SMTL ID : 4f4a.1

Crystal structure of Nucleoside diphosphate kinase B from Trypanosoma brucei, UDP-bound form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 12 residues within 4Å: Chain A: K.15, Y.55, L.58, F.63, L.67, R.91, T.97, R.108, V.115, G.116, N.118 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.15, A:T.97, A:R.108, A:V.115, A:N.118, A:N.118 Water bridges: A:R.91, A:R.108, A:R.108, A:R.108, A:H.121 Salt bridges: A:R.91 pi-Stacking: A:F.63 UDP.3: 11 residues within 4Å: Chain B: K.15, Y.55, L.58, F.63, L.67, R.91, T.97, V.115, G.116, N.118 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.63 Hydrogen bonds: B:K.15, B:T.97, B:T.97, B:R.108, B:V.115, B:N.118, B:N.118 Water bridges: B:R.91, B:R.108, B:R.108, B:R.108, B:N.118 Salt bridges: B:R.91 UDP.5: 12 residues within 4Å: Chain C: K.15, Y.55, L.58, F.63, L.67, R.91, T.97, R.108, V.115, G.116, N.118 Ligands: MG.6 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:V.115 Hydrogen bonds: C:K.15, C:T.97, C:R.108, C:V.115, C:N.118, C:N.118 Water bridges: C:R.108, C:R.108, C:R.108, C:H.121, C:H.121, C:H.121, C:G.122 Salt bridges: C:R.91 pi-Stacking: C:F.63 UDP.7: 12 residues within 4Å: Chain D: K.15, Y.55, L.58, F.63, L.67, R.91, T.97, R.108, V.115, G.116, N.118 Ligands: MG.8 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:K.15, D:T.97, D:T.97, D:R.108, D:V.115, D:N.118, D:N.118 Water bridges: D:Y.55, D:R.91, D:R.108, D:R.108, D:R.108 Salt bridges: D:R.91 pi-Stacking: D:F.63 UDP.9: 11 residues within 4Å: Chain E: K.15, Y.55, L.58, F.63, L.67, R.91, T.97, V.115, G.116, N.118 Ligands: MG.10 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:F.63 Hydrogen bonds: E:K.15, E:T.97, E:R.108, E:V.115, E:N.118, E:N.118 Water bridges: E:R.91, E:R.108, E:R.108, E:N.118, E:H.121, E:H.121, E:H.121, E:H.121, E:H.121 Salt bridges: E:R.91 UDP.11: 12 residues within 4Å: Chain F: K.15, Y.55, L.58, F.63, L.67, R.91, T.97, R.108, V.115, G.116, N.118 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:V.115 Hydrogen bonds: F:K.15, F:T.97, F:T.97, F:R.108, F:V.115, F:N.118, F:N.118 Water bridges: F:Y.55, F:R.108, F:R.108, F:R.108, F:G.122 Salt bridges: F:R.91 pi-Stacking: F:F.63

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

MG.2: 2 residues within 4Å: Chain A: H.121 Ligands: UDP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: H.121 Ligands: UDP.3 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: UDP.5 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain D: H.121 Ligands: UDP.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain E: H.121 Ligands: UDP.9 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: UDP.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seattle Structural Genomics Center for Infectious Disease (SSGCID) et al., Crystal structure of Nucleoside diphosphate kinase B from Trypanosoma brucei, UDP-bound form. To be Published

Release Date

2012-05-30

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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