SMTL ID : 8izj.1

Crystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 10 residues within 4Å: Chain A: L.30, F.31, R.32, L.131, A.133, T.134, L.161, L.164, H.186 Ligands: PO4.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.32, A:R.32, A:T.134, A:T.134 Water bridges: A:E.106, A:A.133, A:T.134 AMP.6: 14 residues within 4Å: Chain B: I.29, L.30, F.31, R.32, D.129, D.130, L.131, A.133, T.134, G.135, G.136, T.137, L.161, H.186 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:R.32, B:L.131, B:L.131, B:A.133, B:T.134, B:T.134, B:G.135, B:G.136, B:T.137, B:T.137, B:H.186, B:H.186 Water bridges: B:R.69, B:R.69, B:R.69, B:R.69, B:R.69, B:I.138

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

CL.2: 3 residues within 4Å: Chain A: I.99, S.100, R.147 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: A.68, R.69 Chain B: R.89 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: R.32, P.184 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: R.89 Chain B: A.68, R.69 Ligand excluded by PLIP

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 5 residues within 4Å: Chain A: R.69, D.129, D.130, L.131 Ligands: AMP.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.69, A:D.130, A:L.131 Water bridges: A:T.66, A:D.130, A:A.133

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

NA.5: 2 residues within 4Å: Chain A: G.28, H.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.186 NA.9: 2 residues within 4Å: Chain B: E.53, K.56 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.53, B:K.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yadav, P. et al., Crystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with AMP. To Be Published

Release Date

2024-04-10

Peptides

Adenine phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenine phosphoribosyltransferase

Related Entries With Identical Sequence