SMTL ID : 7p8n.1

TmHydABC- T. maritima hydrogenase with bridge closed

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

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

FES.1: 10 residues within 4Å: Chain A: C.575, G.577, S.579, C.580, C.612, V.613, E.614, N.615, C.616, N.621 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.575, A:C.580, A:C.612, A:C.616 FES.6: 10 residues within 4Å: Chain A: L.20, N.32, C.34, Y.42, G.43, A.44, C.45, R.46, C.48, C.60 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.34, A:C.45, A:C.48, A:C.60 FES.9: 10 residues within 4Å: Chain B: C.31, G.33, T.34, C.36, C.78, C.79, G.80, R.81, C.82, L.87 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.31, B:C.36, B:C.78, B:C.82 FES.11: 9 residues within 4Å: Chain C: C.106, G.108, A.110, C.111, C.147, L.148, G.149, A.150, C.151 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.106, C:C.111, C:C.147, C:C.151 FES.16: 10 residues within 4Å: Chain D: L.20, N.32, C.34, Y.42, G.43, A.44, C.45, R.46, C.48, C.60 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.34, D:C.45, D:C.48, D:C.60 FES.21: 10 residues within 4Å: Chain E: C.31, G.33, T.34, C.36, C.78, C.79, G.80, R.81, C.82, L.87 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.31, E:C.36, E:C.78, E:C.82 FES.23: 9 residues within 4Å: Chain F: C.106, G.108, A.110, C.111, C.147, L.148, G.149, A.150, C.151 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.106, F:C.111, F:C.147, F:C.151

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

SF4.2: 10 residues within 4Å: Chain A: C.295, P.296, A.297, C.350, M.480, A.481, C.482, G.485, C.486, G.489 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.295, A:C.350, A:C.482, A:C.486 SF4.3: 9 residues within 4Å: Chain A: C.153, V.161, I.162, C.186, V.187, L.188, C.189, G.190, C.192 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.153, A:C.186, A:C.189, A:C.192 SF4.4: 13 residues within 4Å: Chain A: C.143, I.144, L.145, C.146, G.147, D.148, C.149, V.173, C.196, P.197, T.198, A.200, L.201 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.143, A:C.146, A:C.149, A:C.196 SF4.5: 12 residues within 4Å: Chain A: H.92, N.93, D.95, C.96, C.99, N.102, C.105, Q.108, K.142, T.198, G.199 Chain D: T.97 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.92, A:C.96, A:C.99, A:C.105 SF4.7: 13 residues within 4Å: Chain B: V.313, P.331, S.484, C.485, G.486, K.487, C.488, C.491, S.529, L.530, C.531, L.533, G.534 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.485, B:C.488, B:C.491, B:C.531 SF4.12: 11 residues within 4Å: Chain D: C.295, P.296, A.297, C.350, K.353, M.480, A.481, C.482, G.485, C.486, G.489 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.295, D:C.350, D:C.482, D:C.486 SF4.13: 8 residues within 4Å: Chain D: C.153, V.161, C.186, V.187, L.188, C.189, G.190, C.192 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.153, D:C.186, D:C.189, D:C.192 SF4.14: 13 residues within 4Å: Chain D: C.143, I.144, L.145, C.146, G.147, D.148, C.149, V.173, C.196, P.197, T.198, A.200, L.201 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.143, D:C.146, D:C.149, D:C.196 SF4.15: 14 residues within 4Å: Chain A: T.97 Chain D: H.92, N.93, D.95, C.96, C.99, R.101, N.102, C.105, L.107, Q.108, K.142, T.198, G.199 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:H.92, D:C.96, D:C.99, D:C.105 SF4.17: 10 residues within 4Å: Chain E: Y.571, C.588, A.592, I.603, C.608, V.609, K.610, C.611, G.612, C.614 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.588, E:C.608, E:C.611, E:C.614 SF4.18: 10 residues within 4Å: Chain E: I.573, C.578, C.581, G.582, L.583, C.584, Y.601, C.618, F.620, I.623 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.578, E:C.581, E:C.584, E:C.618 SF4.19: 13 residues within 4Å: Chain E: V.313, P.331, S.484, C.485, G.486, K.487, C.488, C.491, S.529, L.530, C.531, L.533, G.534 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.485, E:C.488, E:C.491, E:C.531

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.8: 15 residues within 4Å: Chain B: G.196, G.198, K.207, D.226, E.227, G.228, F.312, G.315, E.316, E.317, I.350, N.351, N.352, G.532, L.533 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.312, B:L.533 Hydrogen bonds: B:G.198, B:K.207, B:D.226, B:G.315, B:E.317, B:E.317, B:I.350, B:N.351, B:N.352 Water bridges: B:N.235, B:N.235 Salt bridges: B:K.207 FMN.20: 18 residues within 4Å: Chain E: G.196, R.197, G.198, K.207, N.224, D.226, E.227, G.228, F.312, G.315, E.316, E.317, I.350, N.351, N.352, T.355, G.532, L.533 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:F.312, E:L.533 Hydrogen bonds: E:G.198, E:D.226, E:G.315, E:E.317, E:N.351, E:N.352 Salt bridges: E:K.207

2 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain B: C.468, H.555, C.560, C.565 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.468, B:H.555, B:C.560, B:C.565 ZN.22: 4 residues within 4Å: Chain E: C.468, H.555, C.560, C.565 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.468, E:H.555, E:C.560, E:C.565

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furlan, C. et al., Structural insight on the mechanism of an electron-bifurcating [FeFe] hydrogenase. Elife (2022)

Release Date

2022-09-14

Peptides

Fe-hydrogenase, subunit alpha: AD
Fe-hydrogenase, subunit beta: BE
Fe-hydrogenase, subunit gamma: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

D
A

B
b

E
B

C
c

F
C

Fe-hydrogenase, subunit alpha

Fe-hydrogenase, subunit beta

Fe-hydrogenase, subunit gamma

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