SMTL ID : 1s57.2 (1 other biounit)

crystal structure of nucleoside diphosphate kinase 2 from Arabidopsis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

18 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 1 residues within 4Å: Chain A: R.89 Ligand excluded by PLIP SO4.2: 6 residues within 4Å: Chain A: R.89, T.95, R.106, V.118, H.119, G.120 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: K.94, T.95 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain B: R.89, D.122 Chain D: K.128 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain B: K.13, R.89, T.95, R.106, H.119 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain B: K.94, T.95 Chain D: D.4, K.128 Ligand excluded by PLIP SO4.9: 1 residues within 4Å: Chain C: R.89 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain C: K.13, R.89, R.106, N.116, H.119 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain C: K.94, T.95 Ligand excluded by PLIP SO4.14: 1 residues within 4Å: Chain D: R.89 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain D: K.13, R.89, R.106, H.119 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain D: K.94, T.95 Ligand excluded by PLIP SO4.18: 1 residues within 4Å: Chain E: R.89 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain E: R.89, T.95, R.106, H.119 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain E: K.94, T.95 Ligand excluded by PLIP SO4.21: 1 residues within 4Å: Chain F: R.89 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain F: K.13, R.89, R.106, V.118, H.119, G.120 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain F: K.94, T.95 Ligand excluded by PLIP

6 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 10 residues within 4Å: Chain A: E.30, G.33, F.34, K.35, W.143, S.145, L.147, A.148, L.151, R.152 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.145 Water bridges: A:G.33, A:K.35, A:E.80, A:R.152, A:R.152 Salt bridges: A:K.35, A:R.152 EPE.8: 10 residues within 4Å: Chain B: E.30, G.33, F.34, K.35, W.143, S.145, L.147, A.148, L.151, R.152 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.145 Water bridges: B:G.33, B:S.145, B:R.152, B:R.152, B:R.152 Salt bridges: B:K.35, B:R.152 EPE.12: 10 residues within 4Å: Chain C: E.30, G.33, F.34, K.35, W.143, S.145, L.147, A.148, L.151, R.152 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.145 Water bridges: C:G.33, C:S.145, C:R.152, C:R.152, C:R.152 Salt bridges: C:K.35, C:R.152 EPE.13: 3 residues within 4Å: Chain C: Q.18, R.19, G.20 No protein-ligand interaction detected (PLIP) EPE.17: 10 residues within 4Å: Chain D: E.30, G.33, F.34, K.35, W.143, S.145, L.147, A.148, L.151, R.152 12 PLIP interactions: 1 interactions with chain E, 11 interactions with chain D Water bridges: E:R.19, D:G.33, D:G.33, D:K.35, D:S.145, D:R.152, D:R.152, D:R.152, D:R.152 Hydrogen bonds: D:S.145 Salt bridges: D:K.35, D:R.152 EPE.24: 10 residues within 4Å: Chain F: E.30, G.33, F.34, K.35, W.143, S.145, L.147, A.148, L.151, R.152 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:S.145 Water bridges: F:G.33, F:S.145, D:R.19 Salt bridges: F:K.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Im, Y.J. et al., Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling. J.Mol.Biol. (2004)

Release Date

2004-11-30

Peptides

Nucleoside diphosphate kinase II: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Nucleoside diphosphate kinase II

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