SMTL ID : 1s2d.1

Purine 2'-Deoxyribosyl complex with arabinoside: Ribosylated Intermediate (AraA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x ADE: ADENINE(Non-covalent)

ADE.1: 7 residues within 4Å: Chain A: P.44, F.45, W.67, T.71, D.75 Chain F: Y.167 Ligands: V3M.2 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:D.75, F:Y.167 pi-Stacking: A:W.67 ADE.3: 8 residues within 4Å: Chain B: P.44, F.45, W.67, T.71, D.75 Chain E: L.129, Y.167 Ligands: V3M.4 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:Y.167, B:D.75 ADE.5: 6 residues within 4Å: Chain C: P.44, F.45, T.71, D.75 Chain D: L.129 Ligands: V3M.6 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Water bridges: D:L.129, D:Y.167, D:Y.167 Hydrogen bonds: C:D.75 pi-Stacking: C:W.67 ADE.7: 7 residues within 4Å: Chain C: Y.167 Chain D: P.44, F.45, W.67, T.71, D.75 Ligands: V3M.8 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.75, C:Y.167 pi-Stacking: D:W.67 ADE.9: 8 residues within 4Å: Chain B: L.129, Y.167 Chain E: P.44, F.45, W.67, T.71, D.75 Ligands: V3M.10 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:D.75, B:Y.167 Water bridges: B:Y.167 ADE.11: 6 residues within 4Å: Chain A: L.129 Chain F: P.44, F.45, T.71, D.75 Ligands: V3M.12 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain F Water bridges: A:L.129, A:Y.167, A:Y.167 Hydrogen bonds: F:D.75 pi-Stacking: F:W.67

6 x V3M: 2-deoxy-2-fluoro-alpha-D-arabinofuranose(Post Translational Modification)

V3M.2: 14 residues within 4Å: Chain A: Y.11, G.13, S.14, Y.17, P.44, F.45, D.75, D.95, G.97, S.98, E.101 Chain F: N.128, M.130 Ligands: ADE.1 6 PLIP interactions: 1 interactions with chain F, 5 interactions with chain A Hydrogen bonds: F:N.128, A:S.14, A:S.14, A:Y.17, A:G.97, A:S.98 V3M.4: 14 residues within 4Å: Chain B: Y.11, G.13, S.14, Y.17, P.44, F.45, D.75, D.95, G.97, S.98, E.101 Chain E: N.128, M.130 Ligands: ADE.3 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:S.14, B:S.14, B:Y.17, B:Y.17, B:G.97, B:S.98, E:N.128 V3M.6: 14 residues within 4Å: Chain C: Y.11, G.13, S.14, Y.17, P.44, F.45, D.75, D.95, G.97, S.98, E.101 Chain D: N.128, M.130 Ligands: ADE.5 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.14, C:S.14, C:Y.17, C:G.97, C:S.98, D:N.128 V3M.8: 14 residues within 4Å: Chain C: N.128, M.130 Chain D: Y.11, G.13, S.14, Y.17, P.44, F.45, D.75, D.95, G.97, S.98, E.101 Ligands: ADE.7 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.14, D:S.14, D:Y.17, D:Y.17, D:G.97, D:S.98, C:N.128 V3M.10: 14 residues within 4Å: Chain B: N.128, M.130 Chain E: Y.11, G.13, S.14, Y.17, P.44, F.45, D.75, D.95, G.97, S.98, E.101 Ligands: ADE.9 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain E Hydrogen bonds: B:N.128, E:S.14, E:S.14, E:Y.17, E:G.97, E:S.98 V3M.12: 14 residues within 4Å: Chain A: N.128, M.130 Chain F: Y.11, G.13, S.14, Y.17, P.44, F.45, D.75, D.95, G.97, S.98, E.101 Ligands: ADE.11 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:S.14, F:S.14, F:Y.17, F:Y.17, F:G.97, F:S.98, A:N.128

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

Nucleoside 2-deoxyribosyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Nucleoside 2-deoxyribosyltransferase

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