SMTL ID : 7t2r.1

Structure of electron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN-free apo state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-mer

Ligands

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

FES.1: 10 residues within 4Å: Chain A: T.34, L.35, C.36, I.44, G.45, A.46, C.47, R.48, 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.7: 7 residues within 4Å: Chain B: C.438, D.441, C.476, H.525, C.531, A.533, C.536 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.476, B:C.531 FES.8: 9 residues within 4Å: Chain C: C.82, A.86, C.87, C.123, L.124, G.125, A.126, C.127, V.132 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.82, C:C.87, C:C.123, C:C.127 FES.12: 10 residues within 4Å: Chain F: T.34, L.35, C.36, I.44, G.45, A.46, C.47, R.48, C.50, C.64 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.36, F:C.47, F:C.50, F:C.64 FES.18: 7 residues within 4Å: Chain G: C.438, D.441, C.476, H.525, C.531, A.533, C.536 2 PLIP interactions: 2 interactions with chain G, Metal complexes: G:C.476, G:C.531 FES.19: 9 residues within 4Å: Chain H: C.82, A.86, C.87, C.123, L.124, G.125, A.126, C.127, V.132 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.82, H:C.87, H:C.123, H:C.127

12 x SF4: IRON/SULFUR CLUSTER(Covalent)

SF4.2: 11 residues within 4Å: Chain A: C.148, V.149, L.150, C.151, Q.152, C.154, C.202, P.203, T.204, T.206, I.207 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.148, A:C.151, A:C.154, A:C.202 SF4.3: 12 residues within 4Å: Chain A: L.141, C.158, V.162, T.166, L.167, C.192, V.193, N.194, C.195, G.196, A.197, C.198 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.158, A:C.192, A:C.195, A:C.198 SF4.4: 10 residues within 4Å: Chain A: C.229, L.231, C.232, G.235, C.236, L.263, C.264, M.266, P.395, V.396 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.229, A:C.232, A:C.236, A:C.264 SF4.5: 11 residues within 4Å: Chain A: F.93, H.98, F.99, C.100, C.103, Q.105, S.106, C.109, Q.112, R.147, T.204 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.98, A:C.100, A:C.103, A:C.109 SF4.6: 10 residues within 4Å: Chain B: P.301, C.455, G.456, K.457, C.458, C.461, S.499, L.500, C.501, G.504 5 PLIP interactions: 5 interactions with chain B, Salt bridges: B:E.286 Metal complexes: B:C.455, B:C.458, B:C.461, B:C.501 SF4.11: 12 residues within 4Å: Chain D: R.62, H.166 Chain E: A.13, C.14, C.17, G.83, D.84, C.85, I.91, G.148, C.149, P.150 5 PLIP interactions: 5 interactions with chain E, Salt bridges: E:D.84 Metal complexes: E:C.14, E:C.17, E:C.85, E:C.149 SF4.13: 11 residues within 4Å: Chain F: C.148, V.149, L.150, C.151, Q.152, C.154, C.202, P.203, T.204, T.206, I.207 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.148, F:C.151, F:C.154, F:C.202 SF4.14: 12 residues within 4Å: Chain F: L.141, C.158, V.162, T.166, L.167, C.192, V.193, N.194, C.195, G.196, A.197, C.198 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.158, F:C.192, F:C.195, F:C.198 SF4.15: 10 residues within 4Å: Chain F: C.229, L.231, C.232, G.235, C.236, L.263, C.264, M.266, P.395, V.396 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.229, F:C.232, F:C.236, F:C.264 SF4.16: 11 residues within 4Å: Chain F: F.93, H.98, F.99, C.100, C.103, Q.105, S.106, C.109, Q.112, R.147, T.204 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:H.98, F:C.100, F:C.103, F:C.109 SF4.17: 10 residues within 4Å: Chain G: P.301, C.455, G.456, K.457, C.458, C.461, S.499, L.500, C.501, G.504 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:E.286 Metal complexes: G:C.455, G:C.458, G:C.461, G:C.501 SF4.22: 12 residues within 4Å: Chain I: R.62, H.166 Chain J: A.13, C.14, C.17, G.83, D.84, C.85, I.91, G.148, C.149, P.150 5 PLIP interactions: 5 interactions with chain J, Salt bridges: J:D.84 Metal complexes: J:C.14, J:C.17, J:C.85, J:C.149

2 x 3NI: NICKEL (III) ION(Non-covalent)

3NI.9: 5 residues within 4Å: Chain D: C.64, C.67, C.444, C.447 Ligands: FCO.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.67, D:C.444, D:C.447 3NI.20: 5 residues within 4Å: Chain I: C.64, C.67, C.444, C.447 Ligands: FCO.21 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.67, I:C.444, I:C.447

2 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-covalent)

FCO.10: 12 residues within 4Å: Chain D: C.67, H.71, A.376, P.377, R.378, G.379, L.381, A.401, T.402, C.444, C.447 Ligands: 3NI.9 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.378, D:G.379, D:A.401, D:T.402 Metal complexes: D:C.67, D:C.447 FCO.21: 12 residues within 4Å: Chain I: C.67, H.71, A.376, P.377, R.378, G.379, L.381, A.401, T.402, C.444, C.447 Ligands: 3NI.20 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:R.378, I:G.379, I:A.401, I:T.402 Metal complexes: I:C.67, I:C.447

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, X. et al., Structure and electron transfer pathways of an electron-bifurcating NiFe-hydrogenase. Sci Adv (2022)

Release Date

2022-03-16

Peptides

NiFe hydrogenase subunit A: AF
NiFe hydrogenase subunit B: BG
NiFe hydrogenase subunit C: CH
NiFe hydrogenase large subunit: DI
NiFe hydrogenase small subunit: EJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
F

B
B

G
G

C
C

H
H

D
D

I
I

E
E

J
J

NiFe hydrogenase subunit A

NiFe hydrogenase subunit B

NiFe hydrogenase subunit C

NiFe hydrogenase large subunit

NiFe hydrogenase small subunit

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