- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x DXP: 1-DEOXY-D-XYLULOSE-5-PHOSPHATE(Non-covalent)
DXP.1: 13 residues within 4Å:- Chain A: N.8, D.10, H.11, H.44, R.46, H.51, E.71, T.101, T.102, F.132, H.192
- Chain E: R.19
- Ligands: G3P.2
15 PLIP interactions:13 interactions with chain A, 2 interactions with chain E- Hydrophobic interactions: A:T.102, A:F.132, A:H.192
- Hydrogen bonds: A:N.8, A:D.10, A:H.44, A:T.101, A:T.101, A:T.102
- Water bridges: A:H.215, E:R.19
- Salt bridges: A:H.11, A:R.46, A:H.51, E:R.19
DXP.3: 12 residues within 4Å:- Chain B: D.10, H.11, H.44, R.46, H.51, E.71, T.101, T.102, F.132, H.192
- Chain G: R.19
- Ligands: G3P.4
17 PLIP interactions:14 interactions with chain B, 3 interactions with chain G- Hydrophobic interactions: B:T.102, B:F.132, B:H.192
- Hydrogen bonds: B:N.8, B:D.10, B:E.71, B:T.101, B:T.102, B:H.192
- Water bridges: B:R.46, B:R.46, G:R.19, G:R.19
- Salt bridges: B:H.11, B:R.46, B:H.51, G:R.19
DXP.5: 14 residues within 4Å:- Chain C: N.8, D.10, H.11, H.44, R.46, H.51, E.71, V.93, T.101, T.102, F.132, H.192
- Chain F: R.19
- Ligands: G3P.6
14 PLIP interactions:12 interactions with chain C, 2 interactions with chain F- Hydrophobic interactions: C:T.102, C:F.132, C:H.192
- Hydrogen bonds: C:N.8, C:H.44, C:T.101, C:T.101, C:T.102
- Water bridges: C:R.50, F:R.19
- Salt bridges: C:H.11, C:R.46, C:H.51, F:R.19
DXP.7: 13 residues within 4Å:- Chain D: N.8, D.10, H.11, H.44, R.46, H.51, E.71, T.101, T.102, F.132, H.192
- Chain H: R.19
- Ligands: G3P.8
10 PLIP interactions:2 interactions with chain H, 8 interactions with chain D- Water bridges: H:R.19
- Salt bridges: H:R.19, D:H.11, D:R.46, D:H.51
- Hydrophobic interactions: D:T.102, D:F.132
- Hydrogen bonds: D:N.8, D:T.101, D:T.102
DXP.9: 13 residues within 4Å:- Chain A: R.19
- Chain E: N.8, D.10, H.11, H.44, R.46, H.51, E.71, T.101, T.102, F.132, H.192
- Ligands: G3P.10
12 PLIP interactions:10 interactions with chain E, 2 interactions with chain A- Hydrophobic interactions: E:T.102, E:F.132, E:H.192
- Hydrogen bonds: E:N.8, E:T.101, E:T.102
- Water bridges: E:H.215, A:R.19
- Salt bridges: E:H.11, E:R.46, E:H.51, A:R.19
DXP.11: 12 residues within 4Å:- Chain C: R.19
- Chain F: D.10, H.11, H.44, R.46, H.51, E.71, T.101, T.102, F.132, H.192
- Ligands: G3P.12
17 PLIP interactions:14 interactions with chain F, 3 interactions with chain C- Hydrophobic interactions: F:T.102, F:F.132, F:H.192
- Hydrogen bonds: F:N.8, F:H.44, F:E.71, F:T.101, F:T.101, F:H.192
- Water bridges: F:R.46, F:R.46, C:R.19, C:R.19
- Salt bridges: F:H.11, F:R.46, F:H.51, C:R.19
DXP.13: 14 residues within 4Å:- Chain B: R.19
- Chain G: N.8, D.10, H.11, H.44, R.46, H.51, E.71, V.93, T.101, T.102, F.132, H.192
- Ligands: G3P.14
13 PLIP interactions:11 interactions with chain G, 2 interactions with chain B- Hydrophobic interactions: G:T.102, G:F.132, G:H.192
- Hydrogen bonds: G:N.8, G:D.10, G:T.101, G:T.102
- Water bridges: G:R.50, B:R.19
- Salt bridges: G:H.11, G:R.46, G:H.51, B:R.19
DXP.15: 13 residues within 4Å:- Chain D: R.19
- Chain H: N.8, D.10, H.11, H.44, R.46, H.51, E.71, T.101, T.102, F.132, H.192
- Ligands: G3P.16
13 PLIP interactions:11 interactions with chain H, 2 interactions with chain D- Hydrophobic interactions: H:T.102, H:F.132
- Hydrogen bonds: H:N.8, H:D.10, H:H.44, H:T.101, H:T.101, H:T.102
- Salt bridges: H:H.11, H:R.46, H:H.51, D:R.19
- Water bridges: D:R.19
- 8 x G3P: SN-GLYCEROL-3-PHOSPHATE(Non-covalent)
G3P.2: 11 residues within 4Å:- Chain A: N.8, E.71, E.152, H.192, G.193, N.212, I.213, G.214, H.215
- Chain E: R.19
- Ligands: DXP.1
11 PLIP interactions:2 interactions with chain E, 9 interactions with chain A- Water bridges: E:R.19, A:H.11, A:H.192, A:L.194
- Salt bridges: E:R.19, A:H.192
- Hydrogen bonds: A:N.8, A:E.71, A:G.193, A:G.214, A:H.215
G3P.4: 11 residues within 4Å:- Chain B: N.8, E.71, E.152, H.192, G.193, N.212, I.213, G.214, H.215
- Chain G: R.19
- Ligands: DXP.3
13 PLIP interactions:11 interactions with chain B, 2 interactions with chain G- Hydrogen bonds: B:N.8, B:E.71, B:E.152, B:G.193, B:G.214, B:H.215
- Water bridges: B:H.11, B:H.192, B:L.194, B:A.216, G:R.19
- Salt bridges: B:H.192, G:R.19
G3P.6: 11 residues within 4Å:- Chain C: N.8, E.71, E.152, H.192, G.193, N.212, I.213, G.214, H.215
- Chain F: R.19
- Ligands: DXP.5
11 PLIP interactions:10 interactions with chain C, 1 interactions with chain F- Hydrogen bonds: C:N.8, C:G.193, C:G.214, C:H.215
- Water bridges: C:H.11, C:H.192, C:H.192, C:A.216, C:A.216
- Salt bridges: C:H.192, F:R.19
G3P.8: 12 residues within 4Å:- Chain D: N.8, T.42, E.71, E.152, H.192, G.193, N.212, I.213, G.214, H.215
- Chain H: R.19
- Ligands: DXP.7
11 PLIP interactions:3 interactions with chain H, 8 interactions with chain D- Water bridges: H:R.19, H:R.19, D:A.216
- Salt bridges: H:R.19, D:H.192
- Hydrogen bonds: D:N.8, D:H.192, D:G.193, D:L.194, D:G.214, D:H.215
G3P.10: 11 residues within 4Å:- Chain A: R.19
- Chain E: N.8, E.71, E.152, H.192, G.193, N.212, I.213, G.214, H.215
- Ligands: DXP.9
12 PLIP interactions:10 interactions with chain E, 2 interactions with chain A- Hydrogen bonds: E:N.8, E:E.71, E:G.193, E:G.214, E:H.215
- Water bridges: E:H.11, E:E.71, E:H.192, E:L.194, A:R.19
- Salt bridges: E:H.192, A:R.19
G3P.12: 11 residues within 4Å:- Chain C: R.19
- Chain F: N.8, E.71, E.152, H.192, G.193, N.212, I.213, G.214, H.215
- Ligands: DXP.11
13 PLIP interactions:11 interactions with chain F, 2 interactions with chain C- Hydrogen bonds: F:N.8, F:E.71, F:E.152, F:G.193, F:G.214, F:H.215
- Water bridges: F:H.11, F:H.192, F:L.194, F:A.216, C:R.19
- Salt bridges: F:H.192, C:R.19
G3P.14: 11 residues within 4Å:- Chain B: R.19
- Chain G: N.8, E.71, E.152, H.192, G.193, N.212, I.213, G.214, H.215
- Ligands: DXP.13
11 PLIP interactions:10 interactions with chain G, 1 interactions with chain B- Hydrogen bonds: G:N.8, G:G.193, G:G.214, G:H.215
- Water bridges: G:H.11, G:H.192, G:H.192, G:A.216, G:A.216
- Salt bridges: G:H.192, B:R.19
G3P.16: 12 residues within 4Å:- Chain D: R.19
- Chain H: N.8, T.42, E.71, E.152, H.192, G.193, N.212, I.213, G.214, H.215
- Ligands: DXP.15
12 PLIP interactions:9 interactions with chain H, 3 interactions with chain D- Hydrogen bonds: H:N.8, H:H.192, H:G.193, H:L.194, H:G.214, H:H.215
- Water bridges: H:E.71, H:A.216, D:R.19, D:R.19
- Salt bridges: H:H.192, D:R.19
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Garrido-Franco, M. et al., Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase: implications for substrate binding and catalysis. J.MOL.BIOL. (2002)
- Release Date
- 2003-02-11
- Peptides
- Pyridoxine 5'-Phosphate Synthase: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
AF
BG
CH
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-octamer
- Ligands
- 8 x DXP: 1-DEOXY-D-XYLULOSE-5-PHOSPHATE(Non-covalent)
- 8 x G3P: SN-GLYCEROL-3-PHOSPHATE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Garrido-Franco, M. et al., Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase: implications for substrate binding and catalysis. J.MOL.BIOL. (2002)
- Release Date
- 2003-02-11
- Peptides
- Pyridoxine 5'-Phosphate Synthase: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
AF
BG
CH
D