SMTL ID : 5u2i.1

Crystal structure of a nucleoside diphosphate kinase from Naegleria fowleri

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-hexamer

Ligands

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: R.13, L.146, N.147, E.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.13, A:R.13, A:N.147, A:E.148 EDO.2: 5 residues within 4Å: Chain B: R.13, L.146, N.147, E.148 Ligands: MG.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.13, B:R.13, B:N.147 EDO.3: 5 residues within 4Å: Chain A: I.48, T.49 Chain B: S.144, E.145, N.147 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:E.145 Hydrogen bonds: A:T.49, A:T.49 EDO.5: 4 residues within 4Å: Chain C: R.13, L.146, N.147, E.148 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.13, C:R.13, C:N.147, C:E.148 Water bridges: C:W.149 EDO.6: 4 residues within 4Å: Chain D: R.13, L.146, N.147, E.148 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.13, D:R.13, D:N.147 Water bridges: D:W.149 EDO.10: 5 residues within 4Å: Chain D: S.144, L.146, N.147 Chain E: I.48, T.49 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain E Water bridges: D:L.146, E:T.49, E:T.49 Hydrogen bonds: E:T.49 EDO.12: 4 residues within 4Å: Chain E: R.13, L.146, N.147, E.148 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.13, E:R.13, E:N.147 Water bridges: E:W.149 EDO.13: 6 residues within 4Å: Chain E: T.101, R.112, I.124, H.125, G.126 Ligands: FMT.14 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:T.101, E:R.112, E:R.112, E:G.126, E:G.126 Water bridges: E:N.122 EDO.15: 4 residues within 4Å: Chain F: R.13, L.146, N.147, E.148 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.13, F:N.147 Water bridges: F:D.143, F:W.149 EDO.16: 4 residues within 4Å: Chain F: D.53, L.54, K.57, L.139 1 PLIP interactions: 1 interactions with chain F Water bridges: F:S.51 EDO.17: 5 residues within 4Å: Chain C: I.48, T.49 Chain F: S.144, L.146, N.147 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:N.147, C:T.49 Water bridges: F:L.146, F:E.148 EDO.18: 4 residues within 4Å: Chain F: R.112, I.124, H.125, G.126 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.112, F:R.112, F:G.126

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

MG.4: 5 residues within 4Å: Chain B: R.13, K.41, E.86, E.148 Ligands: EDO.2 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.86, H2O.10, H2O.12, H2O.12 MG.8: 2 residues within 4Å: Chain D: D.63, G.64 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.63, H2O.36 MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.7: 5 residues within 4Å: Chain D: A.138, L.139, W.140, F.141, Q.142 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.142 Water bridges: D:Q.142 FMT.11: 2 residues within 4Å: Chain D: R.34, Q.37 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.37 Water bridges: D:R.34, D:R.34, D:R.34 FMT.14: 4 residues within 4Å: Chain E: K.19, Y.59, H.125 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.19, E:K.19 Water bridges: E:N.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Conrady, D.G. et al., Crystal structure of a nucleoside diphosphate kinase from Naegleria fowleri. to be published

Release Date

2017-01-25

Peptides

Nucleoside diphosphate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Nucleoside diphosphate kinase