SMTL ID : 9e15.3 (7 other biounits)

Alpha-Delta heterodimeric form of soluble hydrogenase I from Pyrococcus furiosus. Data processed and model refined in P1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: S.22, C.23, Y.24, G.25, C.26, A.94, C.95, G.144, C.145, P.146 Chain B: R.63, H.160 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B, Salt bridges: A:E.67 Metal complexes: A:C.23, A:C.26, A:C.95, A:C.145, B:H.160 SF4.2: 10 residues within 4Å: Chain A: T.197, C.201, R.204, C.205, P.206, C.212, I.213, G.214, C.215 Chain B: R.157 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.201, A:C.205, A:C.212, A:C.215 SF4.3: 11 residues within 4Å: Chain A: V.172, C.173, C.176, R.177, P.182, C.183, I.184, L.185, C.192, G.194, P.195 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.173, A:C.176, A:C.183, A:C.192

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

FCO.4: 11 residues within 4Å: Chain B: C.68, H.72, A.353, P.354, R.355, L.358, T.376, P.377, T.378, C.421 Ligands: NI.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.355, B:R.355, B:T.378, B:T.378 Metal complexes: B:C.68, B:C.421

1 x NI: NICKEL (II) ION(Non-covalent)

NI.5: 5 residues within 4Å: Chain B: C.65, C.68, C.418, C.421 Ligands: FCO.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.65, B:C.68, B:C.418, B:C.421

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.206 PO4.7: 1 residues within 4Å: Chain B: R.266 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.266

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

2025-07-16

Peptides

Sulfhydrogenase 1 subunit delta: A
Sulfhydrogenase 1 subunit alpha: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Sulfhydrogenase 1 subunit delta

Sulfhydrogenase 1 subunit alpha

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