SMTL ID : 1u9z.1

Crystal Structure of Phosphoribosyl Diphosphate Synthase Complexed with AMP and Ribose 5-Phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x R5P: RIBOSE-5-PHOSPHATE(Non-covalent)

R5P.1: 10 residues within 4Å: Chain A: R.92, D.163, D.212, I.214, I.215, S.216, T.217, G.218, G.219, T.220 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.212, A:S.216, A:S.216, A:T.217, A:G.218, A:G.219, A:T.220, A:T.220, A:T.220 Water bridges: A:M.221 R5P.2: 10 residues within 4Å: Chain B: R.92, D.163, D.212, I.214, I.215, S.216, T.217, G.218, G.219, T.220 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.212, B:S.216, B:S.216, B:T.217, B:G.218, B:G.219, B:T.220, B:T.220, B:T.220 Water bridges: B:M.221 R5P.5: 11 residues within 4Å: Chain C: R.92, H.125, D.163, D.212, I.214, I.215, S.216, T.217, G.218, G.219, T.220 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:D.212, C:S.216, C:S.216, C:T.217, C:G.218, C:G.219, C:T.220, C:T.220, C:T.220 Water bridges: C:M.221 R5P.7: 10 residues within 4Å: Chain D: R.92, D.163, D.212, I.214, I.215, S.216, T.217, G.218, G.219, T.220 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:D.212, D:S.216, D:S.216, D:T.217, D:G.218, D:G.219, D:T.220, D:T.220, D:T.220 Water bridges: D:M.221

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 8 residues within 4Å: Chain A: R.92, Q.93, D.94, F.97, H.125 Chain B: F.32, D.34, E.36 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.34, A:R.92 Water bridges: B:D.34, A:Y.90 pi-Stacking: B:F.32, B:F.32 Salt bridges: A:H.125 pi-Cation interactions: A:R.92 AMP.4: 8 residues within 4Å: Chain A: F.32, D.34, E.36 Chain B: R.92, Q.93, D.94, F.97, H.125 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.92, A:D.34 Water bridges: B:Y.90 Salt bridges: B:H.125 pi-Cation interactions: B:R.92 pi-Stacking: A:F.32, A:F.32 AMP.6: 8 residues within 4Å: Chain C: F.32, D.34, E.36 Chain D: R.92, Q.93, D.94, F.97, H.125 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:D.34, C:E.36, D:R.92, D:D.94 pi-Stacking: C:F.32, C:F.32 Water bridges: D:Y.90, D:N.98 Salt bridges: D:H.125 pi-Cation interactions: D:R.92 AMP.8: 8 residues within 4Å: Chain C: R.92, Q.93, D.94, F.97, H.125 Chain D: F.32, D.34, E.36 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:R.92, C:D.94, D:D.34 Water bridges: C:Y.90 Salt bridges: C:H.125 pi-Cation interactions: C:R.92 pi-Stacking: D:F.32, D:F.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kadziola, A. et al., Novel class III phosphoribosyl diphosphate synthase: structure and properties of the tetrameric, phosphate-activated, non-allosterically inhibited enzyme from Methanocaldococcus jannaschii. J.Mol.Biol. (2005)

Release Date

2005-08-23

Peptides

Ribose-phosphate pyrophosphokinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ribose-phosphate pyrophosphokinase

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