- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.20 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.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
10 PLIP interactions:8 interactions with chain A, 2 Ligand-Water 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, H2O.1, H2O.10
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
10 PLIP interactions:8 interactions with chain C, 2 Ligand-Water 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, H2O.30, H2O.36
- 2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
LMT.4: 9 residues within 4Å:- Chain A: I.7, V.9, W.11, I.72, W.112, I.160, M.163, V.164, R.168
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:I.7, A:I.7, A:V.9, A:V.9, A:W.11, A:I.72, A:W.112, A:I.160, A:M.163, A:V.164
LMT.15: 8 residues within 4Å:- Chain C: I.7, V.9, W.11, I.40, I.72, I.160, M.163, V.164
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:I.72, C:I.160, C:M.163, C:V.164
- Water bridges: C:L.169
- 3 x CL: CHLORIDE ION(Non-functional Binders)
- 4 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 3 residues within 4Å:- Chain A: R.125, P.126, N.127
3 PLIP interactions:3 interactions with chain A- Water bridges: A:R.125, A:D.259
- Salt bridges: A:R.125
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:G.480, B:L.482, B:A.483
- Salt bridges: A:R.211
SO4.18: 3 residues within 4Å:- Chain C: D.173, R.174, L.179
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:R.174
- Salt bridges: C:R.174
SO4.22: 2 residues within 4Å:- Chain D: R.394
- Ligands: TRS.24
2 PLIP interactions:2 interactions with chain D- Water bridges: D:R.394
- 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: NI.9
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Hydrogen bonds: B:R.509, B:R.509, B:T.532
- Metal complexes: B:C.579, H2O.22
FCO.19: 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.20
5 PLIP interactions:4 interactions with chain D, 1 Ligand-Water interactions- Hydrogen bonds: D:R.509, D:R.509, D:T.532
- Metal complexes: D:C.579, H2O.47
- 2 x NI: NICKEL (II) ION(Non-covalent)
NI.9: 5 residues within 4Å:- Chain B: C.76, C.79, C.576, C.579
- Ligands: FCO.8
4 PLIP interactions:3 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:C.76, B:C.576, B:C.579, H2O.22
NI.20: 5 residues within 4Å:- Chain D: C.76, C.79, C.576, C.579
- Ligands: FCO.19
4 PLIP interactions:3 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:C.76, D:C.576, D:C.579, H2O.47
- 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.11, H2O.11, H2O.11
MG.21: 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.37, H2O.37, H2O.37
- 2 x LI: LITHIUM ION(Non-covalent)
- 1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Carr, S.B. et al., Kinetic consequences of re-engineering the outer shell "canopy" above the active site of a [NiFe]-hydrogenase. To Be Published
- Release Date
- 2017-08-16
- 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 1.20 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 2 x F3S: FE3-S4 CLUSTER(Non-covalent)
- 2 x SF3: FE4-S3 CLUSTER(Non-covalent)
- 2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
- 3 x CL: CHLORIDE ION(Non-functional Binders)
- 4 x SO4: SULFATE 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 LI: LITHIUM ION(Non-covalent)
- 1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Carr, S.B. et al., Kinetic consequences of re-engineering the outer shell "canopy" above the active site of a [NiFe]-hydrogenase. To Be Published
- Release Date
- 2017-08-16
- Peptides
- Hydrogenase-1 small chain: AC
Hydrogenase-1 large chain: BD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
SC
TB
LD
M