SMTL ID : 3b1r.2 (2 other biounits)

Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with AMP-Mg-AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 19 residues within 4Å: Chain A: S.16, A.18, D.20, G.55, G.56, C.57, N.60, A.111, I.113, Q.121, T.123, F.125, M.130, P.151, Q.177, G.258, D.261 Chain B: S.44 Ligands: MG.3 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.16, A:D.20, A:G.56, A:N.60, A:Q.121, A:Q.177, A:G.258, A:G.258, A:D.261, B:S.44, B:S.44 Water bridges: A:T.123, A:D.152, A:C.259, A:G.260 pi-Stacking: A:F.125 AMP.2: 15 residues within 4Å: Chain A: N.119, T.228, R.229, G.230, E.231, G.233, V.248, C.259, G.260, F.263, S.285, G.288, A.289, I.292 Chain B: H.39 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.119, A:T.228, A:T.228, A:R.229, A:G.230 Water bridges: A:G.233, A:V.248, A:G.260, A:S.285, A:A.289 Salt bridges: B:H.39 AMP.4: 19 residues within 4Å: Chain A: S.44 Chain B: S.16, A.18, D.20, G.55, G.56, C.57, N.60, A.111, Q.121, T.123, F.125, M.130, P.151, Q.177, T.257, G.258, D.261 Ligands: MG.6 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.16, B:D.20, B:G.56, B:N.60, B:Q.121, B:Q.177, B:G.258, B:G.258, B:D.261, A:S.44, A:S.44 Water bridges: B:D.152, B:C.259, B:G.260 pi-Stacking: B:F.125, B:F.125 AMP.5: 16 residues within 4Å: Chain A: H.39 Chain B: N.119, N.200, T.228, R.229, G.230, E.231, G.233, V.248, C.259, G.260, F.263, S.285, G.288, A.289, I.292 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.119, B:T.228, B:R.229, B:G.230 Water bridges: B:L.117, B:N.200, B:G.233, B:P.246, B:A.250, B:G.260, B:R.264, B:A.289, B:A.289, A:H.39 Salt bridges: A:H.39

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 1 residues within 4Å: Ligands: AMP.1 6 PLIP interactions: 5 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.1, H2O.1, H2O.1, H2O.1, H2O.1, AMP.1 MG.6: 2 residues within 4Å: Chain B: Q.177 Ligands: AMP.4 No protein-ligand interaction detected (PLIP)

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
E

Ribokinase, putative

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