SMTL ID : 5y07.1

Crystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis with PRPP.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

2 x PRP: 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose(Non-covalent)

PRP.1: 15 residues within 4Å: Chain A: E.68, A.69, R.70, K.91, D.130, D.131, L.132, A.134, T.135, G.136, G.137, T.138 Chain B: R.90, K.94 Ligands: MG.3 24 PLIP interactions: 21 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.69, A:R.70, A:R.70, A:D.130, A:A.134, A:T.135, A:G.136, A:G.137, A:T.138 Water bridges: A:G.71, A:D.130, A:T.135, A:T.138, A:T.138, A:T.138, A:I.139 Salt bridges: A:R.70, A:R.70, A:R.70, A:K.91, A:K.91, B:R.90, B:K.94, B:K.94 PRP.4: 15 residues within 4Å: Chain A: R.90 Chain B: E.68, A.69, R.70, K.91, D.130, D.131, L.132, L.133, A.134, T.135, G.136, G.137, T.138 Ligands: MG.6 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.68, B:A.69, B:R.70, B:R.70, B:D.130, B:A.134, B:T.135, B:G.136, B:G.137, B:T.138, B:T.138 Water bridges: B:D.130, B:D.131, B:D.131, B:L.132, B:I.139 Salt bridges: B:R.70, B:R.70, B:R.70, B:K.91, B:K.91, A:R.90

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 2 residues within 4Å: Chain A: T.117, I.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.120 NA.5: 2 residues within 4Å: Chain B: T.117, I.120 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.117

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: E.68 Ligands: PRP.1 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: E.68, D.130 Ligands: PRP.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramagopal, U.A. et al., Crystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis with PRPP. To be published

Release Date

2018-08-01

Peptides

Adenine phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenine phosphoribosyltransferase

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