SMTL ID : 9pfc.1

NSF, substrate free, hydrolyzing, class 26

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ATP.1: 22 residues within 4Å: Chain A: I.506, M.507, N.508, G.509, I.510, I.511, K.512, W.513, V.517, P.548, H.549, S.550, G.551, K.552, T.553, A.554, L.555, D.607, I.710, K.711, L.714 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:M.507, A:N.508, A:I.511, A:I.511, A:W.513, A:H.549, A:S.550, A:G.551, A:K.552, A:T.553, A:A.554, A:D.607 Water bridges: A:K.552, A:K.552 Salt bridges: A:H.549, A:K.552, A:K.711, A:K.711, A:K.711 ATP.5: 21 residues within 4Å: Chain A: K.634 Chain B: I.506, M.507, N.508, G.509, I.510, I.511, W.513, V.517, P.548, H.549, S.550, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 Ligands: MG.6 20 PLIP interactions: 1 interactions with chain A, 19 interactions with chain B Salt bridges: A:K.634, B:H.549, B:K.552, B:K.552, B:K.711, B:K.711, B:K.711 Hydrogen bonds: B:M.507, B:N.508, B:G.509, B:I.511, B:I.511, B:W.513, B:H.549, B:S.550, B:G.551, B:K.552, B:T.553, B:A.554 Water bridges: B:T.553 ATP.10: 22 residues within 4Å: Chain B: K.634 Chain C: Y.505, I.506, M.507, N.508, G.509, I.510, I.511, W.513, V.517, P.548, H.549, S.550, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 Ligands: MG.11 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:M.507, C:N.508, C:I.511, C:I.511, C:W.513, C:H.549, C:S.550, C:G.551, C:K.552, C:T.553, C:A.554 Water bridges: C:T.648 Salt bridges: C:H.549, C:K.552, C:K.552, C:K.711, C:K.711, C:K.711, B:K.634 ATP.14: 20 residues within 4Å: Chain C: K.634 Chain D: M.507, N.508, G.509, I.510, I.511, W.513, V.517, P.548, H.549, S.550, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 Ligands: MG.15 22 PLIP interactions: 3 interactions with chain C, 19 interactions with chain D Water bridges: C:K.634, C:N.662 Salt bridges: C:K.634, D:H.549, D:K.552, D:K.552, D:K.711, D:K.711, D:K.711 Hydrogen bonds: D:M.507, D:N.508, D:N.508, D:G.509, D:I.511, D:I.511, D:H.549, D:S.550, D:G.551, D:K.552, D:T.553, D:T.553, D:A.554 ATP.18: 21 residues within 4Å: Chain D: K.634 Chain E: I.506, M.507, N.508, G.509, I.510, I.511, W.513, V.517, P.548, H.549, S.550, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 Ligands: MG.19 21 PLIP interactions: 20 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:M.507, E:N.508, E:N.508, E:G.509, E:I.511, E:I.511, E:W.513, E:H.549, E:S.550, E:G.551, E:K.552, E:T.553, E:T.553, E:A.554 Salt bridges: E:H.549, E:K.552, E:K.552, E:K.711, E:K.711, E:K.711, D:K.634 ATP.21: 22 residues within 4Å: Chain E: K.634 Chain F: Y.505, I.506, M.507, N.508, G.509, I.510, I.511, W.513, V.517, P.548, H.549, S.550, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 Ligands: MG.23 18 PLIP interactions: 18 interactions with chain F Hydrogen bonds: F:M.507, F:N.508, F:G.509, F:I.511, F:I.511, F:W.513, F:H.549, F:S.550, F:G.551, F:K.552, F:T.553, F:A.554 Salt bridges: F:H.549, F:K.552, F:K.552, F:K.711, F:K.711, F:K.711 ATP.22: 18 residues within 4Å: Chain E: R.388, R.391 Chain F: I.223, G.224, P.265, G.266, C.267, G.268, K.269, T.270, L.271, M.375, I.409, I.412, H.413, G.441, A.442, E.445 16 PLIP interactions: 14 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:G.224, F:G.224, F:G.266, F:C.267, F:G.268, F:K.269, F:T.270, F:T.270, F:H.413, F:E.445, F:E.445, E:R.388, E:R.391 Water bridges: F:N.377 Salt bridges: F:K.269, F:K.269

5 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 17 residues within 4Å: Chain A: G.222, I.223, G.224, L.226, P.265, G.266, C.267, G.268, K.269, T.270, L.271, I.409, I.412, H.413, G.441, A.442, E.445 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.224, A:C.267, A:C.267, A:G.268, A:K.269, A:T.270, A:T.270, A:H.413, A:E.445 Water bridges: A:E.445 Salt bridges: A:K.269 ADP.4: 18 residues within 4Å: Chain B: G.222, I.223, G.224, L.226, P.265, G.266, C.267, G.268, K.269, T.270, L.271, I.409, I.412, H.413, G.441, A.442, E.445 Ligands: PO4.8 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.224, B:G.224, B:G.266, B:C.267, B:G.268, B:K.269, B:T.270, B:T.270, B:T.270, B:L.271, B:H.413, B:E.445 Salt bridges: B:K.269 ADP.9: 17 residues within 4Å: Chain C: G.222, I.223, G.224, L.226, P.265, G.266, C.267, G.268, K.269, T.270, L.271, I.409, I.412, H.413, G.441, A.442, E.445 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:G.224, C:G.224, C:G.266, C:C.267, C:G.268, C:K.269, C:T.270, C:T.270, C:T.270, C:L.271, C:H.413, C:E.445 Salt bridges: C:K.269 ADP.13: 17 residues within 4Å: Chain D: G.222, I.223, G.224, L.226, P.265, G.266, C.267, G.268, K.269, T.270, L.271, I.409, I.412, H.413, G.441, A.442, E.445 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.224, D:G.224, D:G.266, D:C.267, D:G.268, D:K.269, D:T.270, D:T.270, D:L.271, D:H.413, D:E.445 Salt bridges: D:K.269 ADP.17: 18 residues within 4Å: Chain E: G.222, I.223, G.224, G.225, L.226, P.265, G.266, C.267, G.268, K.269, T.270, L.271, I.409, I.412, H.413, G.441, A.442, E.445 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.224, E:G.225, E:G.266, E:C.267, E:G.268, E:K.269, E:T.270, E:L.271, E:H.413, E:E.445 Water bridges: E:E.445 Salt bridges: E:K.269

7 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: T.553, D.606, D.607 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.553 MG.6: 2 residues within 4Å: Chain B: T.553 Ligands: ATP.5 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.553, H2O.5 MG.7: 2 residues within 4Å: Chain B: T.270, D.331 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.270 MG.11: 3 residues within 4Å: Chain C: T.553, D.606 Ligands: ATP.10 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.553, H2O.14 MG.15: 3 residues within 4Å: Chain D: T.553, D.606 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.553 MG.19: 3 residues within 4Å: Chain E: T.553, T.648 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.553 MG.23: 2 residues within 4Å: Chain F: T.553 Ligands: ATP.21 No protein-ligand interaction detected (PLIP)

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 7 residues within 4Å: Chain B: P.265, K.269, D.331, E.332, M.375, N.377 Ligands: ADP.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.331, B:N.377 Salt bridges: B:K.269 PO4.12: 5 residues within 4Å: Chain C: K.269, D.331, E.332, M.375, N.377 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.331, C:D.331, C:E.332, C:N.377 Salt bridges: C:K.269 PO4.16: 6 residues within 4Å: Chain D: K.269, D.331, E.332, M.375, T.376, N.377 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.331, D:E.332, D:N.377 Salt bridges: D:K.269 PO4.20: 6 residues within 4Å: Chain E: P.265, K.269, E.332, M.375, T.376, N.377 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.332, E:E.332, E:N.377 Salt bridges: E:K.269

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

White, K.I. et al., Structural remodeling of target-SNARE protein complexes by NSF enables synaptic transmission. Nat Commun (2025)

Release Date

2025-10-08

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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