SMTL ID : 4uof.1

Crystallographic structure of nucleoside diphosphate kinase from Litopenaeus vannamei complexed with dADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

3 x DAT: 2'-DEOXYADENOSINE-5'-DIPHOSPHATE(Non-covalent)

DAT.1: 12 residues within 4Å: Chain A: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.94, R.104, V.111, N.114 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.11, A:R.94, A:N.114 Water bridges: A:K.11 Salt bridges: A:R.87, A:R.104 pi-Stacking: A:F.59, A:F.59 DAT.3: 12 residues within 4Å: Chain B: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.94, R.104, V.111, N.114 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.11, B:R.94, B:N.114 Water bridges: B:R.104, B:R.104, B:R.104, B:I.116 Salt bridges: B:R.87, B:R.104 pi-Stacking: B:F.59, B:F.59 DAT.5: 11 residues within 4Å: Chain C: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, N.114 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:K.11, C:N.114 Water bridges: C:K.11, C:Y.51, C:R.87, C:T.93, C:T.93, C:R.104, C:R.104, C:R.104, C:D.120 Salt bridges: C:R.87, C:R.104 pi-Stacking: C:F.59, C:F.59

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.120 Ligands: DAT.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.120, H2O.4, H2O.4 MG.4: 2 residues within 4Å: Chain B: D.120 Ligands: DAT.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: H.117, D.120 Ligands: DAT.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez-Zavala, A.A. et al., Structure of Nucleoside Diphosphate Kinase from the Pacific Shrimp (Litopenaeus Vannamei) in Binary Complexes with Purine and Pyrimidine Nucleoside Diphosphates. Acta Crystallogr.,Sect.F (2014)

Release Date

2014-09-10

Peptides

NUCLEOSIDE DIPHOSPHATE KINASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

NUCLEOSIDE DIPHOSPHATE KINASE

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