SMTL ID : 6fd6.1

Crystal Structure of Human APRT-Tyr105Phe variant in complex with Adenine, PRPP and Mg2+, 30 days post crystallization (with AMP and PPi products fully generated)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 14 residues within 4Å: Chain A: V.23, F.24, R.25, R.65, D.125, D.126, L.127, A.129, T.130, G.131, G.132, T.133, L.157 Ligands: PPV.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:V.23, A:R.25, A:R.65, A:R.65, A:D.125, A:D.126, A:A.129, A:T.130, A:T.130, A:T.130, A:G.131, A:G.132, A:T.133, A:T.133 Water bridges: A:T.130, A:T.130, A:M.134 pi-Stacking: A:F.24 AMP.3: 16 residues within 4Å: Chain B: V.22, V.23, F.24, R.25, R.65, D.125, D.126, L.127, A.129, T.130, G.131, G.132, T.133, L.157 Ligands: MG.4, PPV.5 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:V.23, B:R.25, B:R.65, B:D.125, B:D.126, B:A.129, B:T.130, B:T.130, B:T.130, B:G.131, B:G.132, B:T.133, B:T.133 Water bridges: B:S.64, B:R.65, B:R.65, B:K.86, B:T.130, B:T.130, B:M.134

2 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.2: 7 residues within 4Å: Chain A: D.63, S.64, R.65, K.86 Chain B: R.85, K.89 Ligands: AMP.1 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain A Water bridges: B:R.85, A:R.65, A:K.86, A:K.86 Salt bridges: B:R.85, B:K.89, B:K.89, A:R.65, A:R.65, A:K.86, A:K.86 Hydrogen bonds: A:D.63, A:S.64, A:R.65 PPV.5: 8 residues within 4Å: Chain A: R.85, K.89 Chain B: D.63, S.64, R.65, K.86 Ligands: AMP.3, MG.4 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.64, B:S.64, B:R.65 Water bridges: B:R.65, B:K.86, B:K.86, B:K.86 Salt bridges: B:R.65, B:R.65, B:K.86, B:K.86, A:R.85, A:K.89, A:K.89

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.4: 2 residues within 4Å: Ligands: AMP.3, PPV.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huyet, J. et al., Structural Insights into the Forward and Reverse Enzymatic Reactions in Human Adenine Phosphoribosyltransferase. Cell Chem Biol (2018)

Release Date

2018-08-15

Peptides

Adenine phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenine phosphoribosyltransferase

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