SMTL ID : 4hx9.2 (1 other biounit)

Designed Phosphodeoxyribosyltransferase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-hexamer

Ligands

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: I.34, L.36, E.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.36, A:E.37 Salt bridges: A:K.3 SO4.2: 5 residues within 4Å: Chain A: Q.91, G.92, T.93, G.94, L.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.91, A:G.92, A:G.94, A:L.95 SO4.3: 4 residues within 4Å: Chain B: I.34, D.35, L.36, E.37 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.36, B:E.37 Salt bridges: B:K.3 SO4.4: 7 residues within 4Å: Chain A: Y.157 Chain B: Q.17, Q.91, G.92, T.93, G.94, L.95 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:Y.157, B:Q.17, B:Q.91, B:G.92, B:G.92, B:G.94, B:L.95 SO4.7: 5 residues within 4Å: Chain C: K.29, I.34, D.35, L.36, E.37 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.36, C:E.37 Salt bridges: C:K.3, C:K.29 SO4.8: 4 residues within 4Å: Chain D: I.34, D.35, L.36, E.37 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.36, D:E.37 SO4.9: 5 residues within 4Å: Chain D: Q.17, G.92, T.93, G.94, L.95 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:S.123, C:Y.157, D:Q.17, D:G.92, D:G.92, D:T.93, D:G.94, D:L.95 SO4.12: 4 residues within 4Å: Chain E: I.34, D.35, L.36, E.37 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.35, E:L.36, E:E.37 SO4.13: 8 residues within 4Å: Chain E: R.13, Q.17, Q.91, G.92, T.93, G.94, L.95 Chain F: Y.157 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:Q.17, E:Q.91, E:G.92, E:G.94, E:L.95, F:Y.157 Salt bridges: E:R.13 SO4.14: 4 residues within 4Å: Chain F: I.34, D.35, L.36, E.37 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.35, F:D.35, F:L.36, F:E.37 SO4.15: 7 residues within 4Å: Chain E: Y.157 Chain F: R.13, Q.17, Q.91, G.92, G.94, L.95 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:Q.17, F:Q.91, F:G.92, F:G.94, F:L.95, E:S.123, E:Y.157 Salt bridges: F:R.13

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 4 residues within 4Å: Chain B: Y.118, G.119, K.120, E.153 No protein-ligand interaction detected (PLIP) PG4.6: 12 residues within 4Å: Chain A: T.66, Y.69, N.70 Chain B: W.127, G.128, F.149 Chain C: W.127, G.128, S.130, F.149 Chain D: T.66, N.70 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:S.130, A:N.70, D:N.70 Water bridges: B:W.127, B:W.127 PG4.10: 4 residues within 4Å: Chain D: D.115, E.116, Y.118, G.119 No protein-ligand interaction detected (PLIP) PG4.11: 12 residues within 4Å: Chain C: T.66, N.70 Chain D: W.127, G.128, S.130, F.149, F.151 Chain E: W.127, G.128, F.149 Chain F: T.66, N.70 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, 1 interactions with chain C Hydrogen bonds: F:N.70, E:W.127, C:N.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaminski, P.A. et al., Phosphodeoxyribosyltransferases, designed enzymes for deoxyribonucleotides synthesis. J.Biol.Chem. (2013)

Release Date

2013-01-16

Peptides

Nucleoside deoxyribosyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
C

D
D

E
G

F
H

Nucleoside deoxyribosyltransferase

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