SMTL ID : 7q4w.1

CryoEM structure of electron bifurcating Fe-Fe hydrogenase HydABC complex A. woodii in the oxidised state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

14 x SF4: IRON/SULFUR CLUSTER(Non-covalent)(Covalent)

SF4.1: 7 residues within 4Å: Chain A: S.301, C.356, M.500, A.501, C.502, G.505, C.506 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:S.301, A:C.356, A:C.502, A:C.506 SF4.2: 8 residues within 4Å: Chain A: C.158, V.164, C.191, I.192, N.193, C.194, G.195, C.197 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.158, A:C.191, A:C.194, A:C.197 SF4.3: 11 residues within 4Å: Chain A: C.148, I.149, L.150, C.151, K.152, R.153, C.154, V.178, C.201, A.205, L.206 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.148, A:C.151, A:C.154, A:C.201 SF4.4: 10 residues within 4Å: Chain A: H.96, N.97, E.99, C.100, C.103, R.105, S.106, C.109, Q.112, V.203 6 PLIP interactions: 6 interactions with chain A, Metal complexes: A:H.96, A:H.96, A:C.100, A:C.100, A:C.103, A:C.109 SF4.7: 9 residues within 4Å: Chain B: C.328, G.329, K.330, C.331, C.334, R.335, L.373, C.374, G.377 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.328, B:C.331, B:C.334, B:C.374 SF4.8: 14 residues within 4Å: Chain B: F.415, K.431, C.432, P.433, A.434, A.436, I.437, C.452, I.453, K.454, C.455, G.456, A.457, C.458 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.432, B:C.452, B:C.455, B:C.458 SF4.9: 12 residues within 4Å: Chain B: C.422, K.423, G.424, C.425, G.426, I.427, C.428, A.461, C.462, P.463, F.464, I.467 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.422, B:C.425, B:C.428, B:C.462 SF4.12: 8 residues within 4Å: Chain D: S.301, C.356, M.500, A.501, C.502, G.505, C.506, G.509 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:S.301, D:C.356, D:C.502, D:C.506 SF4.13: 8 residues within 4Å: Chain D: C.158, V.164, C.191, I.192, N.193, C.194, G.195, C.197 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.158, D:C.191, D:C.194, D:C.197 SF4.14: 11 residues within 4Å: Chain D: C.148, I.149, L.150, C.151, K.152, R.153, C.154, V.178, C.201, V.203, L.206 5 PLIP interactions: 5 interactions with chain D, Metal complexes: D:C.148, D:C.151, D:C.151, D:C.154, D:C.201 SF4.15: 10 residues within 4Å: Chain D: H.96, N.97, E.99, C.100, C.103, R.105, S.106, C.109, Q.112, V.203 6 PLIP interactions: 6 interactions with chain D, Metal complexes: D:H.96, D:C.100, D:C.100, D:C.103, D:C.103, D:C.109 SF4.19: 10 residues within 4Å: Chain E: V.156, P.174, C.328, G.329, K.330, C.331, C.334, L.373, C.374, G.377 5 PLIP interactions: 5 interactions with chain E, Metal complexes: E:C.328, E:C.331, E:C.334, E:C.374, E:C.374 SF4.20: 13 residues within 4Å: Chain E: F.415, K.431, C.432, P.433, A.434, I.437, C.452, I.453, K.454, C.455, G.456, A.457, C.458 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.432, E:C.452, E:C.455, E:C.458 SF4.21: 13 residues within 4Å: Chain E: C.422, K.423, G.424, C.425, G.426, I.427, C.428, Y.445, A.461, C.462, P.463, F.464, I.467 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.422, E:C.425, E:C.428, E:C.462

4 x FES: FE2/S2 (INORGANIC) CLUSTER(Covalent)

FES.5: 8 residues within 4Å: Chain A: P.33, T.34, L.35, C.36, G.45, C.47, C.50, C.64 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.36, A:C.47, A:C.50, A:C.64 FES.11: 9 residues within 4Å: Chain C: C.83, G.85, A.87, C.88, C.124, V.125, G.126, A.127, C.128 5 PLIP interactions: 5 interactions with chain C, Metal complexes: C:C.83, C:C.83, C:C.88, C:C.124, C:C.128 FES.16: 8 residues within 4Å: Chain D: T.34, L.35, C.36, Y.37, G.45, C.47, C.50, C.64 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.36, D:C.47, D:C.50, D:C.64 FES.22: 8 residues within 4Å: Chain F: C.83, G.85, C.88, R.123, C.124, V.125, G.126, C.128 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.83, F:C.88, F:C.124, F:C.128

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.6: 17 residues within 4Å: Chain B: G.37, G.39, G.40, G.41, G.42, F.43, N.67, D.69, E.70, G.71, G.158, E.159, E.160, N.195, S.300, G.375, L.376 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:E.159, B:L.376 Hydrogen bonds: B:G.37, B:G.39, B:G.39, B:G.40, B:G.41, B:G.42, B:N.67, B:G.71, B:G.158, B:E.160, B:E.160, B:N.195, B:S.300 FMN.18: 10 residues within 4Å: Chain E: G.37, G.39, G.41, N.67, D.69, G.71, G.158, E.159, G.375, L.376 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:E.159, E:E.159 Hydrogen bonds: E:G.39, E:G.41, E:G.42, E:N.67, E:D.69, E:G.71, E:G.158 Salt bridges: E:K.48

2 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain B: C.311, H.398, C.404, C.409 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.311, B:H.398, B:C.404, B:C.409 ZN.17: 4 residues within 4Å: Chain E: C.311, H.398, C.404, C.409 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.311, E:H.398, E:C.404, E:C.409

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Katsyv, A. et al., Molecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC. J.Am.Chem.Soc. (2023)

Release Date

2023-02-15

Peptides

Iron hydrogenase HydA1: AD
Iron hydrogenase HydB: BE
Iron hydrogenase HydC: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

B
B

E
F

C
C

F
G

Iron hydrogenase HydA1

Iron hydrogenase HydB

Iron hydrogenase HydC

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