SMTL ID : 8ru6.1

Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 4 amino acid linker peptide derived from CpI of Clostridium pasteurianum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

monomer

Ligands

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 7 residues within 4Å: Chain A: P.46, T.47, Y.185, Y.189, Y.190, K.357, K.364 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.190 PG4.2: 10 residues within 4Å: Chain A: E.90, K.94, V.100, K.212, K.224, Q.225, V.226, Y.227, D.255 Ligands: PG4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.94, A:Q.225 Water bridges: A:Q.225 PG4.3: 6 residues within 4Å: Chain A: E.90, K.93, K.94, D.97, V.100 Ligands: PG4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.94, A:D.97 Water bridges: A:K.94 PG4.4: 3 residues within 4Å: Chain A: T.462, A.463, K.465 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.465

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

SF4.5: 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 SF4.6: 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: MHX.8 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.179, A:C.234, A:C.378, A:C.382 SF4.7: 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 MHX: Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form)(Non-covalent)

MHX.8: 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: SF4.6 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

2025-02-12

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

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