOIPZWDEO-UHFFFAOYSA-N		Interactions Focus chain BC [auth F] Interactions & Density Focus chain BC [auth F]
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] MOL2 format, chain CA [auth D] mmCIF format, chain CA [auth D]	CA [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Interactions & Density Focus chain CA [auth D]
MO (Subject of Investigation/LOI) Query on MO Download:Ideal Coordinates CCD File SDF format, chain UA [auth J] SDF format, chain FB [auth j] MOL2 format, chain UA [auth J] MOL2 format, chain FB [auth j] mmCIF format, chain UA [auth J] mmCIF format, chain FB [auth j]	FB [auth j], UA [auth J]	MOLYBDENUM ATOM Mo ZOKXTWBITQBERF-UHFFFAOYSA-N		Interactions Focus chain FB [auth j] Focus chain UA [auth J] Interactions & Density Focus chain FB [auth j] Focus chain UA [auth J]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain ZA [auth i] SDF format, chain YA [auth i] SDF format, chain QA [auth I] SDF format, chain PA [auth I] MOL2 format, chain ZA [auth i] MOL2 format, chain YA [auth i] MOL2 format, chain QA [auth I] MOL2 format, chain PA [auth I] mmCIF format, chain ZA [auth i] mmCIF format, chain YA [auth i] mmCIF format, chain QA [auth I] mmCIF format, chain PA [auth I]	PA [auth I], QA [auth I], YA [auth i], ZA [auth i]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain PA [auth I] Focus chain QA [auth I] Focus chain YA [auth i] Focus chain ZA [auth i] Interactions & Density Focus chain PA [auth I] Focus chain QA [auth I] Focus chain YA [auth i] Focus chain ZA [auth i]
H2S (Subject of Investigation/LOI) Query on H2S Download:Ideal Coordinates CCD File SDF format, chain VA [auth J] SDF format, chain GB [auth j] MOL2 format, chain VA [auth J] MOL2 format, chain GB [auth j] mmCIF format, chain VA [auth J] mmCIF format, chain GB [auth j]	GB [auth j], VA [auth J]	HYDROSULFURIC ACID H₂ S RWSOTUBLDIXVET-UHFFFAOYSA-N		Interactions Focus chain GB [auth j] Focus chain VA [auth J] Interactions & Density Focus chain GB [auth j] Focus chain VA [auth J]