SMTL ID : 4uog.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

6 x YYY: DEOXYCYTIDINE DIPHOSPHATE(Non-covalent)

YYY.1: 13 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, G.112, N.114 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.11, A:R.94, A:N.114 Water bridges: A:K.11, A:R.104, A:G.118 Salt bridges: A:R.87, A:R.104 pi-Stacking: A:F.59 YYY.3: 12 residues within 4Å: Chain B: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.111 Hydrogen bonds: B:K.11, B:T.93, B:N.114 Water bridges: B:R.87, B:R.87, B:R.104, B:R.104 Salt bridges: B:R.87, B:R.104 pi-Stacking: B:F.59 YYY.5: 12 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 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:V.111 Hydrogen bonds: C:K.11, C:N.114 Water bridges: C:R.87, C:R.87, C:T.93, C:R.104, C:D.120 Salt bridges: C:R.87, C:R.104 pi-Stacking: C:F.59 YYY.7: 13 residues within 4Å: Chain D: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.94, R.104, V.111, G.112, N.114 Ligands: MG.8 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:K.11, D:N.114 Water bridges: D:K.11, D:R.104, D:H.117, D:G.118 Salt bridges: D:R.87, D:R.104 pi-Stacking: D:F.59 YYY.9: 12 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 Ligands: MG.10 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:V.111 Hydrogen bonds: E:K.11, E:N.114 Water bridges: E:Y.51, E:R.87, E:R.104, E:R.104, E:R.104 Salt bridges: E:R.87, E:R.104 pi-Stacking: E:F.59 YYY.11: 12 residues within 4Å: Chain F: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 Ligands: MG.12 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:V.111 Hydrogen bonds: F:K.11, F:N.114 Water bridges: F:R.87, F:R.87, F:R.104 Salt bridges: F:R.87, F:R.104 pi-Stacking: F:F.59

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.120 Ligands: YYY.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: H.117 Ligands: YYY.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: D.120 Ligands: YYY.5 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain D: D.120 Ligands: YYY.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain E: H.117 Ligands: YYY.9 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain F: D.120 Ligands: YYY.11 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 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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

NUCLEOSIDE DIPHOSPHATE KINASE

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