SMTL ID : 9gz4.1

FeFe Hydrogenase from Desulfovibrio desulfuricans labelled with cyanophenylalanine - reduced state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.96 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 16 residues within 4Å: Chain A: C.68, C.178, P.179, G.180, P.232, C.233, A.235, K.236, M.375, A.376, C.377, G.380, C.381, G.384, G.385 Ligands: 4WW.4 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.178, A:C.233, A:C.377, A:C.381 SF4.2: 14 residues within 4Å: Chain A: V.27, C.44, P.45, T.46, A.48, I.49, I.59, C.65, I.66, N.67, C.68, G.69, Q.70, C.71 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.44, A:C.65, A:C.68, A:C.71 SF4.3: 14 residues within 4Å: Chain A: I.29, C.34, I.35, G.36, C.37, D.38, T.39, C.40, H.57, C.75, P.76, E.77, A.79, I.80 5 PLIP interactions: 5 interactions with chain A, pi-Cation interactions: A:H.57 Metal complexes: A:C.34, A:C.37, A:C.40, A:C.75

1 x 4WW: bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+)(Non-covalent)

4WW.4: 20 residues within 4Å: Chain A: A.106, P.107, A.108, T.144, A.148, C.177, C.178, S.201, P.202, I.203, M.231, P.232, C.233, K.236, F.295, G.296, V.301, M.375, C.381 Ligands: SF4.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.108, A:I.203, A:K.236 Metal complexes: A:C.381

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

CL.5: 5 residues within 4Å: Chain A: Y.43, H.74 Chain B: I.4, P.86, Y.87 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: H.13, P.15, D.16, A.19, L.24 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: V.124, T.126, G.127 Ligand excluded by PLIP

1 x LI: LITHIUM ION(Non-covalent)

LI.8: 6 residues within 4Å: Chain A: K.18, A.19, D.20, P.21, L.241, P.243 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.19, A:L.241, H2O.5, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duan, Z. et al., Cyanophenylalanine as an Infrared Probe for Iron-Sulfur Cluster Redox State in Multicenter Metalloenzymes. Chembiochem (2025)

Release Date

2025-05-28

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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