SMTL ID : 5vjn.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

2 x IR8: [(2R,3S,4R,5R)-3,4-dihydroxypyrrolidine-2,5-diyl]bis(methylene) bis[dihydrogen (phosphate)](Non-covalent)

IR8.1: 12 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 Ligands: ADE.5 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.69, A:D.129, A:A.133, A:T.134, A:G.135, A:G.136, A:S.137 Water bridges: A:S.68, A:R.69, A:R.69, A:Y.103, A:D.129, A:S.137, A:S.137, A:A.138, B:R.89, B:R.89 Salt bridges: A:K.90, A:K.105 IR8.6: 11 residues within 4Å: Chain A: K.93 Chain B: R.69, D.129, D.130, I.131, I.132, A.133, T.134, G.135, G.136, S.137 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.69, B:R.69, B:D.129, B:A.133, B:T.134, B:G.135, B:G.136, B:S.137 Water bridges: B:S.68, B:S.68, B:R.69, B:S.137, B:S.137, B:S.137, B:A.138, A:R.89, A:R.89, A:R.89 Salt bridges: A:K.93

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

EDO.2: 6 residues within 4Å: Chain A: Q.115, N.117, A.118 Chain B: L.31, P.32, R.35 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.115, A:N.117, A:N.117, B:L.31 Water bridges: B:Y.17 EDO.3: 7 residues within 4Å: Chain A: L.51, E.52, F.55, V.58, I.60, L.81 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.58 EDO.4: 5 residues within 4Å: Chain A: K.59, I.60, L.81, V.83 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.60, A:L.81 EDO.7: 6 residues within 4Å: Chain B: L.51, E.52, F.55, V.58, I.60 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.58 Water bridges: B:E.52 EDO.8: 5 residues within 4Å: Chain B: K.59, I.60, L.81, V.83 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.59, B:I.60, B:L.81

1 x ADE: ADENINE(Non-covalent)

ADE.5: 8 residues within 4Å: Chain A: L.26, F.27, E.28, R.69, I.131, A.133, L.161 Ligands: IR8.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.26, A:E.28, A:R.69 Water bridges: A:R.69, A:R.69

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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