SMTL ID : 3usc.3 (2 other biounits)

Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

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

SF4.1: 11 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, I.243 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.187, A:C.190, A:C.215, A:C.221 SF4.12: 12 residues within 4Å: Chain C: 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 C, Metal complexes: C:H.187, C:C.190, C:C.215, C:C.221

2 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.2: 10 residues within 4Å: Chain A: T.226, N.228, C.230, W.235, P.242, C.249, L.250, G.251, C.252 Chain B: K.226 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.230, A:C.249, A:C.252 F3S.13: 10 residues within 4Å: Chain C: T.226, N.228, C.230, W.235, P.242, C.249, L.250, G.251, C.252 Chain D: K.226 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.230, C:C.249, C:C.252

2 x SF3: FE4-S3 CLUSTER(Non-covalent)

SF3.3: 12 residues within 4Å: Chain A: E.16, C.17, T.18, C.19, C.20, E.76, T.114, C.115, C.120, G.148, C.149 Chain B: R.74 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 SF3.14: 12 residues within 4Å: Chain C: E.16, C.17, T.18, C.19, C.20, E.76, T.114, C.115, C.120, G.148, C.149 Chain D: R.74 8 PLIP interactions: 8 interactions with chain C, Salt bridges: C:E.76 Metal complexes: C:C.17, C:C.19, C:C.19, C:C.20, C:C.115, C:C.120, C:C.149

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

LMT.4: 10 residues within 4Å: Chain A: I.7, V.9, W.11, I.40, I.72, W.112, I.160, M.163, D.167, R.168 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.7, A:I.7, A:V.9, A:V.9, A:W.11, A:I.40, A:I.72, A:I.72, A:W.112, A:I.160, A:I.160, A:M.163 LMT.15: 11 residues within 4Å: Chain C: I.7, V.9, W.11, I.40, I.72, W.112, I.160, M.163, V.164, D.167, R.168 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.7, C:I.7, C:V.9, C:V.9, C:W.11, C:I.40, C:W.112, C:I.160, C:I.160, C:M.163, C:V.164

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

CL.5: 4 residues within 4Å: Chain A: T.114, W.118, C.120, G.256 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: I.12, H.13, D.46, K.98 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain C: T.114, W.118, G.119, C.120, G.256 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain C: I.12, H.13, D.46, K.98 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain C: D.173, R.174 Ligand excluded by PLIP

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 5 residues within 4Å: Chain A: R.211 Chain B: G.480, N.481, L.482, A.483 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.481, B:L.482, B:A.483 Salt bridges: A:R.211 SO4.19: 5 residues within 4Å: Chain C: R.211 Chain D: G.480, N.481, L.482, A.483 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:L.482, D:A.483 Salt bridges: C:R.211 SO4.20: 2 residues within 4Å: Chain C: K.218, R.266 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.218, C:R.266 SO4.24: 2 residues within 4Å: Chain D: W.373, R.394 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.394

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

FCO.8: 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: 3NI.9 7 PLIP interactions: 6 interactions with chain B, 1 Ligand-Water interactions Hydrogen bonds: B:R.509, B:R.509, B:T.532, B:T.532 Metal complexes: B:C.79, B:C.579, H2O.8 FCO.21: 12 residues within 4Å: Chain D: C.79, V.82, H.83, A.507, P.508, R.509, L.512, V.530, P.531, T.532, C.579 Ligands: 3NI.22 7 PLIP interactions: 6 interactions with chain D, 1 Ligand-Water interactions Hydrogen bonds: D:R.509, D:R.509, D:T.532, D:T.532 Metal complexes: D:C.79, D:C.579, H2O.31

2 x 3NI: NICKEL (III) ION(Non-covalent)

3NI.9: 5 residues within 4Å: Chain B: C.76, C.79, C.576, C.579 Ligands: FCO.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.76, B:C.79, B:C.576, B:C.579, H2O.8 3NI.22: 5 residues within 4Å: Chain D: C.76, C.79, C.576, C.579 Ligands: FCO.21 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.76, D:C.79, D:C.576, D:C.579, H2O.31

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 3 residues within 4Å: Chain B: E.57, 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.8, H2O.8, H2O.8 MG.23: 3 residues within 4Å: Chain D: E.57, C.528, H.582 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.57, D:C.528, D:H.582, H2O.31, H2O.31, H2O.31

1 x LI: LITHIUM ION(Non-covalent)

LI.11: 3 residues within 4Å: Chain B: N.14, N.390, Q.392 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volbeda, A. et al., X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-03-28

Peptides

Hydrogenase-1 small chain: AC
Hydrogenase-1 large chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

C
T

B
L

D
M

Hydrogenase-1 small chain

Hydrogenase-1 large chain

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