SMTL ID : 1f8y.1

CRYSTAL STRUCTURE ANALYSIS OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE COMPLEXED WITH 5-METHYL-2'-DEOXYPSEUDOURIDINE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

6 x 5MD: 2'-deoxy-1-methyl-pseudouridine(Non-covalent)

5MD.1: 15 residues within 4Å: Chain A: Y.7, G.9, A.10, W.12, F.13, P.42, Q.46, D.72, D.92, G.94, E.98 Chain B: N.123, L.124, M.125, Y.157 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.12, A:P.42 Hydrogen bonds: A:A.10, A:Q.46, A:Q.46, A:D.92, B:N.123 pi-Stacking: A:W.12 5MD.2: 16 residues within 4Å: Chain A: N.123, L.124, M.125, Y.157 Chain B: Y.7, G.9, A.10, W.12, F.13, P.42, Q.46, W.64, D.72, D.92, G.94, E.98 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.12, B:P.42 Hydrogen bonds: B:Y.7, B:A.10, B:A.10, B:Q.46, B:Q.46, B:D.92, A:N.123 pi-Stacking: B:W.12 5MD.3: 15 residues within 4Å: Chain C: Y.7, G.9, A.10, W.12, F.13, P.42, Q.46, D.72, D.92, G.94, E.98 Chain D: N.123, L.124, M.125, Y.157 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.12, C:P.42 Hydrogen bonds: C:A.10, C:Q.46, C:Q.46, C:D.92, D:N.123 pi-Stacking: C:W.12 5MD.4: 16 residues within 4Å: Chain C: N.123, L.124, M.125, Y.157 Chain D: Y.7, G.9, A.10, W.12, F.13, P.42, Q.46, W.64, D.72, D.92, G.94, E.98 9 PLIP interactions: 1 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:N.123, D:A.10, D:A.10, D:Q.46, D:Q.46, D:D.92 Hydrophobic interactions: D:W.12, D:P.42 pi-Stacking: D:W.12 5MD.5: 15 residues within 4Å: Chain E: Y.7, G.9, A.10, W.12, F.13, P.42, Q.46, D.72, D.92, G.94, E.98 Chain F: N.123, L.124, M.125, Y.157 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:W.12, E:P.42 Hydrogen bonds: E:Y.7, E:A.10, E:Q.46, E:Q.46, E:D.92, F:N.123 pi-Stacking: E:W.12 5MD.6: 16 residues within 4Å: Chain E: N.123, L.124, M.125, Y.157 Chain F: Y.7, G.9, A.10, W.12, F.13, P.42, Q.46, W.64, D.72, D.92, G.94, E.98 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:W.12, F:P.42 Hydrogen bonds: F:A.10, F:A.10, F:Q.46, F:Q.46, F:D.92, E:N.123 pi-Stacking: F:W.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Armstrong, S.R. et al., Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site. Structure (1996)

Release Date

2000-08-09

Peptides

NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE

Related Entries With Identical Sequence