SMTL ID : 5b6h.1

Crystal structure of an APRT from Yersinia pseudotuberculosis in complex with AMP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 16 residues within 4Å: Chain A: I.24, L.25, F.26, R.27, R.64, D.124, D.125, L.126, L.127, A.128, T.129, G.130, G.131, T.132, L.156 Ligands: NA.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:L.25, A:R.27, A:R.64, A:D.124, A:D.125, A:L.126, A:A.128, A:T.129, A:T.129, A:T.129, A:G.130, A:G.131, A:T.132, A:T.132 Water bridges: A:D.124, A:T.129, A:T.129 AMP.5: 16 residues within 4Å: Chain B: I.24, L.25, F.26, R.27, R.64, D.124, D.125, L.126, L.127, A.128, T.129, G.130, G.131, T.132, L.156 Ligands: NA.6 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:L.25, B:R.27, B:R.64, B:D.124, B:D.125, B:L.126, B:A.128, B:T.129, B:T.129, B:T.129, B:G.130, B:G.131, B:T.132 Water bridges: B:D.125, B:T.132, B:T.132

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

NA.2: 3 residues within 4Å: Chain A: D.124, D.125 Ligands: AMP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.125 Water bridges: A:R.64 NA.3: 3 residues within 4Å: Chain A: T.111, I.114, Q.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.114 NA.6: 3 residues within 4Å: Chain B: D.124, D.125 Ligands: AMP.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.61, B:T.61 Water bridges: B:R.64 NA.7: 3 residues within 4Å: Chain B: T.111, I.114, Q.115 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.114

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: I.94, S.95, R.142 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: I.94, S.95, R.142 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pavithra, G.C. et al., Crystal structure of an APRT from Yersinia pseudotuberculosis in complex with AMP. To be published

Release Date

2017-05-31

Peptides

Adenine phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Adenine phosphoribosyltransferase