SMTL ID : 9nez.1

Structure of the Pyrococcus furiosus SHI complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.47 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: S.13, C.14, G.16, C.17, E.58, G.84, A.85, C.86, C.136, P.137 Chain D: R.63, H.160 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain A, Metal complexes: D:H.160, A:C.14, A:C.17, A:C.86, A:C.136 Salt bridges: A:E.58, A:E.58 SF4.2: 10 residues within 4Å: Chain A: C.192, R.195, C.196, P.197, C.203, I.204, C.206, R.207 Chain D: R.157, E.162 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D, Metal complexes: A:C.192, A:C.196, A:C.203, A:C.206 Salt bridges: D:E.162, D:E.162 SF4.3: 9 residues within 4Å: Chain A: C.164, C.167, R.168, C.174, I.175, C.183, G.185, P.186, P.197 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.164, A:C.167, A:C.174, A:C.183 SF4.4: 11 residues within 4Å: Chain B: C.233, L.234, A.235, C.236, G.237, I.238, C.239, Q.272, F.293, C.322, P.323 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.233, B:C.236, B:C.239, B:C.322 SF4.5: 10 residues within 4Å: Chain B: F.138, C.243, P.244, R.296, K.300, C.312, V.313, C.315, G.316, C.318 6 PLIP interactions: 6 interactions with chain B, pi-Cation interactions: B:F.328, B:F.328 Metal complexes: B:C.243, B:C.312, B:C.315, B:C.318 SF4.6: 9 residues within 4Å: Chain B: N.51, H.94, A.95, C.96, C.131, C.137, C.139, G.314, C.315 7 PLIP interactions: 7 interactions with chain B, Salt bridges: B:D.97 Metal complexes: B:H.94, B:C.96, B:C.131, B:C.137, B:C.137, B:C.139 SF4.7: 8 residues within 4Å: Chain B: N.240, C.246, R.247, C.248, C.271, R.296, C.299, K.300 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.246, B:C.248, B:C.271, B:C.299 SF4.11: 12 residues within 4Å: Chain E: S.13, C.14, G.16, C.17, E.58, G.84, A.85, C.86, C.136, P.137 Chain H: R.63, H.160 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain H, Salt bridges: E:E.58, E:E.58 Metal complexes: E:C.14, E:C.17, E:C.86, E:C.136, H:H.160 SF4.12: 8 residues within 4Å: Chain E: C.192, C.196, P.197, C.203, I.204, C.206, R.207 Chain H: R.157 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.192, E:C.196, E:C.203, E:C.206 SF4.13: 11 residues within 4Å: Chain E: C.164, C.167, R.168, P.173, C.174, I.175, L.176, C.183, G.185, P.186, P.197 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.164, E:C.167, E:C.174, E:C.183 SF4.14: 10 residues within 4Å: Chain F: C.233, L.234, A.235, C.236, G.237, I.238, C.239, Q.272, C.322, P.323 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.233, F:C.236, F:C.239, F:C.322 SF4.15: 12 residues within 4Å: Chain F: F.138, C.243, P.244, R.296, K.300, C.312, V.313, G.314, C.315, G.316, R.317, C.318 5 PLIP interactions: 5 interactions with chain F, pi-Cation interactions: F:F.328 Metal complexes: F:C.243, F:C.312, F:C.315, F:C.318 SF4.16: 9 residues within 4Å: Chain F: H.94, A.95, C.96, C.131, C.137, C.139, T.144, G.314, C.315 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.96, F:C.131, F:C.137, F:C.139 SF4.17: 9 residues within 4Å: Chain F: N.240, C.246, R.247, C.248, D.269, C.271, R.296, C.299, K.300 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.246, F:C.248, F:C.271, F:C.299

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

FES.8: 10 residues within 4Å: Chain C: M.251, C.253, G.254, G.256, K.257, C.258, G.259, C.261, Y.271, C.273 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.253, C:C.258, C:C.261, C:C.273 FES.18: 10 residues within 4Å: Chain G: M.251, C.253, G.254, G.256, K.257, C.258, G.259, C.261, Y.271, C.273 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.253, G:C.258, G:C.261, G:C.273

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.9: 21 residues within 4Å: Chain B: V.279, A.280 Chain C: E.65, V.66, P.67, I.68, S.69, C.83, I.84, R.85, G.88, R.89, V.90, T.91, L.130, A.133, E.248, R.249, R.250, M.251, K.252 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:P.67, C:E.248 Hydrogen bonds: C:E.65, C:P.67, C:S.69, C:C.83, C:R.85, C:R.89, C:V.90, C:T.91, C:E.248, C:M.251, B:A.280 FAD.19: 21 residues within 4Å: Chain F: V.279, A.280 Chain G: E.65, V.66, P.67, I.68, S.69, C.83, I.84, R.85, G.88, R.89, V.90, T.91, L.130, A.133, E.248, R.249, R.250, M.251, K.252 13 PLIP interactions: 12 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:P.67, G:E.248 Hydrogen bonds: G:E.65, G:P.67, G:S.69, G:C.83, G:R.85, G:R.89, G:V.90, G:T.91, G:E.248, G:M.251, F:A.280

2 x NFU: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)(Covalent)(Non-covalent)

NFU.10: 11 residues within 4Å: Chain D: C.65, F.67, C.68, S.69, H.72, R.355, L.358, T.376, P.377, C.418, C.421 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:C.68, D:R.355 Metal complexes: D:C.418, D:C.421, D:C.421 NFU.20: 14 residues within 4Å: Chain H: E.17, C.65, C.68, A.71, H.72, A.353, P.354, R.355, L.358, T.376, P.377, T.378, C.418, C.421 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:R.355, H:T.378 Metal complexes: H:C.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, X. et al., Structural insights into the biotechnologically relevant reversible NADPH-oxidizing NiFe-hydrogenase from P.furiosus. Structure (2025)

Release Date

2025-07-09

Peptides

Sulfhydrogenase 1 subunit delta: AE
Sulfhydrogenase 1 subunit beta: BF
Sulfhydrogenase 1 subunit gamma: CG
Sulfhydrogenase 1 subunit alpha: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

Sulfhydrogenase 1 subunit delta

Sulfhydrogenase 1 subunit beta

Sulfhydrogenase 1 subunit gamma

Sulfhydrogenase 1 subunit alpha

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