SMTL ID : 9p01.1

Cryo-EM structure of S. Mansoni p97 bound to ATPgS

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.20 Å

Oligo State

homo-hexamer

Ligands

12 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 21 residues within 4Å: Chain A: D.238, I.239, G.240, C.242, P.280, G.281, T.282, G.283, K.284, T.285, L.286, N.381, I.413, I.416, H.417, G.441, A.442, A.445 Chain B: R.392, F.393 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.240, A:G.281, A:T.282, A:T.282, A:G.283, A:K.284, A:K.284, A:T.285, A:T.285, A:L.286, A:N.381, A:H.417 Salt bridges: A:K.284 AGS.3: 22 residues within 4Å: Chain A: D.511, I.512, G.514, L.515, P.553, G.554, C.555, G.556, K.557, T.558, L.559, N.657, I.689, A.692, N.693, G.717, A.718, T.721 Chain B: R.668, P.669, R.798 Ligands: MG.4 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.512, A:G.554, A:C.555, A:G.556, A:K.557, A:T.558, A:L.559, A:N.657, A:N.657, A:T.721, B:R.798, B:R.798 Salt bridges: A:K.557 AGS.5: 22 residues within 4Å: Chain B: D.238, I.239, G.240, C.242, P.280, G.281, T.282, G.283, K.284, T.285, L.286, E.338, N.381, I.413, I.416, H.417, G.441, A.442, A.445 Chain F: R.392, F.393 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.240, B:G.281, B:T.282, B:G.283, B:K.284, B:K.284, B:T.285, B:L.286, B:E.338, B:E.338, B:N.381, B:H.417 Salt bridges: B:K.284 AGS.7: 21 residues within 4Å: Chain B: D.511, I.512, L.515, P.553, G.554, C.555, G.556, K.557, T.558, L.559, N.657, I.689, A.692, N.693, G.717, A.718, T.721 Chain F: R.668, P.669, R.798 Ligands: MG.8 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:G.554, B:C.555, B:C.555, B:G.556, B:K.557, B:T.558, B:L.559, B:N.657, B:N.657, F:R.798 Salt bridges: B:K.557 AGS.9: 21 residues within 4Å: Chain A: R.392, F.393 Chain C: D.238, I.239, G.240, C.242, P.280, G.281, T.282, G.283, K.284, T.285, L.286, N.381, I.413, I.416, H.417, G.441, A.442, A.445 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.240, C:G.281, C:T.282, C:T.282, C:G.283, C:K.284, C:K.284, C:T.285, C:L.286, C:N.381, C:H.417 Salt bridges: C:K.284 AGS.11: 22 residues within 4Å: Chain A: R.668, P.669, R.798 Chain C: D.511, I.512, G.513, L.515, P.553, G.554, C.555, G.556, K.557, T.558, L.559, N.657, I.689, A.692, N.693, G.717, A.718, T.721 Ligands: MG.12 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.513, C:G.554, C:C.555, C:C.555, C:G.556, C:K.557, C:T.558, C:L.559, C:N.657, C:N.657, C:N.693, C:T.721, A:R.798 Salt bridges: C:K.557 AGS.13: 20 residues within 4Å: Chain C: R.392, F.393 Chain D: D.238, I.239, G.240, P.280, G.281, T.282, G.283, K.284, T.285, L.286, N.381, I.413, I.416, H.417, G.441, A.442, A.445 Ligands: MG.14 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.240, D:G.281, D:T.282, D:T.282, D:G.283, D:K.284, D:K.284, D:T.285, D:T.285, D:N.381, D:H.417 Salt bridges: D:K.284 AGS.15: 22 residues within 4Å: Chain C: R.668, P.669, R.798 Chain D: D.511, I.512, G.514, L.515, P.553, G.554, C.555, G.556, K.557, T.558, L.559, N.657, I.689, A.692, N.693, G.717, A.718, T.721 Ligands: MG.16 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.554, D:C.555, D:C.555, D:G.556, D:K.557, D:T.558, D:T.558, D:L.559, D:N.657, D:N.657, D:T.721, C:R.798 Salt bridges: D:K.557 AGS.17: 21 residues within 4Å: Chain D: R.392, F.393 Chain E: D.238, I.239, G.240, P.280, G.281, T.282, G.283, K.284, T.285, L.286, E.338, N.381, I.413, I.416, H.417, G.441, A.442, A.445 Ligands: MG.18 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.240, E:G.281, E:T.282, E:T.282, E:G.283, E:K.284, E:K.284, E:T.285, E:L.286, E:E.338, E:E.338, E:N.381, E:H.417 Salt bridges: E:K.284 AGS.19: 22 residues within 4Å: Chain D: R.668, P.669, R.798 Chain E: D.511, I.512, G.514, L.515, P.553, G.554, C.555, G.556, K.557, T.558, L.559, N.657, I.689, A.692, N.693, G.717, A.718, T.721 Ligands: MG.20 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:G.554, E:C.555, E:C.555, E:G.556, E:K.557, E:T.558, E:L.559, E:N.657, E:N.657, E:N.693, D:R.798, D:R.798 Salt bridges: E:K.557 AGS.21: 21 residues within 4Å: Chain E: R.392, F.393 Chain F: D.238, I.239, G.240, C.242, P.280, G.281, T.282, G.283, K.284, T.285, L.286, N.381, I.413, I.416, H.417, G.441, A.442, A.445 Ligands: MG.22 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.240, F:G.281, F:T.282, F:T.282, F:G.283, F:K.284, F:K.284, F:T.285, F:N.381, F:H.417, F:G.441 Salt bridges: F:K.284 AGS.23: 22 residues within 4Å: Chain E: R.668, P.669, R.798 Chain F: D.511, I.512, G.513, L.515, P.553, G.554, C.555, G.556, K.557, T.558, L.559, N.657, I.689, A.692, N.693, G.717, A.718, T.721 Ligands: MG.24 12 PLIP interactions: 1 interactions with chain E, 11 interactions with chain F Hydrogen bonds: E:R.798, F:G.513, F:G.513, F:G.554, F:C.555, F:G.556, F:K.557, F:T.558, F:L.559, F:N.657, F:N.657 Salt bridges: F:K.557

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.285, D.337 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.285 MG.4: 3 residues within 4Å: Chain A: T.558, D.610 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.558 MG.6: 4 residues within 4Å: Chain B: T.285, D.337, E.338 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.285 MG.8: 3 residues within 4Å: Chain B: T.558, D.610 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.558 MG.10: 3 residues within 4Å: Chain C: T.285, D.337 Ligands: AGS.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.285 MG.12: 3 residues within 4Å: Chain C: T.558, D.610 Ligands: AGS.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.558 MG.14: 3 residues within 4Å: Chain D: T.285, D.337 Ligands: AGS.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.285 MG.16: 3 residues within 4Å: Chain D: T.558, D.610 Ligands: AGS.15 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.558 MG.18: 4 residues within 4Å: Chain E: T.285, D.337, E.338 Ligands: AGS.17 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.285 MG.20: 4 residues within 4Å: Chain D: R.668 Chain E: T.558, D.610 Ligands: AGS.19 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.558 MG.22: 3 residues within 4Å: Chain F: T.285, D.337 Ligands: AGS.21 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.285 MG.24: 3 residues within 4Å: Chain F: T.558, D.610 Ligands: AGS.23 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.558

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
F

D
E

E
D

F
C

vesicle-fusing ATPase

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