SMTL ID : 9nf0.1

Structure of the NADPH-bound Pyrococcus furiosus SHI complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.06 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: S.13, C.14, Y.15, G.16, C.17, A.85, C.86, C.136, P.137 Chain D: R.63, H.160 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D, Salt bridges: A:E.58 Metal complexes: A:C.14, A:C.17, A:C.86, A:C.136, D:H.160 SF4.2: 10 residues within 4Å: Chain A: T.188, C.192, R.195, C.196, P.197, C.203, I.204, G.205, C.206, R.207 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D, Metal complexes: A:C.192, A:C.196, A:C.203, A:C.206 Salt bridges: D:E.162 SF4.3: 10 residues within 4Å: Chain A: C.164, C.167, R.168, C.174, I.175, L.176, 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: 12 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, A.324 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.233, B:C.236, B:C.239, B:C.322 SF4.5: 12 residues within 4Å: Chain B: F.138, T.242, C.243, P.244, R.296, K.300, C.312, V.313, C.315, G.316, R.317, C.318 5 PLIP interactions: 5 interactions with chain B, pi-Cation interactions: B:F.328 Metal complexes: B:C.243, B:C.312, B:C.315, B:C.318 SF4.6: 10 residues within 4Å: Chain B: N.51, H.94, A.95, C.96, C.131, P.133, C.137, C.139, G.314, C.315 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.96, B:C.131, B:C.137, B:C.139 SF4.7: 11 residues within 4Å: Chain B: N.240, C.246, R.247, C.248, D.269, C.271, H.276, N.295, 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 SF4.13: 10 residues within 4Å: Chain E: T.188, C.192, R.195, C.196, P.197, C.203, I.204, G.205, C.206, R.207 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain H, Metal complexes: E:C.192, E:C.196, E:C.203, E:C.206 Salt bridges: H:E.162 SF4.14: 13 residues within 4Å: Chain E: S.13, C.14, G.16, C.17, E.58, G.84, A.85, C.86, G.135, C.136, P.137 Chain H: R.63, H.160 5 PLIP interactions: 5 interactions with chain E, Salt bridges: E:E.58 Metal complexes: E:C.14, E:C.17, E:C.86, E:C.136 SF4.15: 10 residues within 4Å: Chain E: C.164, C.167, R.168, 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 SF4.16: 12 residues within 4Å: Chain F: C.233, L.234, A.235, C.236, G.237, I.238, C.239, Q.272, F.293, C.322, P.323, A.324 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.233, F:C.236, F:C.239, F:C.322 SF4.17: 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 SF4.18: 12 residues within 4Å: Chain F: N.240, C.246, R.247, C.248, D.269, S.270, C.271, N.295, R.296, C.299, K.300 Chain G: N.262 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.246, F:C.248, F:C.271, F:C.299 SF4.19: 10 residues within 4Å: Chain F: N.51, H.94, C.96, C.131, P.133, C.137, C.139, F.204, 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

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

FES.8: 10 residues within 4Å: Chain C: M.251, K.252, C.253, G.254, G.256, K.257, C.258, G.259, C.261, 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.20: 10 residues within 4Å: Chain G: M.251, K.252, C.253, G.254, G.256, K.257, C.258, G.259, C.261, 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: 22 residues within 4Å: Chain B: V.279, A.280 Chain C: F.55, E.65, V.66, P.67, I.68, S.69, C.83, I.84, R.85, A.87, G.88, R.89, V.90, T.91, L.130, E.248, R.249, R.250, M.251, K.252 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.55, C:E.248 Hydrogen bonds: C:E.65, C:P.67, C:S.69, C:C.83, C:R.85, C:G.88, C:R.89, C:V.90, C:T.91, C:T.91, C:T.91, C:E.248, C:M.251, C:K.252, C:K.252, B:A.280 FAD.21: 23 residues within 4Å: Chain F: V.279, A.280 Chain G: F.55, E.65, V.66, P.67, I.68, S.69, C.83, I.84, R.85, A.87, G.88, R.89, V.90, T.91, L.130, E.248, R.249, R.250, M.251, K.252 Ligands: NAP.22 15 PLIP interactions: 15 interactions with chain G Hydrophobic interactions: G:F.55, G:P.67, G:E.248 Hydrogen bonds: G:E.65, G:P.67, G:S.69, G:C.83, G:R.85, G:G.88, G:R.89, G:V.90, G:T.91, G:T.91, G:E.248, G:M.251

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Covalent)

NAP.10: 20 residues within 4Å: Chain C: R.85, A.128, G.129, L.130, G.131, T.132, P.134, A.158, R.159, T.189, R.190, R.200, P.201, G.221, P.222, R.224, M.225, S.228, T.246, E.248 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:E.248 Hydrogen bonds: C:S.69, C:R.85, C:L.130, C:L.130, C:A.158, C:R.159, C:T.189, C:R.200, C:R.224, C:S.228 Salt bridges: C:R.85, C:R.159, C:R.159, C:R.200, C:R.224 pi-Cation interactions: C:R.200, C:R.200 NAP.22: 22 residues within 4Å: Chain G: R.85, A.128, G.129, L.130, G.131, P.134, A.158, R.159, T.189, R.190, R.200, P.201, Q.202, C.220, G.221, P.222, R.224, M.225, S.228, T.246, E.248 Ligands: FAD.21 16 PLIP interactions: 16 interactions with chain G Hydrophobic interactions: G:P.134 Hydrogen bonds: G:L.130, G:A.158, G:R.159, G:T.189, G:R.200, G:Q.202, G:S.228 Salt bridges: G:R.85, G:R.159, G:R.159, G:R.190, G:R.200, G:R.224 pi-Cation interactions: G:R.200, G:R.200

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

NFU.11: 13 residues within 4Å: Chain D: 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 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.355, D:T.378, D:T.378 Metal complexes: D:C.68, D:C.68 NFU.23: 13 residues within 4Å: Chain H: 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 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:R.355, H:R.355, H:T.378, H:T.378 Metal complexes: H:C.68, H:C.68

2 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 3 residues within 4Å: Chain D: E.46, I.374, H.424 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.46, D:I.374, D:H.424 MG.24: 4 residues within 4Å: Chain H: E.46, E.250, I.374, H.424 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.46, H:I.374, H:H.424

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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