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

Designed Phosphodeoxyribosyltransferase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: I.34, D.35, L.36, E.37 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.35, A:L.36, A:E.37 Salt bridges: A:K.3 SO4.2: 8 residues within 4Å: Chain A: G.92, T.93, G.94, G.96 Chain B: T.93, G.94, L.95, G.96 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.93, B:G.94, B:G.96, A:G.92, A:G.94, A:G.96, A:M.97 SO4.4: 4 residues within 4Å: Chain B: I.34, D.35, L.36, E.37 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.35, B:L.36, B:E.37 Salt bridges: B:K.3 SO4.6: 4 residues within 4Å: Chain C: I.34, D.35, L.36, E.37 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.35, C:L.36, C:E.37 Salt bridges: C:K.3 SO4.7: 8 residues within 4Å: Chain C: G.92, T.93, G.94, G.96 Chain D: T.93, G.94, L.95, G.96 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.92, C:G.94, C:G.96, C:M.97, D:G.94, D:G.96 SO4.9: 4 residues within 4Å: Chain D: I.34, D.35, L.36, E.37 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.35, D:L.36, D:E.37 Salt bridges: D:K.3 SO4.11: 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:L.36, E:E.37 Salt bridges: E:K.3 SO4.12: 8 residues within 4Å: Chain E: G.92, T.93, G.94, G.96 Chain F: T.93, G.94, L.95, G.96 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:T.93, F:G.94, F:G.96, E:G.92, E:G.94, E:G.96, E:M.97 SO4.14: 4 residues within 4Å: Chain F: I.34, D.35, L.36, E.37 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:L.36, F:E.37 Salt bridges: F:K.3

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

PG4.3: 13 residues within 4Å: Chain A: T.66, N.70 Chain B: W.127, S.130, F.149, F.151 Chain C: W.127, G.128, S.130, F.149, F.151 Chain D: T.66, N.70 7 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D, 4 interactions with chain B Hydrogen bonds: C:S.130, A:N.70, D:N.70 Water bridges: B:W.127, B:W.127, B:S.130, B:D.131 PG4.5: 3 residues within 4Å: Chain B: Y.118, G.119, E.153 No protein-ligand interaction detected (PLIP) PG4.8: 13 residues within 4Å: Chain C: T.66, N.70 Chain D: W.127, S.130, F.149, F.151 Chain E: W.127, G.128, S.130, F.149, F.151 Chain F: T.66, N.70 7 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D, 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: C:N.70, E:S.130, F:N.70 Water bridges: D:W.127, D:W.127, D:S.130, D:D.131 PG4.10: 3 residues within 4Å: Chain D: Y.118, G.119, E.153 No protein-ligand interaction detected (PLIP) PG4.13: 13 residues within 4Å: Chain A: W.127, G.128, S.130, F.149, F.151 Chain B: T.66, N.70 Chain E: T.66, N.70 Chain F: W.127, S.130, F.149, F.151 7 PLIP interactions: 4 interactions with chain F, 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain B Water bridges: F:W.127, F:W.127, F:S.130, F:D.131 Hydrogen bonds: E:N.70, A:S.130, B:N.70 PG4.15: 3 residues within 4Å: Chain F: Y.118, G.119, E.153 No protein-ligand interaction detected (PLIP)

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
A

B
B

C
A

D
B

E
A

F
B

Nucleoside deoxyribosyltransferase

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