SMTL ID : 4uoh.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 11 residues within 4Å: Chain B: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.94, V.111, N.114 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:K.11, B:N.114, B:N.114 Water bridges: B:K.11, B:R.87, B:R.87, B:T.93, B:R.104, B:H.117, B:D.120, B:D.120 Salt bridges: B:R.87 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.94, V.111, N.114 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:K.11, C:T.93, C:R.104, C:N.114, C:N.114 Water bridges: C:K.11, C:R.87, C:R.104, C:R.104, C:R.104, C:D.120 Salt bridges: C:R.87 pi-Stacking: C:F.59, C: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.94, V.111, N.114 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:K.11, E:N.114, E:N.114 Water bridges: E:K.11, E:R.87, E:R.87, E:R.104, E:H.117, E:D.120 Salt bridges: E:R.87 pi-Stacking: E:F.59, E:F.59 ADP.7: 11 residues within 4Å: Chain F: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.94, V.111, N.114 Ligands: MG.8 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:K.11, F:R.104, F:N.114, F:N.114 Water bridges: F:K.11, F:R.87, F:R.104, F:R.104, F:R.104, F:H.117, F:D.120, F:D.120, F:D.120 Salt bridges: F:R.87 pi-Stacking: F:F.59, F:F.59

4 x MG: MAGNESIUM ION(Non-covalent)

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