SMTL ID : 9gnk.1

Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from CpI of Clostridium pasteurianum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-dimer

Ligands

2 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.1: 5 residues within 4Å: Chain A: C.178, P.203, F.296, V.302 Ligands: 402.2 No protein-ligand interaction detected (PLIP) CMO.13: 5 residues within 4Å: Chain B: C.178, P.203, F.296, V.302 Ligands: 402.14 No protein-ligand interaction detected (PLIP)

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

402.2: 22 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: CMO.1, 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.382 402.14: 22 residues within 4Å: Chain B: 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: CMO.13, SF4.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.109, B:I.204, B:K.237 Metal complexes: B:C.382

6 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: 402.2 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.179, A:C.234, A:C.378, A:C.382 SF4.4: 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 SF4.5: 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 SF4.15: 16 residues within 4Å: Chain B: 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: 402.14 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.179, B:C.234, B:C.378, B:C.382 SF4.16: 14 residues within 4Å: Chain B: 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 B, Metal complexes: B:C.45, B:C.66, B:C.69, B:C.72 SF4.17: 14 residues within 4Å: Chain B: 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 B, pi-Cation interactions: B:H.58 Metal complexes: B:C.35, B:C.38, B:C.41, B:C.76

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 6 residues within 4Å: Chain A: R.8, K.34, I.36, P.77, E.78, N.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.79 Salt bridges: A:E.78, A:E.78 EPE.18: 7 residues within 4Å: Chain A: H.441 Chain B: R.8, K.34, I.36, P.77, E.78, N.79 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.79 Salt bridges: B:E.78, B:E.78, A:H.441 Water bridges: A:H.441

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

PG4.7: 5 residues within 4Å: Chain A: K.357, D.361, K.364, A.365 Ligands: PEG.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.357, A:K.364 Water bridges: A:Y.190 PG4.11: 7 residues within 4Å: Chain A: Q.135, D.279, G.280, K.281, R.282, D.283, S.284 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.135, A:G.280, A:K.281, A:R.282 Water bridges: A:S.284 PG4.12: 10 residues within 4Å: Chain A: K.201, E.245, L.246, K.247, S.248, H.448, T.449, H.450, F.452 Chain B: K.268 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.245, A:F.452 Hydrogen bonds: A:T.449, A:H.450, A:H.450 Water bridges: A:S.248 PG4.19: 5 residues within 4Å: Chain B: K.357, D.361, K.364, A.365 Ligands: PEG.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.357, B:K.364 Water bridges: B:Y.190 PG4.23: 7 residues within 4Å: Chain B: Q.135, D.279, G.280, K.281, R.282, D.283, S.284 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.135, B:G.280, B:K.281, B:R.282 Water bridges: B:S.284 PG4.24: 9 residues within 4Å: Chain B: K.201, E.245, L.246, K.247, S.248, H.448, T.449, H.450, F.452 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:E.245, B:F.452 Hydrogen bonds: B:T.449, B:H.450, B:H.450 Water bridges: B:S.248

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 8 residues within 4Å: Chain A: P.46, T.47, A.48, Y.185, Y.189, Y.190, K.357 Ligands: PG4.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.47, A:Y.190, A:Y.190 PEG.9: 7 residues within 4Å: Chain A: D.21, P.22, D.23, Y.239, R.243, P.244, K.454 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.454 PEG.10: 5 residues within 4Å: Chain A: K.325, A.326, R.328, G.329, Y.410 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.328 PEG.20: 8 residues within 4Å: Chain B: P.46, T.47, A.48, Y.185, Y.189, Y.190, K.357 Ligands: PG4.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.47, B:Y.190, B:Y.190 PEG.21: 7 residues within 4Å: Chain B: D.21, P.22, D.23, Y.239, R.243, P.244, K.454 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.454 PEG.22: 5 residues within 4Å: Chain B: K.325, A.326, R.328, G.329, Y.410 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.328

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

2025-09-24

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

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