SMTL ID : 1ucn.1

X-ray structure of human nucleoside diphosphate kinase A complexed with ADP at 2 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: A.10, K.12, H.51, Y.52, G.118, G.119 Ligands: CA.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.10, A:Y.52 Salt bridges: A:K.12, A:H.51 PO4.4: 8 residues within 4Å: Chain B: A.10, K.12, H.51, Y.52, M.68, G.118, G.119 Ligands: CA.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.10, B:Y.52 Water bridges: B:G.119, B:G.119 Salt bridges: B:K.12, B:H.51 PO4.9: 5 residues within 4Å: Chain C: A.10, H.51, Y.52, G.118, G.119 5 PLIP interactions: 5 interactions with chain C Water bridges: C:H.51, C:G.119, C:G.119 Salt bridges: C:K.12, C:H.51 PO4.13: 7 residues within 4Å: Chain D: A.10, K.12, H.51, Y.52, G.118, G.119 Ligands: CA.14 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.10 Salt bridges: D:K.12, D:H.51 PO4.16: 8 residues within 4Å: Chain E: A.10, K.12, H.51, Y.52, M.68, G.118, G.119 Ligands: CA.17 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:A.10 Water bridges: E:G.119, E:G.119 Salt bridges: E:K.12, E:H.51 PO4.21: 5 residues within 4Å: Chain F: A.10, H.51, Y.52, G.118, G.119 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Y.52 Water bridges: F:G.119, F:G.119 Salt bridges: F:K.12, F:H.51

10 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: R.88, G.119, D.121 Ligands: PO4.1, ADP.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.121, H2O.2, H2O.3 CA.5: 4 residues within 4Å: Chain B: R.88, G.119 Ligands: PO4.4, ADP.7 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.119, H2O.6, H2O.7 CA.6: 2 residues within 4Å: Chain B: G.131, F.134 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:G.131, H2O.6, H2O.8, H2O.9, H2O.9 CA.10: 3 residues within 4Å: Chain C: R.88, G.119 Ligands: ADP.12 No protein-ligand interaction detected (PLIP) CA.11: 2 residues within 4Å: Chain C: G.131, F.134 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:G.131, H2O.11, H2O.11, H2O.11 CA.14: 5 residues within 4Å: Chain D: R.88, G.119, D.121 Ligands: PO4.13, ADP.15 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.121, H2O.15, H2O.16 CA.17: 4 residues within 4Å: Chain E: R.88, G.119 Ligands: PO4.16, ADP.19 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:G.119, H2O.19, H2O.20 CA.18: 2 residues within 4Å: Chain E: G.131, F.134 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:G.131, H2O.19, H2O.21, H2O.22, H2O.22 CA.22: 3 residues within 4Å: Chain F: R.88, G.119 Ligands: ADP.24 No protein-ligand interaction detected (PLIP) CA.23: 2 residues within 4Å: Chain F: G.131, F.134 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:G.131, H2O.24, H2O.24, H2O.24

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

ADP.3: 12 residues within 4Å: Chain A: K.12, Y.52, L.55, W.60, L.64, R.88, T.94, R.105, V.112, N.115, D.121 Ligands: CA.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.12, A:R.105, A:N.115, A:N.115 Salt bridges: A:R.88, A:R.105 pi-Stacking: A:W.60, A:W.60, A:W.60 ADP.7: 12 residues within 4Å: Chain B: K.12, Y.52, L.55, W.60, L.64, R.88, T.94, R.105, V.112, N.115, G.119 Ligands: CA.5 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.12, B:R.105, B:N.115, B:N.115 Water bridges: B:R.88, B:G.119 Salt bridges: B:R.88, B:R.105 pi-Stacking: B:W.60, B:W.60, B:W.60 ADP.12: 11 residues within 4Å: Chain C: K.12, Y.52, L.55, W.60, L.64, R.88, T.94, R.105, V.112, N.115 Ligands: CA.10 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:K.12, C:N.115, C:N.115 Water bridges: C:R.88, C:G.119 Salt bridges: C:R.88, C:R.105 pi-Stacking: C:W.60, C:W.60, C:W.60 ADP.15: 12 residues within 4Å: Chain D: K.12, Y.52, L.55, W.60, L.64, R.88, T.94, R.105, V.112, N.115, D.121 Ligands: CA.14 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:K.12, D:R.105, D:N.115, D:N.115 Salt bridges: D:R.88, D:R.105 pi-Stacking: D:W.60, D:W.60, D:W.60 ADP.19: 12 residues within 4Å: Chain E: K.12, Y.52, L.55, W.60, L.64, R.88, T.94, R.105, V.112, N.115, G.119 Ligands: CA.17 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:K.12, E:R.105, E:N.115, E:N.115 Water bridges: E:R.88, E:G.119, E:D.121 Salt bridges: E:R.88, E:R.105 pi-Stacking: E:W.60, E:W.60, E:W.60 ADP.24: 11 residues within 4Å: Chain F: K.12, Y.52, L.55, W.60, L.64, R.88, T.94, R.105, V.112, N.115 Ligands: CA.22 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:K.12, F:N.115, F:N.115 Water bridges: F:R.88, F:G.119 Salt bridges: F:R.88, F:R.105 pi-Stacking: F:W.60, F:W.60, F:W.60

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.8: 2 residues within 4Å: Chain B: N.148, E.152 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.148, B:E.152 TRS.20: 2 residues within 4Å: Chain E: N.148, E.152 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.148, E:E.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Nucleotide Binding to Nucleoside Diphosphate Kinases: X-ray Structure of Human NDPK-A in Complex with ADP and Comparison to Protein Kinases. J.Mol.Biol. (2003)

Release Date

2003-09-30

Peptides

nucleoside diphosphate kinase A: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

nucleoside diphosphate kinase A