SMTL ID : 3ngu.1

Structure of Leishmania NDKb complexed with ADP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 11 residues within 4Å: Chain A: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.11, A:N.114, A:N.114 Salt bridges: A:R.87, A:R.104 pi-Stacking: A:F.59, A:F.59 ADP.2: 10 residues within 4Å: Chain B: K.11, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.11, B:N.114, B:N.114 Salt bridges: B:R.87, B:R.104 pi-Stacking: B:F.59, B:F.59 ADP.3: 11 residues within 4Å: Chain C: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.11, C:N.114, C:N.114 Salt bridges: C:R.87, C:R.104 pi-Stacking: C:F.59, C:F.59 ADP.4: 10 residues within 4Å: Chain D: K.11, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:K.11, D:N.114, D:N.114 Salt bridges: D:R.87, D:R.104 pi-Stacking: D:F.59, D:F.59 ADP.5: 11 residues within 4Å: Chain E: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:K.11, E:N.114, E:N.114 Salt bridges: E:R.87, E:R.104 pi-Stacking: E:F.59, E:F.59 ADP.6: 10 residues within 4Å: Chain F: K.11, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:K.11, F:N.114, F:N.114 Salt bridges: F:R.87, F:R.104 pi-Stacking: F:F.59, F:F.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Souza, T.A. et al., Molecular adaptability of nucleoside diphosphate kinase b from trypanosomatid parasites: stability, oligomerization and structural determinants of nucleotide binding. Mol Biosyst (2011)

Release Date

2011-04-27

Peptides

Nucleoside diphosphate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Nucleoside diphosphate kinase

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