SMTL ID : 5yol.1

Crystal structure of octameric form of Nucleoside diphosphate kinase from Acinetobacter baumannii at 2.2 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-octamer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: N.136 Chain G: D.46 5 PLIP interactions: 1 interactions with chain G, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: G:D.46, A:N.136, H2O.1, H2O.1, H2O.3 MG.2: 1 residues within 4Å: Chain A: D.120 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.120, H2O.1, H2O.3 MG.3: 2 residues within 4Å: Chain B: N.136 Chain F: D.46 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: B:N.136, F:D.46, H2O.5, H2O.13 MG.4: 1 residues within 4Å: Chain C: N.136 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain D: N.136 Chain H: D.46 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: D:N.136, H:D.46, H2O.9, H2O.10, H2O.17 MG.6: 4 residues within 4Å: Chain A: D.112 Chain E: E.53, D.120, S.124 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: E:D.120, A:D.112, H2O.11, H2O.11, H2O.11 MG.7: 2 residues within 4Å: Chain C: D.46 Chain E: N.136 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: C:D.46, E:N.136, H2O.7, H2O.12, H2O.12 MG.8: 2 residues within 4Å: Chain B: D.46 Chain F: N.136 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: B:D.46, F:N.136, H2O.13, H2O.14, H2O.14 MG.9: 2 residues within 4Å: Chain A: D.46 Chain G: N.136 5 PLIP interactions: 1 interactions with chain G, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: G:N.136, A:D.46, H2O.2, H2O.2, H2O.3 MG.10: 1 residues within 4Å: Chain G: D.112 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain D: D.46 Chain H: N.136 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: H:N.136, D:D.46, H2O.8, H2O.17, H2O.19 MG.12: 3 residues within 4Å: Chain H: E.53, D.120, S.124 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.120, H:D.120, H:S.124, H2O.17, H2O.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, P.K. et al., Crystal structure of octameric form of Nucleoside diphosphate kinase from Acinetobacter baumannii at 2.2 A resolution. To Be Published

Release Date

2017-11-08

Peptides

Nucleoside diphosphate kinase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Nucleoside diphosphate kinase

Related Entries With Identical Sequence