SMTL ID : 8rtg.1

Desulfovibrio desulfuricans [FeFe] hydrogenase in apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 15 residues within 4Å: Chain A: C.69, C.179, P.180, G.181, P.233, C.234, A.236, K.237, M.376, A.377, C.378, G.381, C.382, G.385, G.386 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.179, A:C.234, A:C.378, A:C.382 SF4.2: 14 residues within 4Å: Chain A: V.28, C.45, P.46, T.47, A.49, I.50, I.60, C.66, I.67, N.68, C.69, G.70, Q.71, C.72 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.45, A:C.66, A:C.69, A:C.72 SF4.3: 14 residues within 4Å: Chain A: I.30, C.35, I.36, G.37, C.38, D.39, T.40, C.41, H.58, C.76, P.77, E.78, A.80, I.81 5 PLIP interactions: 5 interactions with chain A, pi-Cation interactions: A:H.58 Metal complexes: A:C.35, A:C.38, A:C.41, A:C.76

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 6 residues within 4Å: Chain A: T.145, S.202, P.203, I.204, M.232, K.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.202, A:I.204, A:K.237

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

CL.5: 6 residues within 4Å: Chain A: A.107, P.108, A.109, P.233, G.297, C.382 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bikbaev, K. et al., Structure of [FeFe] hydrogenase in the holo and apo forms at room temperature. To Be Published

Release Date

2025-02-12

Peptides

Periplasmic [Fe] hydrogenase large subunit: A
Periplasmic [Fe] hydrogenase small subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Periplasmic [Fe] hydrogenase large subunit

Periplasmic [Fe] hydrogenase small subunit

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