SMTL ID : 5vjp.1

Crystal Structure of Adenine Phosphoribosyltransferase from Saccharomyces cerevisiae Complexed with L-2,5-Dideoxy-2,5-Imino-Altritol 1,6-Bisphosphate (L-DIAB) and Adenine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

2 x IR9: [(2S,3R,4S,5S)-3,4-dihydroxypyrrolidine-2,5-diyl]bis(methylene) bis[dihydrogen (phosphate)](Non-covalent)

IR9.1: 11 residues within 4Å: Chain A: R.69, K.90, D.129, D.130, I.131, I.132, A.133, T.134, G.135, G.136, S.137 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.69, A:D.129, A:D.130, A:A.133, A:T.134, A:T.134, A:T.134, A:G.135, A:G.136, A:S.137, A:S.137 Water bridges: A:S.68, A:R.69, A:D.129, A:D.130, A:A.138 Salt bridges: A:K.90 IR9.4: 11 residues within 4Å: Chain B: R.69, K.90, D.129, D.130, I.131, I.132, A.133, T.134, G.135, G.136, S.137 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.69, B:D.129, B:D.130, B:A.133, B:T.134, B:T.134, B:T.134, B:G.135, B:G.136, B:S.137, B:S.137 Water bridges: B:R.69, B:R.69, B:A.138, A:R.89 Salt bridges: B:K.90, A:K.93

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: L.51, E.52, F.55, V.58, I.60 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.58, A:I.60 EDO.3: 5 residues within 4Å: Chain A: K.59, I.60, L.81, V.83 Ligands: EDO.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.59, A:I.60, A:L.81 EDO.5: 6 residues within 4Å: Chain B: L.51, F.55, P.56, V.58, I.60 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.51, B:P.56 EDO.6: 6 residues within 4Å: Chain B: V.58, K.59, I.60, L.81, V.83 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.58, B:I.60, B:L.81 EDO.7: 4 residues within 4Å: Chain B: A.54, F.55, E.154, P.173 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.50, B:E.154 EDO.8: 8 residues within 4Å: Chain A: V.86, P.87, Q.115, N.117, A.118 Chain B: L.31, P.32, R.35 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:H.15 Hydrogen bonds: A:N.117, A:N.117 EDO.9: 6 residues within 4Å: Chain A: L.31, P.32, R.35 Chain B: Q.115, N.117, A.118 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.117 Water bridges: B:Q.115, A:L.31

1 x ADE: ADENINE(Non-covalent)

ADE.10: 7 residues within 4Å: Chain B: L.26, F.27, E.28, R.69, I.131, A.133, L.161 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.26, B:E.28, B:R.69, B:R.69 pi-Stacking: B:F.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harris, L.D. et al., Synthesis of bis-Phosphate Iminoaltritol Enantiomers and Structural Characterization with Adenine Phosphoribosyltransferase. ACS Chem. Biol. (2018)

Release Date

2017-12-27

Peptides

Adenine phosphoribosyltransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenine phosphoribosyltransferase 1

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