- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.67 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 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.16: 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
- 4 x F4S: FE4-S3 CLUSTER(Non-covalent)
F4S.3: 12 residues within 4Å:- Chain A: E.16, C.17, T.18, C.19, C.20, T.114, C.115, C.120, G.148, C.149
- Chain B: R.74
- Ligands: SF3.4
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.4: 13 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
- Ligands: F4S.3
9 PLIP interactions:8 interactions with chain A, 1 Ligand-Ligand interactions- 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, SF3.4
F4S.17: 12 residues within 4Å:- Chain C: E.16, C.17, T.18, C.19, C.20, T.114, C.115, C.120, G.148, C.149
- Chain D: R.74
- Ligands: SF3.18
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
F4S.18: 13 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
- Ligands: F4S.17
9 PLIP interactions:8 interactions with chain C, 1 Ligand-Ligand interactions- 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, SF3.18
- 2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
LMT.5: 11 residues within 4Å:- Chain A: I.7, V.9, W.11, I.40, I.72, I.160, M.163, V.164, D.167, R.168, L.169
11 PLIP interactions:11 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.160, A:I.160, A:M.163, A:V.164
LMT.19: 10 residues within 4Å:- Chain C: I.7, V.9, W.11, I.40, I.72, I.160, M.163, V.164, D.167, R.168
9 PLIP interactions:9 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:I.160, C:M.163, C:V.164
- 6 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 5 residues within 4Å:- Chain A: R.211
- Chain B: G.480, N.481, L.482, A.483
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:L.482, B:A.483
- Salt bridges: A:R.211
SO4.7: 2 residues within 4Å:- Chain A: K.218, R.266
2 PLIP interactions:2 interactions with chain A- Salt bridges: A:K.218, A:R.266
SO4.20: 5 residues within 4Å:- Chain C: R.211
- Chain D: G.480, N.481, L.482, A.483
3 PLIP interactions:1 interactions with chain C, 2 interactions with chain D- Salt bridges: C:R.211
- Hydrogen bonds: D:L.482, D:A.483
SO4.21: 3 residues within 4Å:- Chain C: Q.203, K.218, R.266
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:Q.203
- Salt bridges: C:K.218, C:R.266
SO4.22: 2 residues within 4Å:- Chain C: D.173, R.174
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:R.174
- Salt bridges: C:R.174
SO4.27: 2 residues within 4Å:- Chain D: N.375, R.394
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:N.375
- Salt bridges: D:R.394
- 3 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-covalent)
FCO.9: 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.10
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.24: 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: 3NI.26
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.10: 5 residues within 4Å:- Chain B: C.76, C.79, C.576, C.579
- Ligands: FCO.9
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.26: 5 residues within 4Å:- Chain D: C.76, C.79, C.576, C.579
- Ligands: FCO.24
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.11: 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.25: 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
- 2 x LI: LITHIUM ION(Non-covalent)
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.13: 3 residues within 4Å:- Chain B: F.331, H.421, Q.446
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:Q.446
- Water bridges: B:D.298, B:G.329, B:S.443, B:Q.446
GOL.14: 7 residues within 4Å:- Chain B: L.135, L.179, F.182, R.183, N.184, G.185, W.187
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:N.184, B:G.185
- 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
SC
TB
LD
M
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.67 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 2 x F3S: FE3-S4 CLUSTER(Non-covalent)
- 4 x F4S: FE4-S3 CLUSTER(Non-covalent)
- 2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
- 6 x SO4: SULFATE ION(Non-functional Binders)
- 3 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-covalent)
- 2 x 3NI: NICKEL (III) ION(Non-covalent)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 2 x LI: LITHIUM ION(Non-covalent)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- 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
SC
TB
LD
M