SMTL ID : 4dz6.1

Transition state mimic of nucleoside-diphosphate kinase from borrelia burgdorferi with bound vanadate and adp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: K.34, R.82, H.83, V.87, L.91, R.115, T.121, R.132, F.140, S.143, S.149, I.150, N.152 Ligands: VN4.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.34, A:R.132, A:S.143, A:I.150, A:N.152, A:N.152 Salt bridges: A:R.82, A:H.83, A:R.115, A:R.132 pi-Stacking: A:H.83 ADP.6: 14 residues within 4Å: Chain C: K.34, R.82, H.83, V.87, L.91, R.115, T.121, R.132, F.140, S.143, S.149, I.150, N.152 Ligands: VN4.7 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:K.34, C:T.121, C:S.143, C:I.150, C:N.152, C:N.152 Salt bridges: C:R.82, C:H.83, C:R.115, C:R.132 pi-Stacking: C:H.83 ADP.8: 17 residues within 4Å: Chain D: K.34, Y.74, R.82, H.83, V.87, L.91, R.115, T.121, R.132, F.140, S.143, N.144, F.148, S.149, I.150, N.152 Ligands: VN4.9 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:K.34, D:S.143, D:N.144, D:I.150, D:N.152, D:N.152 Salt bridges: D:R.82, D:H.83, D:R.115, D:R.132 pi-Stacking: D:H.83

3 x VN4: oxido(dioxo)vanadium(Non-covalent)

VN4.2: 7 residues within 4Å: Chain A: K.34, Y.74, R.115, R.132, H.155, A.156 Ligands: ADP.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.34, A:R.115, A:R.132, A:H.155, A:A.156, A:A.156 VN4.7: 7 residues within 4Å: Chain C: K.34, Y.74, R.115, R.132, H.155, A.156 Ligands: ADP.6 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.34, C:R.115, C:R.132, C:A.156 VN4.9: 7 residues within 4Å: Chain D: K.34, Y.74, R.115, R.132, H.155, A.156 Ligands: ADP.8 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.34, D:Y.74, D:R.115, D:R.132, D:A.156, D:A.156

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: K.61, L.63, L.69, I.169, W.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.169 EDO.5: 6 residues within 4Å: Chain A: D.182, D.183 Chain B: R.40 Chain C: R.40 Chain E: D.182, D.183 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: A:D.182, B:R.40 Water bridges: A:D.183, A:D.183, E:D.182

3 x VO4: VANADATE ION(Non-covalent)

VO4.4: 6 residues within 4Å: Chain B: K.34, Y.74, R.115, R.132, H.155, A.156 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.34, B:Y.74, B:R.115, B:R.132, B:A.156, B:A.156 VO4.10: 6 residues within 4Å: Chain E: K.34, Y.74, R.115, R.132, H.155, A.156 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:K.34, E:Y.74, E:R.115, E:R.132, E:A.156 VO4.11: 7 residues within 4Å: Chain F: K.34, Y.74, R.115, T.121, R.132, H.155, A.156 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:K.34, F:K.34, F:R.115, F:R.132, F:N.152, F:H.155, F:A.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dumais, M. et al., Structure and analysis of nucleoside diphosphate kinase from Borrelia burgdorferi prepared in a transition-state complex with ADP and vanadate moieties. Acta Crystallogr F Struct Biol Commun (2018)

Release Date

2012-03-14

Peptides

Nucleoside diphosphate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Nucleoside diphosphate kinase

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