SMTL ID : 7k3z.1

P. falciparum Cpn60 D474A mutant bound to ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.69 Å

Oligo State

homo-heptamer

Ligands

7 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.89, A.153, N.155 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.89 MG.3: 4 residues within 4Å: Chain B: D.89, I.152, N.155 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain C: D.89, I.152, N.155 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.89 MG.7: 3 residues within 4Å: Chain D: D.89, N.155 Ligands: ATP.8 No protein-ligand interaction detected (PLIP) MG.9: 5 residues within 4Å: Chain E: D.89, I.152, A.153, N.155 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.89 MG.11: 4 residues within 4Å: Chain F: D.89, A.153, N.155 Ligands: ATP.12 No protein-ligand interaction detected (PLIP) MG.13: 5 residues within 4Å: Chain G: D.89, I.152, A.153, N.155 Ligands: ATP.14 No protein-ligand interaction detected (PLIP)

7 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 25 residues within 4Å: Chain A: T.32, L.33, G.34, P.35, V.56, G.88, D.89, G.90, T.91, S.92, S.93, I.152, N.155, N.156, G.426, G.427, G.428, I.494, Y.520, D.521, V.522, N.523, I.535, D.537 Ligands: MG.1 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.34, A:G.90, A:G.90, A:T.91, A:S.92, A:S.92, A:S.93, A:N.155, A:N.156, A:G.427, A:G.428, A:V.522, A:D.537 ATP.4: 25 residues within 4Å: Chain B: T.32, L.33, G.34, P.35, V.56, G.88, D.89, G.90, T.91, S.92, S.93, I.152, N.155, N.156, G.426, G.427, G.428, I.494, Y.520, D.521, V.522, N.523, I.535, D.537 Ligands: MG.3 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.34, B:G.90, B:T.91, B:S.92, B:S.92, B:S.93, B:N.156, B:G.427, B:G.428, B:D.521, B:V.522, B:D.537 ATP.6: 25 residues within 4Å: Chain C: T.32, L.33, G.34, P.35, V.56, G.88, D.89, G.90, T.91, S.92, S.93, I.152, N.155, N.156, G.426, G.427, G.428, I.494, Y.520, D.521, V.522, N.523, I.535, D.537 Ligands: MG.5 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:G.34, C:G.90, C:G.90, C:T.91, C:S.92, C:S.92, C:S.93, C:N.155, C:N.155, C:N.156, C:G.427, C:G.428, C:D.521, C:V.522, C:N.523, C:D.537 ATP.8: 26 residues within 4Å: Chain D: T.32, L.33, G.34, P.35, D.54, V.56, G.88, D.89, G.90, T.91, S.92, S.93, I.152, N.155, N.156, G.426, G.427, G.428, I.494, Y.520, D.521, V.522, N.523, I.535, D.537 Ligands: MG.7 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.34, D:G.90, D:G.90, D:T.91, D:S.92, D:S.92, D:S.93, D:G.427, D:G.428, D:D.521, D:V.522, D:D.537 ATP.10: 26 residues within 4Å: Chain E: T.32, L.33, G.34, P.35, D.54, V.56, G.88, D.89, G.90, T.91, S.92, S.93, I.152, N.155, N.156, G.426, G.427, G.428, I.494, Y.520, D.521, V.522, N.523, I.535, D.537 Ligands: MG.9 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.34, E:G.90, E:G.90, E:T.91, E:S.92, E:S.92, E:S.93, E:N.155, E:N.155, E:G.427, E:G.428, E:D.521, E:V.522, E:D.537 ATP.12: 26 residues within 4Å: Chain F: T.32, L.33, G.34, P.35, D.54, G.55, V.56, G.88, D.89, G.90, T.91, S.92, S.93, I.152, N.155, G.426, G.427, G.428, I.494, Y.520, D.521, V.522, N.523, I.535, D.537 Ligands: MG.11 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:G.34, F:G.55, F:G.90, F:G.90, F:S.92, F:S.92, F:S.93, F:N.155, F:N.156, F:G.427, F:G.428, F:D.521, F:V.522, F:N.523, F:D.537 ATP.14: 24 residues within 4Å: Chain G: T.32, L.33, G.34, P.35, V.56, G.88, D.89, G.90, T.91, S.92, S.93, I.152, N.155, G.426, G.427, G.428, I.494, Y.520, D.521, V.522, N.523, I.535, D.537 Ligands: MG.13 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:G.34, G:G.90, G:G.90, G:T.91, G:S.92, G:S.92, G:S.93, G:N.155, G:N.156, G:G.427, G:G.428, G:D.521, G:V.522, G:D.537

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, B. et al., Crystal structure of P. falciparum Cpn60 bound to ATP reveals an open dynamic conformation before substrate binding. Sci Rep (2021)

Release Date

2021-04-21

Peptides

60 kDa chaperonin: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

60 kDa chaperonin