SMTL ID : 2bef.1

CRYSTAL STRUCTURE OF NDP KINASE COMPLEXED WITH MG, ADP, AND BEF3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 2 residues within 4Å: Ligands: BEF.2, ADP.3 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Ligands: BEF.5, ADP.6 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Ligands: BEF.8, ADP.9 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Ligands: BEF.11, ADP.12 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Ligands: BEF.14, ADP.15 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Ligands: BEF.17, ADP.18 No protein-ligand interaction detected (PLIP)

6 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 8 residues within 4Å: Chain A: K.16, Y.56, R.92, R.109, H.122, G.123 Ligands: MG.1, ADP.3 No protein-ligand interaction detected (PLIP) BEF.5: 9 residues within 4Å: Chain B: K.16, Y.56, R.92, R.109, I.121, H.122, G.123 Ligands: MG.4, ADP.6 No protein-ligand interaction detected (PLIP) BEF.8: 8 residues within 4Å: Chain C: K.16, Y.56, R.109, I.121, H.122, G.123 Ligands: MG.7, ADP.9 No protein-ligand interaction detected (PLIP) BEF.11: 8 residues within 4Å: Chain D: K.16, Y.56, R.92, R.109, H.122, G.123 Ligands: MG.10, ADP.12 No protein-ligand interaction detected (PLIP) BEF.14: 9 residues within 4Å: Chain E: K.16, Y.56, R.92, R.109, I.121, H.122, G.123 Ligands: MG.13, ADP.15 No protein-ligand interaction detected (PLIP) BEF.17: 8 residues within 4Å: Chain F: K.16, Y.56, R.109, I.121, H.122, G.123 Ligands: MG.16, ADP.18 No protein-ligand interaction detected (PLIP)

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

ADP.3: 12 residues within 4Å: Chain A: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Ligands: MG.1, BEF.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.16, A:R.109, A:N.119, A:N.119 Water bridges: A:R.92, A:R.92, A:T.98 Salt bridges: A:H.59, A:R.92, A:R.109 pi-Stacking: A:F.64, A:F.64 ADP.6: 13 residues within 4Å: Chain B: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Chain C: E.155 Ligands: MG.4, BEF.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.16, B:R.109, B:N.119, B:N.119 Salt bridges: B:H.59, B:R.92, B:R.109 pi-Stacking: B:F.64 ADP.9: 12 residues within 4Å: Chain C: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Ligands: MG.7, BEF.8 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:K.16, C:R.109, C:N.119, C:N.119 Water bridges: C:R.92, C:D.125 Salt bridges: C:H.59, C:R.92, C:R.109 pi-Stacking: C:F.64 ADP.12: 12 residues within 4Å: Chain D: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Ligands: MG.10, BEF.11 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:K.16, D:R.109, D:N.119, D:N.119 Water bridges: D:R.92, D:R.92, D:T.98, D:T.98 Salt bridges: D:H.59, D:R.92, D:R.109 pi-Stacking: D:F.64, D:F.64 ADP.15: 13 residues within 4Å: Chain E: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Chain F: E.155 Ligands: MG.13, BEF.14 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:K.16, E:T.98, E:R.109, E:N.119, E:N.119 Salt bridges: E:H.59, E:R.92, E:R.109 pi-Stacking: E:F.64 ADP.18: 12 residues within 4Å: Chain F: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Ligands: MG.16, BEF.17 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:K.16, F:T.98, F:N.119, F:N.119 Water bridges: F:R.92 Salt bridges: F:H.59, F:R.92, F:R.109 pi-Stacking: F:F.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y.W. et al., AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP. Proc.Natl.Acad.Sci.USA (1997)

Release Date

1998-08-12

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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