SMTL ID : 7t30.1

Structure of electron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN/NAD(H) bound state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

FES.1: 7 residues within 4Å: Chain A: C.36, 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.9: 7 residues within 4Å: Chain B: C.438, D.441, C.476, H.525, C.531, A.533, C.536 5 PLIP interactions: 5 interactions with chain B, Metal complexes: B:C.438, B:C.476, B:H.525, B:C.531, B:C.536 FES.13: 7 residues within 4Å: Chain F: C.36, 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.21: 7 residues within 4Å: Chain G: C.438, D.441, C.476, H.525, C.531, A.533, C.536 5 PLIP interactions: 5 interactions with chain G, Metal complexes: G:C.438, G:C.476, G:H.525, G:C.531, G:C.536

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

SF4.2: 13 residues within 4Å: Chain A: C.148, V.149, L.150, C.151, Q.152, R.153, C.154, V.178, 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: 10 residues within 4Å: Chain A: L.141, C.158, A.164, 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, G.267, 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: 12 residues within 4Å: Chain A: F.93, H.98, F.99, C.100, C.103, Q.105, S.106, C.109, L.111, R.147, T.204, G.205 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.98, A:C.100, A:C.103, A:C.109 SF4.7: 11 residues within 4Å: Chain B: V.283, S.454, C.455, G.456, K.457, C.458, C.461, S.499, C.501, L.503, G.504 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.455, B:C.458, B:C.461, B:C.501 SF4.12: 13 residues within 4Å: Chain D: R.62, H.166 Chain E: A.13, C.14, G.16, C.17, S.57, G.83, D.84, C.85, 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 SF4.14: 13 residues within 4Å: Chain F: C.148, V.149, L.150, C.151, Q.152, R.153, C.154, V.178, 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 SF4.15: 10 residues within 4Å: Chain F: L.141, C.158, A.164, 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 SF4.16: 10 residues within 4Å: Chain F: C.229, L.231, C.232, G.235, C.236, L.263, C.264, G.267, 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 SF4.17: 12 residues within 4Å: Chain F: F.93, H.98, F.99, C.100, C.103, Q.105, S.106, C.109, L.111, R.147, T.204, G.205 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:H.98, F:C.100, F:C.103, F:C.109 SF4.19: 11 residues within 4Å: Chain G: V.283, S.454, C.455, G.456, K.457, C.458, C.461, S.499, C.501, L.503, G.504 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.455, G:C.458, G:C.461, G:C.501 SF4.24: 13 residues within 4Å: Chain I: R.62, H.166 Chain J: A.13, C.14, G.16, C.17, S.57, G.83, D.84, C.85, 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 NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.6: 20 residues within 4Å: Chain B: G.168, G.169, A.170, F.172, K.177, F.180, E.197, F.282, E.286, E.287, R.304, F.307, P.308, A.309, S.400, I.424, M.425, G.426, S.427 Ligands: FMN.8 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.282 Hydrogen bonds: B:K.177, B:E.197, B:E.287, B:S.427 Salt bridges: B:R.304, B:R.304 pi-Stacking: B:F.172, B:F.307, B:F.307 NAD.18: 20 residues within 4Å: Chain G: G.168, G.169, A.170, F.172, K.177, F.180, E.197, F.282, E.286, E.287, R.304, F.307, P.308, A.309, S.400, I.424, M.425, G.426, S.427 Ligands: FMN.20 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:F.282 Hydrogen bonds: G:K.177, G:E.197, G:E.287, G:S.427 Salt bridges: G:R.304, G:R.304 pi-Stacking: G:F.172, G:F.307, G:F.307

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.8: 21 residues within 4Å: Chain B: G.166, R.167, G.168, G.169, A.170, K.177, N.194, D.196, E.197, F.282, G.285, E.286, E.287, R.304, I.320, N.321, N.322, T.325, G.502, L.503 Ligands: NAD.6 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.503 Hydrogen bonds: B:G.168, B:G.169, B:A.170, B:N.194, B:N.194, B:E.287, B:R.304, B:N.321, B:N.322 Salt bridges: B:K.177 FMN.20: 21 residues within 4Å: Chain G: G.166, R.167, G.168, G.169, A.170, K.177, N.194, D.196, E.197, F.282, G.285, E.286, E.287, R.304, I.320, N.321, N.322, T.325, G.502, L.503 Ligands: NAD.18 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:L.503 Hydrogen bonds: G:G.168, G:G.169, G:A.170, G:N.194, G:N.194, G:E.287, G:R.304, G:N.321, G:N.322 Salt bridges: G:K.177

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

3NI.10: 5 residues within 4Å: Chain D: C.64, C.67, C.444, C.447 Ligands: FCO.11 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.64, D:C.67, D:C.444, D:C.447 3NI.22: 5 residues within 4Å: Chain I: C.64, C.67, C.444, C.447 Ligands: FCO.23 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.64, I:C.67, I:C.444, I:C.447

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

FCO.11: 13 residues within 4Å: Chain D: C.67, S.70, H.71, A.376, P.377, R.378, L.381, V.400, A.401, T.402, C.444, C.447 Ligands: 3NI.10 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.70, D:R.378, D:R.378, D:A.401, D:T.402 Metal complexes: D:C.67, D:C.447 FCO.23: 13 residues within 4Å: Chain I: C.67, S.70, H.71, A.376, P.377, R.378, L.381, V.400, A.401, T.402, C.444, C.447 Ligands: 3NI.22 7 PLIP interactions: 7 interactions with chain I Hydrogen bonds: I:S.70, I:R.378, I:R.378, 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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