SMTL ID : 9e15.5 (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(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 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.67 Metal complexes: A:C.23, A:C.26, A:C.95, A:C.145 SF4.2: 10 residues within 4Å: Chain A: T.197, C.201, R.204, C.205, P.206, C.212, I.213, C.215, R.216 Chain B: R.157 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B, Salt bridges: A:E.148, B:E.162 Metal complexes: A:C.201, A:C.205, A:C.212, A:C.215 SF4.3: 10 residues within 4Å: Chain A: V.172, C.173, C.176, C.183, I.184, L.185, C.192, P.195, P.206, F.226 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.173, A:C.176, A:C.183, A:C.192

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

PO4.4: 1 residues within 4Å: Chain A: Q.38 No protein-ligand interaction detected (PLIP) PO4.7: 3 residues within 4Å: Chain B: E.365, N.366, R.368 No protein-ligand interaction detected (PLIP)

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

FCO.5: 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.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.355, B:R.355, B:T.378 Metal complexes: B:C.68, B:C.421

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

NI.6: 5 residues within 4Å: Chain B: C.65, C.68, C.418, C.421 Ligands: FCO.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.65, B:C.68, B:C.418, B:C.421

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
I

B
J

Sulfhydrogenase 1 subunit delta

Sulfhydrogenase 1 subunit alpha

Related Entries With Identical Sequence