SMTL ID : 8rxj.1

Desulfovibrio desulfuricans [FeFe] hydrogenase C178A mutant in Hinact-like state derivatized with krypton

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

hetero-1-1-mer

Ligands

10 x KR: KRYPTON(Non-covalent)

KR.1: 7 residues within 4Å: Chain A: I.153, E.156, T.176, V.302, A.306, F.372 Ligands: KR.8 No protein-ligand interaction detected (PLIP) KR.2: 5 residues within 4Å: Chain A: F.160, A.306, L.307, A.310, F.372 No protein-ligand interaction detected (PLIP) KR.3: 7 residues within 4Å: Chain A: F.160, V.161, L.164, A.310, V.314, V.340, V.345 No protein-ligand interaction detected (PLIP) KR.4: 4 residues within 4Å: Chain A: F.309, E.312, A.313 Chain B: Q.28 No protein-ligand interaction detected (PLIP) KR.5: 7 residues within 4Å: Chain A: S.202, I.204, G.205, E.240, G.241, L.246, I.254 No protein-ligand interaction detected (PLIP) KR.6: 8 residues within 4Å: Chain A: T.47, E.64, A.65, I.67, K.184, Y.185, T.188, Y.189 No protein-ligand interaction detected (PLIP) KR.7: 5 residues within 4Å: Chain A: L.134, Q.135, F.139, H.141, C.142 No protein-ligand interaction detected (PLIP) KR.8: 6 residues within 4Å: Chain A: E.156, G.157, F.160, A.306, F.372 Ligands: KR.1 No protein-ligand interaction detected (PLIP) KR.9: 7 residues within 4Å: Chain A: V.327, K.334, E.335, A.336, V.347, A.348, V.349 No protein-ligand interaction detected (PLIP) KR.10: 5 residues within 4Å: Chain A: L.307, A.310, Y.311, V.338, V.340 No protein-ligand interaction detected (PLIP)

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

402.11: 22 residues within 4Å: Chain A: A.107, P.108, A.109, T.145, A.149, A.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: SF4.12, CYN.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.109, A:I.204, A:K.237 Metal complexes: A:C.382

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

SF4.12: 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: 402.11 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.179, A:C.234, A:C.378, A:C.382 SF4.13: 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 SF4.14: 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 CYN: CYANIDE ION(Non-covalent)

CYN.15: 5 residues within 4Å: Chain A: A.178, P.203, F.296, V.302 Ligands: 402.11 No protein-ligand interaction detected (PLIP)

1 x TOE: 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL(Non-covalent)

TOE.16: 9 residues within 4Å: Chain A: P.46, T.47, A.48, Y.185, Y.189, Y.190, K.357 Chain B: A.78, F.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.185, A:Y.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bikbaev, K. et al., Krypton Derivatization of [FeFe] Hydrogenase from Desulfovibrio desulfuricans Reveals its Gas Channel. To Be Published

Release Date

2025-02-19

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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