SMTL ID : 9e1j.1 (1 other biounit)

Alpha-Delta heterodimeric form of soluble hydrogenase I from Pyrococcus furiosus. Data processed and model refined in P21221

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 14 residues within 4Å: Chain A: S.12, C.13, Y.14, G.15, C.16, E.57, G.83, A.84, C.85, G.134, C.135, P.136 Chain B: R.58, H.155 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.57 Metal complexes: A:C.13, A:C.16, A:C.85, A:C.135 SF4.2: 11 residues within 4Å: Chain A: T.187, C.191, R.194, C.195, P.196, C.202, I.203, G.204, C.205, R.206 Chain B: R.152 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.191, A:C.195, A:C.202, A:C.205 SF4.3: 11 residues within 4Å: Chain A: V.162, C.163, C.166, C.173, I.174, L.175, C.182, G.184, P.185, P.196, F.216 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.163, A:C.166, A:C.173, A:C.182

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

FCO.4: 11 residues within 4Å: Chain B: C.63, H.67, A.348, P.349, R.350, L.353, T.371, P.372, T.373, C.416 Ligands: NI.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.350, B:R.350, B:T.373, B:T.373 Metal complexes: B:C.63, B:C.416

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

NI.5: 5 residues within 4Å: Chain B: C.60, C.63, C.413, C.416 Ligands: FCO.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.60, B:C.63, B:C.413, B:C.416

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 1 residues within 4Å: Chain B: M.405 Ligand excluded by PLIP

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
A

B
B

Sulfhydrogenase 1 subunit delta

Sulfhydrogenase 1 subunit alpha

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