SMTL ID : 9ox9.1

Cryo-EM structure of S. Mansoni p97 bound to CB-5083

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.85 Å

Oligo State

homo-hexamer

Ligands

6 x JDP: 1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide(Non-covalent)

JDP.1: 19 residues within 4Å: Chain A: V.507, D.511, I.512, L.515, G.554, C.555, G.556, L.559, L.560, P.681, S.685, N.688, I.689, A.692, N.693, R.695, G.717, A.718, T.721 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.512, A:L.559, A:L.559, A:I.689, A:I.689 Hydrogen bonds: A:D.511 JDP.2: 18 residues within 4Å: Chain B: V.507, D.511, I.512, L.515, G.554, C.555, G.556, L.559, L.560, P.681, S.685, N.688, I.689, A.692, N.693, G.717, A.718, T.721 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.559, B:I.689, B:I.689 Hydrogen bonds: B:N.688, B:T.721 JDP.3: 18 residues within 4Å: Chain C: V.507, D.511, I.512, L.515, G.554, C.555, G.556, L.559, L.560, P.681, S.685, N.688, I.689, A.692, N.693, G.717, A.718, T.721 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.512, C:L.559, C:I.689 Hydrogen bonds: C:G.554, C:N.688, C:T.721 JDP.4: 18 residues within 4Å: Chain D: V.507, D.511, I.512, L.515, G.554, C.555, G.556, L.559, L.560, P.681, S.685, N.688, I.689, A.692, N.693, G.717, A.718, T.721 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.512, D:L.559, D:I.689, D:I.689, D:A.692 Hydrogen bonds: D:G.554, D:N.688, D:T.721 JDP.5: 18 residues within 4Å: Chain E: V.507, D.511, I.512, G.554, C.555, G.556, L.559, L.560, P.681, S.685, N.688, I.689, A.692, N.693, R.695, G.717, A.718, T.721 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:I.512, E:L.559 Hydrogen bonds: E:N.688, E:T.721 JDP.6: 18 residues within 4Å: Chain F: V.507, D.511, I.512, L.515, G.554, C.555, G.556, L.559, L.560, P.681, S.685, N.688, I.689, A.692, N.693, G.717, A.718, T.721 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:I.512, F:L.559, F:I.689, F:I.689, F:A.692 Hydrogen bonds: F:G.554, F:N.688, F:T.721

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stephens, D.R. et al., Leveraging the Human Druggable Genome to Uncover Therapeutic Targets in the Human Parasite Schistosoma mansoni. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-08-13

Peptides

vesicle-fusing ATPase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

vesicle-fusing ATPase

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