SMTL ID : 8a5e.1

Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Acetobacterium woodii in the reduced state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

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

SF4.1: 6 residues within 4Å: Chain A: C.158, V.166, C.191, 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 SF4.2: 10 residues within 4Å: Chain A: C.148, I.149, C.151, K.152, R.153, C.154, C.201, P.202, V.203, L.206 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.148, A:C.151, A:C.154, A:C.201 SF4.3: 9 residues within 4Å: Chain A: H.96, N.97, E.99, C.100, C.103, S.106, C.109, L.111, V.203 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.96, A:C.100, A:C.103, A:C.109 SF4.5: 8 residues within 4Å: Chain A: S.301, C.356, M.500, A.501, C.502, C.506, G.509 Ligands: HC1.6 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.356, A:C.502, A:C.506 SF4.8: 10 residues within 4Å: Chain B: F.544, C.561, P.562, I.566, C.581, I.582, K.583, C.584, G.585, C.587 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.561, B:C.581, B:C.584, B:C.587 SF4.9: 12 residues within 4Å: Chain B: I.546, C.551, K.552, G.553, C.554, G.555, I.556, C.557, C.591, P.592, F.593, I.596 5 PLIP interactions: 5 interactions with chain B, pi-Cation interactions: B:Y.574 Metal complexes: B:C.551, B:C.554, B:C.557, B:C.591 SF4.11: 9 residues within 4Å: Chain B: V.285, P.303, C.457, G.458, K.459, C.460, C.463, C.503, G.506 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.457, B:C.460, B:C.463, B:C.503 SF4.14: 8 residues within 4Å: Chain D: C.158, V.164, V.166, C.191, I.192, 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 SF4.15: 13 residues within 4Å: Chain D: R.143, C.148, I.149, C.151, K.152, R.153, C.154, N.200, C.201, P.202, V.203, A.205, L.206 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.148, D:C.151, D:C.154, D:C.201 SF4.16: 10 residues within 4Å: Chain D: H.96, N.97, E.99, C.100, C.103, S.106, C.109, L.111, Q.112, V.203 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:H.96, D:C.100, D:C.103, D:C.109 SF4.18: 8 residues within 4Å: Chain D: S.301, P.302, C.356, A.501, C.502, C.506, G.509 Ligands: HC1.19 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.356, D:C.502, D:C.506

3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)(Covalent)

FES.4: 7 residues within 4Å: Chain A: 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.13: 9 residues within 4Å: Chain C: C.83, G.85, A.87, C.88, R.123, C.124, V.125, C.128, V.133 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.17: 9 residues within 4Å: Chain D: T.34, L.35, C.36, G.45, A.46, C.47, R.48, 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

2 x HC1: 2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER(Non-covalent)

HC1.6: 10 residues within 4Å: Chain A: C.300, P.325, M.354, P.355, C.356, K.359, F.418, M.500, C.506 Ligands: SF4.5 2 PLIP interactions: 2 interactions with chain A, Hydrogen bonds: A:K.359, A:F.418 HC1.19: 12 residues within 4Å: Chain D: P.232, T.269, S.301, S.324, P.325, M.354, P.355, K.359, F.418, G.419, C.506 Ligands: SF4.18 4 PLIP interactions: 4 interactions with chain D, Hydrogen bonds: D:T.269, D:K.359, D:G.419 Metal complexes: D:C.506

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain B: C.440, H.527, C.533, C.538 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.440, B:H.527, B:C.533, B:C.538

1 x FMN: FLAVIN MONONUCLEOTIDE(Covalent)

FMN.10: 15 residues within 4Å: Chain B: G.166, G.168, F.172, K.177, N.196, D.198, G.287, E.288, E.289, L.322, N.323, N.324, G.504, L.505 Ligands: NAI.12 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.505 Hydrogen bonds: B:G.168, B:E.289, B:N.323, B:N.324, B:N.324, B:T.327 Salt bridges: B:K.177

1 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Covalent)

NAI.12: 15 residues within 4Å: Chain A: R.58 Chain B: G.168, G.169, G.170, F.172, K.177, F.180, N.196, D.201, R.306, F.309, S.402, M.426, T.508 Ligands: FMN.10 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Salt bridges: A:R.58, B:R.306 Hydrogen bonds: B:K.177, B:R.306, B:G.428 pi-Stacking: B:F.172, B:F.180, B:F.309, B:F.309

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

2023-02-22

Peptides

Iron hydrogenase HydA1: AD
Iron hydrogenase HydB: B
Iron hydrogenase HydC: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

Iron hydrogenase HydA1

Iron hydrogenase HydB

Iron hydrogenase HydC

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