- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.64 Å
- Oligo State
- homo-dimer
- Ligands
- 8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 4 x BEN: BENZAMIDINE(Non-functional Binders)
BEN.5: 5 residues within 4Å:- Chain A: F.189, E.190, P.253, E.254
- Ligands: PGE.17
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:F.189, A:P.253, A:E.254
- Hydrogen bonds: A:E.190, A:E.254
BEN.12: 4 residues within 4Å:- Chain A: A.257, E.260, M.261
- Ligands: PGE.17
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:E.260
- Water bridges: A:E.260
BEN.24: 5 residues within 4Å:- Chain B: F.189, E.190, P.253, E.254
- Ligands: PGE.36
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:F.189, B:P.253, B:E.254
- Hydrogen bonds: B:E.190, B:E.254, B:E.254
BEN.31: 4 residues within 4Å:- Chain B: A.257, E.260, M.261
- Ligands: PGE.36
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:E.260
- Water bridges: B:E.260, B:E.260
- 10 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 3 residues within 4Å:- Chain A: R.252, R.298, N.299
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.299
- Salt bridges: A:R.252, A:R.298
SO4.7: 3 residues within 4Å:- Chain A: D.309, Y.310, R.311
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.310, A:R.311
- Salt bridges: A:R.311
SO4.8: 1 residues within 4Å:- Chain A: R.292
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:R.292
SO4.9: 4 residues within 4Å:- Chain A: F.68, P.69, G.70, K.194
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:F.68, A:G.70
- Salt bridges: A:K.194
SO4.10: 1 residues within 4Å:- Chain A: R.122
3 PLIP interactions:3 interactions with chain A- Water bridges: A:R.122, A:R.122
- Salt bridges: A:R.122
SO4.25: 3 residues within 4Å:- Chain B: R.252, R.298, N.299
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:N.299
- Salt bridges: B:R.252, B:R.298
SO4.26: 3 residues within 4Å:- Chain B: D.309, Y.310, R.311
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Y.310, B:R.311
- Salt bridges: B:R.311
SO4.27: 1 residues within 4Å:- Chain B: R.292
1 PLIP interactions:1 interactions with chain B- Salt bridges: B:R.292
SO4.28: 4 residues within 4Å:- Chain B: F.68, P.69, G.70, K.194
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:F.68, B:G.70
- Salt bridges: B:K.194
SO4.29: 1 residues within 4Å:- Chain B: R.122
3 PLIP interactions:3 interactions with chain B- Water bridges: B:R.122, B:R.122
- Salt bridges: B:R.122
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.11: 24 residues within 4Å:- Chain A: M.16, L.20, I.24, L.38, L.41, D.42, D.43, D.59, D.84, T.223, R.224, C.338
- Chain B: N.97, M.99, T.130, G.131, D.132, T.133, K.134
- Ligands: MG.1, MG.2, MG.3, MG.4, PO4.19
19 PLIP interactions:11 interactions with chain A, 8 interactions with chain B- Hydrogen bonds: A:L.41, A:T.223, A:R.224, B:N.97, B:T.130, B:G.131, B:D.132, B:T.133, B:T.133
- Water bridges: A:D.42, A:T.223, A:T.223, A:R.224, A:R.224, A:R.224, B:T.133
- Salt bridges: A:R.224, A:R.224, B:K.134
ATP.30: 24 residues within 4Å:- Chain A: N.97, M.99, T.130, G.131, D.132, T.133, K.134
- Chain B: M.16, L.20, I.24, L.38, L.41, D.42, D.43, D.59, D.84, T.223, R.224, C.338
- Ligands: MG.20, MG.21, MG.22, MG.23, PO4.38
18 PLIP interactions:11 interactions with chain B, 7 interactions with chain A- Hydrogen bonds: B:L.41, B:T.223, B:R.224, A:N.97, A:T.130, A:T.130, A:G.131, A:T.133
- Water bridges: B:D.42, B:T.223, B:T.223, B:R.224, B:R.224, B:R.224, A:T.133
- Salt bridges: B:R.224, B:R.224, A:K.134
- 6 x GOL: GLYCEROL(Non-functional Binders)
GOL.13: 6 residues within 4Å:- Chain A: S.32, G.35, I.36, G.37, D.39, A.40
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.32, A:S.32, A:G.37
GOL.14: 3 residues within 4Å:- Chain A: K.64, P.65, R.184
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.184
- Water bridges: A:E.141, A:E.141, A:E.141
GOL.15: 7 residues within 4Å:- Chain A: T.172, D.175, K.194, S.195, D.196, R.252, K.274
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:K.194, A:R.252, A:K.274, A:K.274
- Water bridges: A:R.298, A:R.298
GOL.32: 6 residues within 4Å:- Chain B: S.32, G.35, I.36, G.37, D.39, A.40
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.32, B:S.32, B:G.37
GOL.33: 3 residues within 4Å:- Chain B: K.64, P.65, R.184
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:R.184
- Water bridges: B:E.141, B:E.141, B:E.141
GOL.34: 7 residues within 4Å:- Chain B: T.172, D.175, K.194, S.195, D.196, R.252, K.274
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:K.194, B:R.252, B:K.274, B:K.274
- Water bridges: B:R.298, B:R.298
- 2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.16: 2 residues within 4Å:- Chain A: F.67, R.112
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:R.112, A:R.112
- Water bridges: A:F.67, A:F.67, A:F.68, A:G.71
PEG.35: 2 residues within 4Å:- Chain B: F.67, R.112
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:R.112, B:R.112
- Water bridges: B:F.67, B:F.67, B:F.68, B:G.71
- 4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.17: 5 residues within 4Å:- Chain A: P.253, R.256, A.257
- Ligands: BEN.5, BEN.12
No protein-ligand interaction detected (PLIP)PGE.18: 7 residues within 4Å:- Chain A: R.256, S.259, E.260, I.264, S.265, P.266, Y.267
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.260, A:S.265
- Water bridges: A:S.265
PGE.36: 5 residues within 4Å:- Chain B: P.253, R.256, A.257
- Ligands: BEN.24, BEN.31
No protein-ligand interaction detected (PLIP)PGE.37: 7 residues within 4Å:- Chain B: R.256, S.259, E.260, I.264, S.265, P.266, Y.267
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:S.265
- Water bridges: B:S.265
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.19: 10 residues within 4Å:- Chain A: D.59, G.60, T.223, R.224, C.338
- Chain B: D.132, K.134
- Ligands: MG.1, MG.2, ATP.11
7 PLIP interactions:6 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:D.59, A:D.59, A:T.223, A:R.224
- Water bridges: A:R.224
- Salt bridges: A:R.224, B:K.134
PO4.38: 10 residues within 4Å:- Chain A: D.132, K.134
- Chain B: D.59, G.60, T.223, R.224, C.338
- Ligands: MG.20, MG.21, ATP.30
7 PLIP interactions:6 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:D.59, B:D.59, B:R.224
- Water bridges: B:D.59, B:R.224
- Salt bridges: B:R.224, A:K.134
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Tominaga, T. et al., Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation. Proc.Natl.Acad.Sci.USA (2013)
- Release Date
- 2013-12-18
- Peptides
- Hydrogenase expression/formation protein HypE: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.64 Å
- Oligo State
- homo-dimer
- Ligands
- 8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 4 x BEN: BENZAMIDINE(Non-functional Binders)
- 10 x SO4: SULFATE ION(Non-functional Binders)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 6 x GOL: GLYCEROL(Non-functional Binders)
- 2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Tominaga, T. et al., Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation. Proc.Natl.Acad.Sci.USA (2013)
- Release Date
- 2013-12-18
- Peptides
- Hydrogenase expression/formation protein HypE: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A