SMTL ID : 3ngt.1 (7 other biounits)

Structure of Leishmania NDKb complexed with AMP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

homo-pentamer

Ligands

5 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 10 residues within 4Å: Chain A: K.11, Y.51, F.59, L.63, T.93, V.111, G.112, N.114, H.117 Chain E: E.151 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.51, A:N.114, A:C.116 Water bridges: A:G.112 Salt bridges: A:K.11, A:H.117 pi-Stacking: A:F.59 AMP.2: 9 residues within 4Å: Chain B: K.11, Y.51, L.54, F.59, T.93, R.104, V.111, N.114, H.117 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.104, B:N.114, B:N.114 Water bridges: B:G.112 Salt bridges: B:K.11, B:H.117 pi-Stacking: B:F.59, B:F.59 AMP.3: 10 residues within 4Å: Chain C: K.11, Y.51, L.54, F.59, R.87, T.93, R.104, V.111, N.114, H.117 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Y.51, C:R.87, C:R.104, C:N.114, C:N.114 Salt bridges: C:K.11, C:H.117 pi-Stacking: C:F.59, C:F.59 AMP.4: 9 residues within 4Å: Chain D: K.11, Y.51, L.54, F.59, L.63, T.93, V.111, N.114, H.117 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.104, D:N.114 Salt bridges: D:K.11, D:H.117 pi-Stacking: D:F.59, D:F.59 AMP.5: 11 residues within 4Å: Chain C: E.151 Chain E: K.11, Y.51, F.59, L.63, T.93, R.104, V.111, G.112, N.114, H.117 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:Y.51, E:R.104, C:E.151 Salt bridges: E:K.11, E:H.117 pi-Stacking: E:F.59, E: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: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

E
F

Nucleoside diphosphate kinase

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