SMTL ID : 1s2g.1

Purine 2'deoxyribosyltransferase + 2'-deoxyadenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x 3D1: (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol(Non-covalent)

3D1.1: 17 residues within 4Å: Chain A: Y.11, G.13, S.14, Y.17, P.44, F.45, W.67, T.71, D.75, D.95, G.97, S.98, E.101 Chain F: N.128, L.129, M.130, Y.167 9 PLIP interactions: 3 interactions with chain F, 6 interactions with chain A Hydrogen bonds: F:N.128, F:Y.167, A:S.14, A:S.14, A:Y.17, A:Y.17, A:S.98 Water bridges: F:L.129 Hydrophobic interactions: A:P.44 3D1.2: 17 residues within 4Å: Chain B: Y.11, G.13, S.14, Y.17, P.44, F.45, W.67, T.71, D.75, D.95, G.97, S.98, E.101 Chain E: N.128, L.129, M.130, Y.167 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: B:P.44 Hydrogen bonds: B:Y.11, B:S.14, B:S.14, B:Y.17, B:Y.17, B:G.97, B:S.98, E:N.128, E:L.129, E:Y.167 3D1.3: 17 residues within 4Å: Chain C: Y.11, G.13, S.14, Y.17, P.44, F.45, W.67, T.71, D.75, D.95, G.97, S.98, E.101 Chain D: N.128, L.129, M.130, Y.167 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:P.44, C:F.45 Hydrogen bonds: C:S.14, C:S.14, C:Y.17, C:Y.17, C:G.97, C:S.98, D:N.128, D:L.129, D:Y.167 3D1.4: 17 residues within 4Å: Chain C: N.128, L.129, M.130, Y.167 Chain D: Y.11, G.13, S.14, Y.17, P.44, F.45, W.67, T.71, D.75, D.95, G.97, S.98, E.101 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:P.44 Hydrogen bonds: D:Y.11, D:S.14, D:S.14, D:Y.17, D:Y.17, D:S.98, C:N.128, C:Y.167 Water bridges: C:L.129 3D1.5: 17 residues within 4Å: Chain B: N.128, L.129, M.130, Y.167 Chain E: Y.11, G.13, S.14, Y.17, P.44, F.45, W.67, T.71, D.75, D.95, G.97, S.98, E.101 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain E Hydrogen bonds: B:N.128, B:L.129, B:Y.167, E:S.14, E:S.14, E:Y.17, E:Y.17, E:G.97, E:S.98 Hydrophobic interactions: E:P.44 3D1.6: 17 residues within 4Å: Chain A: N.128, L.129, M.130, Y.167 Chain F: Y.11, G.13, S.14, Y.17, P.44, F.45, W.67, T.71, D.75, D.95, G.97, S.98, E.101 11 PLIP interactions: 8 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:P.44, F:F.45 Hydrogen bonds: F:S.14, F:S.14, F:Y.17, F:Y.17, F:G.97, F:S.98, A:N.128, A:L.129, A:Y.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anand, R. et al., Structures of purine 2'-deoxyribosyltransferase, substrate complexes, and the ribosylated enzyme intermediate at 2.0 A resolution. Biochemistry (2004)

Release Date

2004-03-30

Peptides

purine trans deoxyribosylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

purine trans deoxyribosylase

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