SMTL ID : 8bew.1

Cryo-EM structure of the electron bifurcating Fe-Fe hydrogenase HydABC complex from Thermoanaerobacter kivui in the oxidised state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

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

SF4.1: 8 residues within 4Å: Chain A: C.299, P.300, S.301, C.354, M.494, C.496, C.500, G.503 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.299, A:C.354, A:C.496, A:C.500 SF4.3: 9 residues within 4Å: Chain A: H.95, N.96, C.99, C.102, C.108, L.110, T.201, G.202 Chain D: F.100 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:D.98 Metal complexes: A:H.95, A:C.99, A:C.102, A:C.108 SF4.4: 10 residues within 4Å: Chain A: C.146, I.147, L.148, C.149, G.150, C.152, I.176, C.199, P.200, T.201 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.146, A:C.149, A:C.152, A:C.199 SF4.5: 7 residues within 4Å: Chain A: I.139, C.156, I.162, C.189, C.192, G.193, C.195 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.156, A:C.189, A:C.192, A:C.195 SF4.7: 12 residues within 4Å: Chain B: V.316, P.334, S.487, C.488, G.489, K.490, C.491, C.494, S.532, C.534, L.536, G.537 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.488, B:C.491, B:C.494, B:C.534 SF4.10: 10 residues within 4Å: Chain B: Y.575, C.588, C.592, A.596, I.597, I.607, C.612, C.615, G.616, C.618 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.592, B:C.612, B:C.618 SF4.11: 12 residues within 4Å: Chain B: I.577, C.582, I.583, G.584, C.585, G.586, C.588, H.605, C.622, K.624, A.626, I.627 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.582, B:C.585, B:C.622 SF4.13: 8 residues within 4Å: Chain D: C.299, S.301, C.354, M.494, A.495, C.496, C.500, G.503 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.299, D:C.354, D:C.496, D:C.500 SF4.15: 7 residues within 4Å: Chain A: F.100 Chain D: H.95, C.99, C.102, C.108, T.201, G.202 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:H.95, D:C.99, D:C.102, D:C.108 SF4.16: 10 residues within 4Å: Chain D: C.146, I.147, C.149, G.150, C.152, I.176, C.199, T.201, A.203, L.204 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.146, D:C.149, D:C.152, D:C.199 SF4.17: 7 residues within 4Å: Chain D: C.156, I.162, A.164, C.189, C.192, G.193, C.195 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.156, D:C.189, D:C.192, D:C.195 SF4.19: 9 residues within 4Å: Chain E: P.334, C.488, G.489, K.490, C.491, C.494, C.534, L.536, G.537 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.488, E:C.491, E:C.494, E:C.534 SF4.22: 11 residues within 4Å: Chain E: Y.575, C.588, C.592, A.596, I.597, I.607, C.612, K.614, C.615, G.616, C.618 3 PLIP interactions: 3 interactions with chain E, Metal complexes: E:C.592, E:C.612, E:C.618 SF4.23: 12 residues within 4Å: Chain E: I.577, C.582, I.583, G.584, C.585, G.586, C.588, H.605, C.622, K.624, A.626, I.627 3 PLIP interactions: 3 interactions with chain E, Metal complexes: E:C.582, E:C.585, E:C.622

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

FES.2: 9 residues within 4Å: Chain A: C.36, D.37, G.45, A.46, C.47, R.48, C.50, A.61, C.63 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.36, A:C.47, A:C.50, A:C.63 FES.9: 10 residues within 4Å: Chain B: C.31, G.33, G.35, C.36, C.82, Q.83, G.84, F.85, C.86, L.91 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.31, B:C.36, B:C.82, B:C.86 FES.12: 9 residues within 4Å: Chain C: C.87, G.89, T.90, A.91, C.92, C.128, L.129, G.130, C.132 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.87, C:C.92, C:C.128, C:C.132 FES.14: 8 residues within 4Å: Chain D: L.35, C.36, G.45, A.46, C.47, R.48, C.50, C.63 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.36, D:C.47, D:C.50, D:C.63 FES.21: 8 residues within 4Å: Chain E: C.31, G.35, C.36, G.81, C.82, Q.83, G.84, C.86 3 PLIP interactions: 3 interactions with chain E, Metal complexes: E:C.31, E:C.36, E:C.86 FES.24: 7 residues within 4Å: Chain F: C.87, G.89, A.91, C.92, C.128, L.129, C.132 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.87, F:C.92, F:C.128, F:C.132

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)(Covalent)

FMN.6: 16 residues within 4Å: Chain B: G.199, G.201, A.203, F.205, K.210, N.227, E.230, G.231, F.315, G.318, E.319, L.353, N.354, N.355, G.535, L.536 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.315, B:E.319, B:L.536 Hydrogen bonds: B:G.201, B:N.227, B:N.227, B:E.230, B:G.231, B:G.318, B:L.353, B:N.354, B:T.358 Salt bridges: B:K.210 FMN.18: 16 residues within 4Å: Chain E: G.199, G.201, K.210, N.227, D.229, E.230, G.231, F.315, G.318, E.319, S.320, L.353, N.354, N.355, G.535, L.536 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:E.319, E:L.536 Hydrogen bonds: E:G.204, E:N.227, E:G.231, E:E.319, E:N.355 Salt bridges: E:K.210

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain B: C.471, H.558, C.564, C.569 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.471, B:H.558, B:C.564, B:C.569 ZN.20: 4 residues within 4Å: Chain E: C.471, H.558, C.564, C.569 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.471, E:H.558, E:C.564, E:C.569

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

Electron bifurcating hydrogenase subunit HydA1: AD
Electron bifurcating hydrogenase subunit HydB: BE
Electron bifurcating hydrogenase subunit HydC: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Electron bifurcating hydrogenase subunit HydA1

Electron bifurcating hydrogenase subunit HydB

Electron bifurcating hydrogenase subunit HydC

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