SMTL ID : 3b1q.2 (2 other biounits)

Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with inosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x NOS: INOSINE(Non-covalent)

NOS.1: 15 residues within 4Å: Chain A: S.8, A.10, D.12, G.47, G.48, C.49, N.52, A.103, F.117, M.122, P.143, Q.169, D.253, P.289 Chain B: S.36 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.8, A:G.48, A:N.52, A:Q.169, B:S.36 Water bridges: A:D.144, A:Q.169, A:G.250, A:G.250, A:D.253 pi-Stacking: A:F.117, A:F.117 NOS.8: 16 residues within 4Å: Chain A: S.36, L.38 Chain B: S.8, A.10, D.12, G.47, G.48, C.49, N.52, A.103, F.117, M.122, P.143, Q.169, D.253, P.289 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:S.36, B:S.8, B:G.48, B:N.52, B:Q.169 Water bridges: B:D.144, B:Q.169, B:G.250, B:D.253 pi-Stacking: B:F.117, B:F.117

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 3 residues within 4Å: Chain A: H.286, Q.287, T.291 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.287, A:T.291, A:T.291 Water bridges: A:R.244 Salt bridges: A:R.244, A:H.286 ACT.9: 6 residues within 4Å: Chain A: N.34 Chain B: P.248, T.249, G.250, C.251, G.252 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.250, B:C.251, B:G.252 Water bridges: B:D.253

2 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.3: 7 residues within 4Å: Chain A: Y.11, R.44, E.45, F.46, D.74, P.77, Q.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.44, A:R.44, A:D.74, A:Q.102 P33.4: 8 residues within 4Å: Chain A: V.240, R.241, A.242, E.243, L.278, L.282, A.301, R.302 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.243, A:R.302 Water bridges: A:A.281, A:T.305

4 x NA: SODIUM ION(Non-functional Binders)

NA.5: 6 residues within 4Å: Chain A: I.183, E.184, L.185, A.186, R.213, V.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.186 NA.6: 1 residues within 4Å: Chain A: G.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.204 NA.7: 1 residues within 4Å: Chain A: R.231 No protein-ligand interaction detected (PLIP) NA.10: 6 residues within 4Å: Chain B: I.183, E.184, L.185, A.186, R.213, V.214 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yasutake, Y. et al., Structures of Burkholderia thailandensis nucleoside kinase: implications for the catalytic mechanism and nucleoside selectivity. Acta Crystallogr.,Sect.D (2011)

Release Date

2011-11-02

Peptides

Ribokinase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Ribokinase, putative

Related Entries With Identical Sequence