SMTL ID : 3b1n.1

Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with ADP-mizoribine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x MZR: 5-hydroxy-1-(beta-D-ribofuranosyl)-1H-imidazole-4-carboxamide(Non-covalent)

MZR.1: 17 residues within 4Å: Chain A: S.8, A.10, D.12, G.47, G.48, C.49, N.52, A.103, I.105, Q.113, T.115, F.117, M.122, P.143, Q.169, D.253 Chain B: S.36 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.8, A:D.12, A:G.48, A:N.52, A:Q.169, B:S.36 Water bridges: A:Q.113, A:T.115, A:D.144, A:Q.169, A:G.250 pi-Stacking: A:F.117 MZR.4: 15 residues within 4Å: Chain A: S.36 Chain B: S.8, A.10, D.12, G.47, G.48, C.49, N.52, A.103, T.115, F.117, M.122, P.143, Q.169, D.253 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.8, B:D.12, B:G.48, B:N.52, B:P.143, B:Q.169, A:S.36 Water bridges: B:Q.113, B:Q.113, B:T.115, B:D.144, B:Q.169, B:G.250, B:D.253 pi-Stacking: B:F.117

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 17 residues within 4Å: Chain A: N.111, N.192, T.220, R.221, G.222, E.223, G.225, V.240, V.245, C.251, G.252, F.255, S.277, G.280, A.281, I.284 Chain B: H.31 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.111, A:N.192, A:T.220, A:R.221, A:G.222, A:G.252 Water bridges: A:L.109, A:D.110, A:N.111, A:Q.113, A:E.223, A:E.223, A:E.223, A:G.225, A:P.238, A:A.242, A:C.251, A:A.281, A:A.281 Salt bridges: B:H.31, B:H.31 ADP.5: 15 residues within 4Å: Chain A: H.31 Chain B: N.111, N.192, T.220, R.221, G.222, E.223, G.225, V.240, A.242, C.251, G.252, S.277, G.280, I.284 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.192, B:T.220, B:T.220, B:R.221, B:G.222, B:G.252 Water bridges: B:L.109, B:N.111, B:Q.113, B:Q.113, B:Q.113, B:G.225, B:P.238, B:A.242, B:P.248, B:G.250, B:C.251, B:D.253, B:A.281, B:A.281 Salt bridges: A:H.31, A:H.31

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

NA.3: 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:E.184 NA.6: 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:R.213

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain B: Q.124, H.126 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.124 Water bridges: B:M.123, B:Q.147

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
A

B
B

Ribokinase, putative

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