SMTL ID : 9gbu.2 (1 other biounit)

Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from a group A1 type [FeFe]-hydrogenase of Solobacterium moorei

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 7 residues within 4Å: Chain A: L.172, P.173, K.346, S.368, P.369, Y.370, H.371 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.172, A:K.346 MPD.2: 7 residues within 4Å: Chain A: L.164, T.165, V.314, T.343, D.344, V.345, H.371 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.165

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

SF4.3: 16 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 Ligands: 402.4 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.179, A:C.234, A:C.378, A:C.382 SF4.5: 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 SF4.6: 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

1 x 402: dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)(Non-covalent)

402.4: 21 residues within 4Å: Chain A: A.107, P.108, A.109, T.145, A.149, C.178, C.179, P.180, S.202, P.203, I.204, M.232, P.233, C.234, K.237, F.296, G.297, V.302, M.376, C.382 Ligands: SF4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.109, A:I.204, A:K.237 Metal complexes: A:C.382

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bikbaev, K. et al., Enhancing maturation of [FeFe]-hydrogenase by interlinking the large and small subunits. To Be Published

Release Date

2025-08-13

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit

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