SMTL ID : 1s3f.1

Purine 2'-deoxyribosyltransferase + selenoinosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x SNI: 9-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YL)-1,9-DIHYDRO-PURINE-6-THIONE(Non-covalent)

SNI.1: 16 residues within 4Å: Chain A: Y.11, G.13, S.14, 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 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:S.14, A:S.14, A:D.75, A:S.98, F:N.128 SNI.2: 16 residues within 4Å: Chain B: Y.11, G.13, S.14, 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 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:Y.11, B:S.14, B:S.14, B:D.75, B:D.95, B:G.97, B:S.98, E:N.128 pi-Stacking: B:F.45 SNI.3: 12 residues within 4Å: Chain C: Y.11, S.14, P.44, F.45, W.67, T.71, D.75, E.101 Chain D: N.128, L.129, M.130, Y.167 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:N.128, D:Y.167, C:S.14, C:E.101 pi-Stacking: C:F.45 SNI.4: 16 residues within 4Å: Chain C: N.128, L.129, M.130, Y.167 Chain D: Y.11, G.13, S.14, P.44, F.45, W.67, T.71, D.75, D.95, G.97, S.98, E.101 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:N.128, D:Y.11, D:S.14, D:S.14, D:D.75, D:S.98 SNI.5: 16 residues within 4Å: Chain B: N.128, L.129, M.130, Y.167 Chain E: Y.11, G.13, S.14, P.44, F.45, W.67, T.71, D.75, D.95, G.97, S.98, E.101 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:S.14, E:S.14, E:D.75, E:D.95, E:G.97, E:S.98, B:N.128 pi-Stacking: E:F.45 SNI.6: 12 residues within 4Å: Chain A: N.128, L.129, M.130, Y.167 Chain F: Y.11, S.14, P.44, F.45, W.67, T.71, D.75, E.101 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:Y.11, F:S.14, F:E.101, A:N.128, A:Y.167 pi-Stacking: F:F.45

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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