- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.55 Å
- Oligo State
- homo-dimer
- Ligands
- 6 x FE: FE (III) ION(Non-covalent)
FE.1: 6 residues within 4Å:- Chain A: D.228, H.256, H.282, H.283
- Ligands: FE.2, SIN.4
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.228, A:H.256, A:H.282, A:H.283, H2O.1
FE.2: 8 residues within 4Å:- Chain A: E.191, D.228, K.231
- Ligands: FE.1, FE.3, SIN.4, SIN.5, IMD.7
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:E.191, A:D.228, H2O.1, H2O.1
FE.3: 7 residues within 4Å:- Chain A: E.191, H.195, H.227, D.311
- Ligands: FE.2, SIN.5, IMD.7
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:E.191, A:H.195, A:D.311, H2O.1
FE.8: 6 residues within 4Å:- Chain B: D.228, H.256, H.282, H.283
- Ligands: FE.9, SIN.12
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.228, B:H.256, B:H.282, B:H.283, H2O.3
FE.9: 8 residues within 4Å:- Chain B: E.191, D.228, K.231
- Ligands: FE.8, FE.10, 5GP.11, SIN.12, IMD.14
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:E.191, B:D.228, H2O.3, H2O.3
FE.10: 8 residues within 4Å:- Chain B: E.191, H.195, H.227, D.228, D.311
- Ligands: FE.9, 5GP.11, IMD.14
5 PLIP interactions:3 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions- Metal complexes: B:H.195, B:H.227, B:D.311, H2O.3, 5GP.11
- 5 x SIN: SUCCINIC ACID(Non-covalent)
SIN.4: 11 residues within 4Å:- Chain A: E.191, D.228, K.231, W.250, M.253, H.256, H.283, Y.291
- Ligands: FE.1, FE.2, SIN.5
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:Y.291
- Salt bridges: A:K.231, A:H.256, A:H.256, A:H.283, A:H.283
SIN.5: 9 residues within 4Å:- Chain A: E.191, H.195, D.311, V.312, A.315
- Ligands: FE.2, FE.3, SIN.4, IMD.7
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:A.315
- Salt bridges: A:H.195, A:K.231
SIN.6: 11 residues within 4Å:- Chain A: E.281, E.284, W.286, I.300, G.304, R.305, S.308, I.309, H.342, F.343, D.344
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:I.300
- Hydrogen bonds: A:E.284, A:W.286, A:S.308, A:S.308, A:D.344
SIN.12: 10 residues within 4Å:- Chain B: D.228, K.231, W.250, M.253, H.256, H.283, Y.291
- Ligands: FE.8, FE.9, 5GP.11
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:Y.291
- Water bridges: B:Y.291
- Salt bridges: B:K.231, B:H.256, B:H.283, B:H.283
SIN.13: 12 residues within 4Å:- Chain B: E.281, E.284, R.285, W.286, I.300, G.304, R.305, S.308, I.309, H.342, F.343, D.344
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:W.286, B:R.305
- Hydrogen bonds: B:S.308, B:I.309, B:D.344
- 2 x IMD: IMIDAZOLE(Non-covalent)
IMD.7: 9 residues within 4Å:- Chain A: E.191, H.195, I.196, H.227, D.228, D.311
- Ligands: FE.2, FE.3, SIN.5
5 PLIP interactions:5 interactions with chain A- Water bridges: A:E.191, A:E.191, A:D.228, A:D.228
- pi-Stacking: A:H.227
IMD.14: 9 residues within 4Å:- Chain B: E.191, H.195, I.196, H.227, D.228, D.311
- Ligands: FE.9, FE.10, 5GP.11
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.228
- pi-Cation interactions: B:K.231
- 1 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)
5GP.11: 14 residues within 4Å:- Chain B: E.191, H.195, H.283, D.311, A.315, L.316, R.320, K.323, F.334, H.342
- Ligands: FE.9, FE.10, SIN.12, IMD.14
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:E.191, B:E.191, B:H.283, B:R.320, B:K.323
- Salt bridges: B:H.195
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Bellini, D. et al., Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre. Mol.Microbiol. (2014)
- Release Date
- 2014-02-19
- Peptides
- Metal dependent phosphohydrolase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.55 Å
- Oligo State
- homo-dimer
- Ligands
- 6 x FE: FE (III) ION(Non-covalent)
- 5 x SIN: SUCCINIC ACID(Non-covalent)
- 2 x IMD: IMIDAZOLE(Non-covalent)
- 1 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Bellini, D. et al., Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre. Mol.Microbiol. (2014)
- Release Date
- 2014-02-19
- Peptides
- Metal dependent phosphohydrolase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B