SMTL ID : 6fd5.1

Crystal Structure of Human APRT-Tyr105Phe variant in complex with Adenine, PRPP and Mg2+, 14 days post crystallization (with AMP and PPi products partially generated)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 16 residues within 4Å: Chain A: 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: PPV.2, MG.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:V.23, A:R.25, A:R.65, A:R.65, 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:V.23, A:K.86, A:T.130, A:T.130, A:M.134 AMP.6: 17 residues within 4Å: Chain B: V.23, F.24, R.25, R.65, D.125, D.126, L.127, L.128, A.129, T.130, G.131, G.132, T.133, L.157 Ligands: PRP.5, MG.7, PPV.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:V.23, B:R.25, B:R.65, B:R.65, B:D.125, B:A.129, B:T.130, B:T.130, B:G.131, B:G.132, B:T.133, B:T.133 Water bridges: B:S.64, B:T.130, B:T.130, B:M.134

2 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.2: 8 residues within 4Å: Chain A: D.63, S.64, R.65, K.86 Chain B: R.85, K.89 Ligands: AMP.1, MG.3 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.64, A:R.65 Water bridges: A:S.64, A:R.65, A:K.86, A:K.86, A:K.86, A:K.86 Salt bridges: A:R.65, A:R.65, A:K.86, A:K.86, B:R.85, B:K.89, B:K.89 PPV.8: 8 residues within 4Å: Chain A: R.85, K.89 Chain B: D.63, S.64, R.65 Ligands: PRP.5, AMP.6, MG.7 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.64, B:R.65 Water bridges: B:S.64, 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

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 2 residues within 4Å: Ligands: AMP.1, PPV.2 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain B: D.63, S.64 Ligands: PRP.5, AMP.6, PPV.8 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: K.49, G.53, G.54, R.55, I.56, L.77 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.56, A:I.56, A:L.77 Water bridges: A:G.54

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

PRP.5: 16 residues within 4Å: Chain A: R.85, K.89 Chain B: D.63, S.64, R.65, D.125, D.126, L.127, A.129, T.130, G.131, G.132, T.133 Ligands: AMP.6, MG.7, PPV.8 25 PLIP interactions: 21 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.64, B:R.65, B:D.125, B:A.129, B:T.130, B:G.131, B:G.132, B:T.133, B:T.133 Water bridges: B:R.65, B:K.86, B:K.86, B:D.125, B:T.130, B:T.130, B:M.134, A:R.85 Salt bridges: B:R.65, B:R.65, B:R.65, B:K.86, B:K.86, A:R.85, A:K.89, A:K.89

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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