SMTL ID : 1ibs.1

PHOSPHORIBOSYLDIPHOSPHATE SYNTHETASE IN COMPLEX WITH CADMIUM IONS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: D.228, T.229, A.230, G.231, T.232 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.228, A:D.228, A:T.229, A:T.229, A:T.229, A:A.230, A:G.231, A:T.232 SO4.2: 6 residues within 4Å: Chain A: S.311, V.312, S.313 Chain B: R.110 Chain E: S.53, R.55 7 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 4 interactions with chain E Hydrogen bonds: A:V.312, A:S.313, E:S.53 Salt bridges: B:R.110, E:R.55 Water bridges: E:R.55, E:R.55 SO4.6: 6 residues within 4Å: Chain B: I.227, D.228, T.229, A.230, G.231, T.232 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.228, B:T.229, B:T.229, B:A.230, B:G.231, B:T.232, B:T.232 Water bridges: B:T.232, B:I.233, B:I.233 SO4.7: 6 residues within 4Å: Chain A: R.110 Chain B: S.311, V.312, S.313 Chain D: S.53, R.55 5 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B, 1 interactions with chain A Salt bridges: D:R.55, A:R.110 Hydrogen bonds: B:S.311, B:V.312, B:S.313 SO4.11: 5 residues within 4Å: Chain C: D.228, T.229, A.230, G.231, T.232 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.228, C:D.228, C:T.229, C:T.229, C:T.229, C:A.230, C:G.231, C:T.232 SO4.12: 6 residues within 4Å: Chain A: S.53, R.55 Chain C: S.311, V.312, S.313 Chain D: R.110 7 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:V.312, C:S.313, A:S.53 Water bridges: A:R.55, A:R.55 Salt bridges: A:R.55, D:R.110 SO4.16: 6 residues within 4Å: Chain D: I.227, D.228, T.229, A.230, G.231, T.232 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:D.228, D:T.229, D:T.229, D:A.230, D:G.231, D:T.232, D:T.232 Water bridges: D:T.232, D:I.233, D:I.233 SO4.17: 6 residues within 4Å: Chain C: R.110 Chain D: S.311, V.312, S.313 Chain F: S.53, R.55 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F, 1 interactions with chain C Hydrogen bonds: D:S.311, D:V.312, D:S.313 Salt bridges: F:R.55, C:R.110 SO4.21: 5 residues within 4Å: Chain E: D.228, T.229, A.230, G.231, T.232 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:D.228, E:D.228, E:T.229, E:T.229, E:T.229, E:A.230, E:G.231, E:T.232 SO4.22: 6 residues within 4Å: Chain C: S.53, R.55 Chain E: S.311, V.312, S.313 Chain F: R.110 7 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E, 4 interactions with chain C Salt bridges: F:R.110, C:R.55 Hydrogen bonds: E:V.312, E:S.313, C:S.53 Water bridges: C:R.55, C:R.55 SO4.26: 6 residues within 4Å: Chain F: I.227, D.228, T.229, A.230, G.231, T.232 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:D.228, F:T.229, F:T.229, F:A.230, F:G.231, F:T.232, F:T.232 Water bridges: F:T.232, F:I.233, F:I.233 SO4.27: 6 residues within 4Å: Chain B: S.53, R.55 Chain E: R.110 Chain F: S.311, V.312, S.313 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E, 1 interactions with chain B Hydrogen bonds: F:S.311, F:V.312, F:S.313 Salt bridges: E:R.110, B:R.55

12 x CD: CADMIUM ION(Non-covalent)

CD.3: 4 residues within 4Å: Chain A: D.104, R.105, H.136 Ligands: ABM.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.136 CD.4: 2 residues within 4Å: Chain A: D.175, D.224 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.175, A:D.224, A:D.224 CD.8: 3 residues within 4Å: Chain B: R.105, H.136 Ligands: ABM.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.136 CD.9: 2 residues within 4Å: Chain B: D.175, D.224 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.175, B:D.224, B:D.224 CD.13: 4 residues within 4Å: Chain C: D.104, R.105, H.136 Ligands: ABM.15 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.136 CD.14: 2 residues within 4Å: Chain C: D.175, D.224 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.175, C:D.224, C:D.224 CD.18: 3 residues within 4Å: Chain D: R.105, H.136 Ligands: ABM.20 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.136 CD.19: 2 residues within 4Å: Chain D: D.175, D.224 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.175, D:D.224, D:D.224 CD.23: 4 residues within 4Å: Chain E: D.104, R.105, H.136 Ligands: ABM.25 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.136 CD.24: 2 residues within 4Å: Chain E: D.175, D.224 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.175, E:D.224, E:D.224 CD.28: 3 residues within 4Å: Chain F: R.105, H.136 Ligands: ABM.30 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:H.136 CD.29: 2 residues within 4Å: Chain F: D.175, D.224 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.175, F:D.224, F:D.224

6 x ABM: METHYL PHOSPHONIC ACID ADENOSINE ESTER(Non-covalent)

ABM.5: 8 residues within 4Å: Chain A: R.102, Q.103, R.105, H.136 Chain D: F.41, D.43, E.45 Ligands: CD.3 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:R.102, A:R.102, A:Q.103, A:R.105, D:D.43, D:E.45, D:E.45 pi-Cation interactions: A:R.102 pi-Stacking: D:F.41 ABM.10: 10 residues within 4Å: Chain B: R.102, Q.103, R.105, E.111, H.136 Chain E: F.41, D.43, E.45, Q.47 Ligands: CD.8 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain E Hydrogen bonds: B:R.105, B:E.111, E:D.43 Water bridges: B:R.102, E:D.43 pi-Stacking: E:F.41, E:F.41 ABM.15: 8 residues within 4Å: Chain C: R.102, Q.103, R.105, H.136 Chain F: F.41, D.43, E.45 Ligands: CD.13 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain F Hydrogen bonds: C:R.102, C:R.102, C:Q.103, C:R.105, F:D.43, F:E.45, F:E.45 pi-Cation interactions: C:R.102 pi-Stacking: F:F.41 ABM.20: 10 residues within 4Å: Chain A: F.41, D.43, E.45, Q.47 Chain D: R.102, Q.103, R.105, E.111, H.136 Ligands: CD.18 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:D.43, D:R.105, D:E.111 Water bridges: A:D.43, D:R.102 pi-Stacking: A:F.41, A:F.41 ABM.25: 8 residues within 4Å: Chain B: F.41, D.43, E.45 Chain E: R.102, Q.103, R.105, H.136 Ligands: CD.23 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain B Hydrogen bonds: E:R.102, E:R.102, E:Q.103, E:R.105, B:D.43, B:E.45, B:E.45 pi-Cation interactions: E:R.102 pi-Stacking: B:F.41 ABM.30: 10 residues within 4Å: Chain C: F.41, D.43, E.45, Q.47 Chain F: R.102, Q.103, R.105, E.111, H.136 Ligands: CD.28 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain C Hydrogen bonds: F:R.105, F:E.111, C:D.43 Water bridges: F:R.102, C:D.43 pi-Stacking: C:F.41, C:F.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eriksen, T.A. et al., Binding of cations in Bacillus subtilis phosphoribosyldiphosphate synthetase and their role in catalysis. Protein Sci. (2002)

Release Date

2002-02-06

Peptides

RIBOSE-PHOSPHATE PYROPHOSPHOKINASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

RIBOSE-PHOSPHATE PYROPHOSPHOKINASE

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