- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.30 Å
- Oligo State
- hetero-2-2-1-mer
- Ligands
- 4 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 2 x F4S: FE4-S3 CLUSTER(Non-covalent)
F4S.3: 11 residues within 4Å:- Chain A: C.17, T.18, C.19, C.20, 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
F4S.12: 12 residues within 4Å:- Chain C: C.17, T.18, C.19, C.20, E.76, G.113, T.114, C.115, C.120, C.149
- Chain D: R.74, H.229
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
- 5 x CL: CHLORIDE ION(Non-functional Binders)
CL.4: 5 residues within 4Å:- Chain A: W.118, G.119, C.120, N.255, G.256
Ligand excluded by PLIPCL.5: 3 residues within 4Å:- Chain A: H.29, D.237
- Chain D: L.259
Ligand excluded by PLIPCL.9: 2 residues within 4Å:- Chain B: F.212, R.266
Ligand excluded by PLIPCL.14: 6 residues within 4Å:- Chain C: E.22, R.26
- Chain D: G.77, V.78, T.80, H.117
Ligand excluded by PLIPCL.18: 5 residues within 4Å:- Chain A: M.180
- Chain D: N.242, I.243, N.253, M.254
Ligand excluded by PLIP- 2 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
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:R.509, B:R.509, B:T.532, B:T.532
- Metal complexes: B:C.79, B:C.579
FCO.15: 13 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.576, C.579
- Ligands: NI.16
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:R.509, D:R.509, D:T.532
- Metal complexes: D:C.79, D:C.579
- 2 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
NI.16: 5 residues within 4Å:- Chain D: C.76, C.79, C.576, C.579
- Ligands: FCO.15
4 PLIP interactions:4 interactions with chain D- Metal complexes: D:C.76, D:C.79, D:C.576, D:C.579
- 2 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
MG.17: 4 residues within 4Å:- Chain D: E.57, Q.527, 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.1, H2O.1, H2O.1
- 2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
LMT.13: 4 residues within 4Å:- Chain C: T.281, L.284, T.285, G.288
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:T.285, C:T.285
LMT.20: 5 residues within 4Å:- Chain C: Q.203, K.218
- Chain E: P.42, L.43, P.44
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:Q.203, C:K.218, C:K.218
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.19: 21 residues within 4Å:- Chain E: 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 E,- Hydrophobic interactions: E:L.32, E:L.32, E:I.39, E:F.64, E:F.148, E:F.148, E:L.150, E:I.191
- Salt bridges: E:R.60, E:H.181, E:H.181, E:R.185
- Metal complexes: E:H.63, E: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: AC
Hydrogenase-1 large chain: BD
Ni/Fe-hydrogenase 1 B-type cytochrome subunit: E - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
QC
RB
JD
KE
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.30 Å
- Oligo State
- hetero-2-2-1-mer
- Ligands
- 4 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 2 x F4S: FE4-S3 CLUSTER(Non-covalent)
- 5 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-covalent)
- 2 x NI: NICKEL (II) ION(Non-covalent)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 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: AC
Hydrogenase-1 large chain: BD
Ni/Fe-hydrogenase 1 B-type cytochrome subunit: E - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
QC
RB
JD
KE
B