SMTL ID : 9pf2.1

NSF, substrate free, hydrolyzing, class 25

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: G.222, I.223, G.224, L.226, 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:G.224, A:G.266, A:G.268, A:K.269, A:T.270, A:T.270, A:L.271, A:H.413, A:E.445 Salt bridges: A:K.269 ADP.4: 16 residues within 4Å: Chain B: G.222, I.223, G.224, L.226, G.266, C.267, G.268, K.269, T.270, L.271, I.409, I.412, H.413, G.441, A.442, E.445 10 PLIP interactions: 10 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:L.271 Salt bridges: B:K.269 ADP.7: 18 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 Ligands: PO4.10 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.224, C:G.224, C:G.266, C:G.268, C:K.269, C:T.270, C:H.413 Salt bridges: C:K.269 ADP.11: 17 residues within 4Å: Chain D: G.222, I.223, G.224, L.226, 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: PO4.14 10 PLIP interactions: 10 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:L.271, D:H.413 Salt bridges: D:K.269 ADP.15: 17 residues within 4Å: Chain E: G.222, I.223, G.224, G.225, L.226, G.266, C.267, G.268, K.269, T.270, L.271, I.409, I.412, H.413, G.441, A.442, E.445 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.224, E:G.225, E:G.266, E:G.268, E:K.269, E:T.270, E:T.270, E:H.413 Salt bridges: E:K.269 ADP.18: 16 residues within 4Å: Chain F: G.222, I.223, G.224, 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 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:G.224, F:G.268, F:K.269, F:T.270, F:T.270, F:T.270, F:L.271, F:H.413, F:E.445

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

ATP.2: 19 residues within 4Å: Chain A: I.506, M.507, N.508, G.509, I.510, I.511, W.513, V.517, H.549, S.550, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 Ligands: MG.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:M.507, A:N.508, A:I.511, A:I.511, A:H.549, A:G.551, A:K.552, A:T.553, A:T.553, A:A.554 Salt bridges: A:H.549, A:K.711, A:K.711, A:K.711 ATP.5: 21 residues within 4Å: Chain A: K.634 Chain B: Y.505, I.506, M.507, N.508, G.509, I.510, I.511, W.513, V.517, H.549, S.550, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 Ligands: MG.6 14 PLIP interactions: 1 interactions with chain A, 13 interactions with chain B Salt bridges: A:K.634, B:K.552, B:K.711 Hydrogen bonds: B:N.508, B:N.508, B:G.509, B:I.511, B:I.511, B:W.513, B:H.549, B:G.551, B:K.552, B:T.553, B:A.554 ATP.8: 20 residues within 4Å: Chain B: K.634 Chain C: I.506, M.507, N.508, G.509, I.510, I.511, W.513, V.517, P.548, H.549, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 Ligands: MG.9 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.508, C:I.511, C:W.513, C:H.549, C:G.551, C:K.552, C:T.553, C:T.553, C:A.554 Salt bridges: C:K.552, C:K.552, C:K.711, C:K.711, C:K.711, B:K.634 ATP.12: 22 residues within 4Å: Chain C: K.634 Chain D: Y.505, I.506, M.507, N.508, G.509, I.510, I.511, W.513, V.517, H.549, S.550, G.551, K.552, T.553, A.554, L.555, D.607, I.710, K.711, L.714 Ligands: MG.13 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.508, D:N.508, D:I.511, D:I.511, D:H.549, D:G.551, D:K.552, D:T.553 Salt bridges: D:K.552, D:K.711, D:K.711, C:K.634 ATP.16: 20 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, H.549, S.550, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 Ligands: MG.17 17 PLIP interactions: 16 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:N.508, E:N.508, 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 Salt bridges: E:K.552, E:K.552, E:K.711, E:K.711, E:K.711, D:K.634 ATP.19: 23 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, D.607, I.710, K.711, L.714 Ligands: MG.20 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:N.508, F:I.511, F:I.511, F:W.513, F:H.549, F:S.550, F:G.551, F:K.552, F:T.553 Salt bridges: F:K.552, F:K.552, F:K.711, E:K.634

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: T.553 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.553 MG.6: 3 residues within 4Å: Chain B: T.553, D.607 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain C: T.553 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.553 MG.13: 3 residues within 4Å: Chain D: T.553, D.607 Ligands: ATP.12 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain D: K.634 Chain E: T.553 Ligands: ATP.16 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.553 MG.20: 3 residues within 4Å: Chain F: T.553, D.607 Ligands: ATP.19 No protein-ligand interaction detected (PLIP)

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

PO4.10: 6 residues within 4Å: Chain B: R.388 Chain C: K.269, D.331, M.375, N.377 Ligands: ADP.7 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.377 Salt bridges: C:K.269 PO4.14: 8 residues within 4Å: Chain D: P.265, G.266, K.269, T.270, D.331, M.375, N.377 Ligands: ADP.11 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.270 Salt bridges: D: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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