SMTL ID : 9okc.1

22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 17

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: 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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.224, A:G.266, A:C.267, A:G.268, A:K.269, A:T.270, A:T.270, A:H.413 Salt bridges: A:K.269 ADP.5: 18 residues within 4Å: Chain B: 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 Ligands: PO4.3 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: 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 Salt bridges: B:K.269 ADP.7: 20 residues within 4Å: Chain B: Q.366, R.388 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: PO4.8 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.224, C:G.266, C:C.267, C:C.267, C:G.268, C:K.269, C:T.270, C:L.271, C:H.413 Salt bridges: C:K.269, B:R.388 ADP.10: 20 residues within 4Å: Chain C: D.362, R.388 Chain D: G.222, I.223, G.224, G.225, L.226, G.266, C.267, G.268, K.269, T.270, L.271, I.409, H.413, G.441, A.442, E.445 Ligands: MG.11, PO4.12 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.224, D:G.266, D:C.267, D:C.267, D:G.268, D:K.269, D:T.270, D:T.270, D:H.413 Salt bridges: D:K.269, C:R.388, C:R.388

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

ATP.2: 22 residues within 4Å: Chain A: Y.505, 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, I.710, K.711, L.714 Chain F: K.634 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.508, A:N.508, A:G.509, A:G.509, A:I.511, A:I.511, A:W.513, A:H.549, A:G.551, A:K.552, A:T.553, A:T.553, A:A.554 Salt bridges: A:K.552, A:K.552, A:K.711, A:K.711, A:K.711 ATP.4: 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, P.548, H.549, S.550, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.508, 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 Salt bridges: B:K.552, B:K.552, B:K.711, B:K.711, A:K.634 ATP.6: 19 residues within 4Å: Chain B: K.634 Chain C: 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 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:N.508, C:N.508, C:I.511, C:I.511, C:W.513, C:H.549, C:G.551, C:K.552, C:T.553, C:A.554 Salt bridges: C:K.552, C:K.552, C:K.711, C:K.711, C:K.711 ATP.9: 20 residues within 4Å: Chain D: 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 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:N.508, D:N.508, D:I.511, D:I.511, D:W.513, D:H.549, D:S.550, D:G.551, D:K.552, D:T.553, D:T.553, D:T.553, D:A.554 Salt bridges: D:K.552, D:K.552, D:K.711 ATP.13: 21 residues within 4Å: Chain D: R.388, R.391 Chain E: G.222, I.223, G.224, L.226, P.265, G.266, C.267, G.268, K.269, T.270, L.271, N.377, I.409, I.412, H.413, G.441, A.442, E.445 Ligands: MG.15 19 PLIP interactions: 3 interactions with chain D, 16 interactions with chain E Salt bridges: D:R.388, D:R.388, D:R.391, E:K.269, E:K.269 Hydrogen bonds: E:G.224, E:G.224, E:G.266, E:G.268, E:K.269, E:T.270, E:T.270, E:T.270, E:L.271, E:N.377, E:N.377, E:H.413, E:E.445, E:E.445 ATP.14: 21 residues within 4Å: Chain D: K.634 Chain E: 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 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:N.508, 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, E:T.553, E:A.554, E:D.607 Salt bridges: E:K.552, E:K.552, E:K.711, E:K.711, E:K.711 ATP.16: 18 residues within 4Å: Chain E: R.388 Chain F: I.223, G.224, G.225, G.266, C.267, G.268, K.269, T.270, L.271, N.377, P.401, I.409, I.412, H.413, S.440, G.441, A.442 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:G.266, F:C.267, F:G.268, F:K.269, F:T.270, F:T.270, F:L.271, F:N.377, F:G.441 Salt bridges: F:K.269, E:R.388, E:R.388 ATP.17: 20 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, H.549, S.550, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 18 PLIP interactions: 17 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:M.507, F:M.507, F:M.507, 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, E:K.634

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

PO4.3: 3 residues within 4Å: Chain A: D.362, R.391 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.391 PO4.8: 7 residues within 4Å: Chain B: R.388, R.391 Chain C: K.269, T.270, D.331, E.332 Ligands: ADP.7 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.270, C:E.332, B:R.391 Salt bridges: C:K.269 PO4.12: 8 residues within 4Å: Chain C: R.388, R.391 Chain D: K.269, T.270, D.331, E.332 Ligands: ADP.10, MG.11 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Salt bridges: C:R.391, D:K.269 Hydrogen bonds: D:E.332

2 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 4 residues within 4Å: Chain D: T.270, M.375 Ligands: ADP.10, PO4.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.270 MG.15: 4 residues within 4Å: Chain D: G.363 Chain E: T.270, D.331 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

White, K.I. et al., Pre-fusion AAA+ remodeling of target-SNARE protein complexes enables synaptic transmission. Biorxiv (2024)

Release Date

2025-08-06

Peptides

Vesicle-fusing ATPase: ABCDEF
Undefined N-terminus of SNAP-25 or syntaxin-1a: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Vesicle-fusing ATPase

Undefined N-terminus of SNAP-25 or syntaxin-1a

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