SMTL ID : 4gd3.6 (5 other biounits)

Structure of E. coli hydrogenase-1 in complex with cytochrome b

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: H.187, C.190, R.192, R.193, F.196, C.215, L.216, Y.217, C.221, G.223, P.224, I.243 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.187, A:C.190, A:C.215, A:C.221 SF4.2: 10 residues within 4Å: Chain A: T.226, N.228, C.230, W.235, C.242, C.249, L.250, G.251, C.252 Chain B: K.226 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.230, A:C.242, A:C.249, A:C.252

1 x F4S: FE4-S3 CLUSTER(Non-covalent)

F4S.3: 12 residues within 4Å: Chain A: C.17, T.18, C.19, C.20, E.76, G.113, T.114, C.115, C.120, C.149 Chain B: R.74, H.229 8 PLIP interactions: 8 interactions with chain A, Salt bridges: A:E.76 Metal complexes: A:C.17, A:C.19, A:C.19, A:C.20, A:C.115, A:C.120, A:C.149

2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.4: 4 residues within 4Å: Chain A: T.281, L.284, T.285, G.288 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.285, A:T.285 LMT.11: 5 residues within 4Å: Chain A: Q.203, K.218 Chain C: P.42, L.43, P.44 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.203, A:K.218, A:K.218

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

CL.5: 6 residues within 4Å: Chain A: E.22, R.26 Chain B: G.77, V.78, T.80, H.117 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: N.242, I.243, N.253, M.254 Ligand excluded by PLIP

1 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-covalent)

FCO.6: 13 residues within 4Å: Chain B: C.79, V.82, H.83, A.507, P.508, R.509, L.512, V.530, P.531, T.532, C.576, C.579 Ligands: NI.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.509, B:R.509, B:T.532 Metal complexes: B:C.79, B:C.579

1 x NI: NICKEL (II) ION(Non-covalent)

NI.7: 5 residues within 4Å: Chain B: C.76, C.79, C.576, C.579 Ligands: FCO.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.76, B:C.79, B:C.576, B:C.579

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain B: E.57, Q.527, C.528, H.582 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.57, B:C.528, B:H.582, H2O.1, H2O.1, H2O.1

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.10: 21 residues within 4Å: Chain C: L.32, M.33, G.36, Y.37, I.39, G.40, R.60, H.63, F.64, G.67, T.71, M.143, G.147, F.148, L.150, Y.151, H.181, H.184, R.185, M.188, I.191 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:L.32, C:L.32, C:I.39, C:F.64, C:F.148, C:F.148, C:L.150, C:I.191 Salt bridges: C:R.60, C:H.181, C:H.181, C:R.185 Metal complexes: C:H.63, C:H.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volbeda, A. et al., Crystal Structure of the O(2)-Tolerant Membrane-Bound Hydrogenase 1 from Escherichia coli in Complex with Its Cognate Cytochrome b. Structure (2013)

Release Date

2013-01-02

Peptides

Hydrogenase-1 small chain: A
Hydrogenase-1 large chain: B
Ni/Fe-hydrogenase 1 B-type cytochrome subunit: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
K

C
B

Hydrogenase-1 small chain

Hydrogenase-1 large chain

Ni/Fe-hydrogenase 1 B-type cytochrome subunit

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