SMTL ID : 9olj.1

22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 18

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

5 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, H.413, G.441, A.442, E.445 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.224, A:G.225, A:G.266, A:C.267, A:G.268, A:K.269, A:T.270, A:T.270, A:T.270, A:L.271, A:E.445 Salt bridges: A:K.269 ADP.5: 17 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 Ligands: MG.7 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.224, B:G.224, B:G.266, B:G.268, B:K.269, B:T.270, B:H.413, B:E.445, B:E.445 Salt bridges: B:K.269 Water bridges: A:D.362 ADP.9: 21 residues within 4Å: Chain B: D.362, R.388, R.391 Chain C: G.222, I.223, G.224, G.266, C.267, G.268, K.269, T.270, L.271, R.274, I.409, I.412, H.413, G.441, A.442, E.445 Ligands: MG.10, PO4.12 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain B 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:H.413, C:E.445, B:R.391 Salt bridges: C:K.269, B:R.388, B:R.388 ADP.14: 22 residues within 4Å: Chain C: D.362, R.388, R.391 Chain D: G.222, I.223, G.224, L.226, G.266, C.267, G.268, K.269, T.270, L.271, R.274, I.409, I.412, H.413, G.441, A.442, E.445 Ligands: MG.16, PO4.17 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C 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:E.445 Salt bridges: C:R.388, C:R.388 ADP.23: 14 residues within 4Å: Chain F: I.223, G.224, P.265, G.266, C.267, G.268, K.269, T.270, L.271, I.409, H.413, G.441, A.442, E.445 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:G.266, F:C.267, F:G.268, F:K.269, F:T.270, F:T.270, F:L.271, F:G.441

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

ATP.2: 23 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, H.549, S.550, G.551, K.552, T.553, A.554, L.555, S.650, I.710, K.711, L.714 Chain F: K.634 Ligands: MG.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:M.507, A:N.508, A:N.508, A:G.509, A:I.511, A:I.511, A:H.549, A:G.551, A:K.552, A:T.553, A:T.553, A:T.553, A:A.554 Salt bridges: A:K.552, A:K.552, 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, H.549, S.550, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 Ligands: MG.6 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:M.507, B:N.508, B:N.508, 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:T.553, B:A.554 Salt bridges: B:K.552, B:K.711, B:K.711, B:K.711 ATP.8: 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:T.553, C:A.554 Salt bridges: C:H.549, C:K.552, C:K.552, C:K.711, C:K.711, C:K.711, B:K.634 ATP.13: 21 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, I.710, K.711, L.714 Ligands: MG.15 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:M.507, 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:A.554 Salt bridges: D:H.549, D:K.711, D:K.711, D:K.711 ATP.18: 23 residues within 4Å: Chain D: K.254, R.388, R.391 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, N.377, I.409, I.412, H.413, G.441, A.442, E.445 Ligands: MG.20 18 PLIP interactions: 13 interactions with chain E, 5 interactions with chain D Hydrogen bonds: E:G.224, E:G.266, E:C.267, E:C.267, E:G.268, E:K.269, E:T.270, E:L.271, E:N.377, E:N.377, E:H.413, E:E.445, D:K.254 Salt bridges: E:K.269, D:R.388, D:R.388, D:R.388, D:R.391 ATP.19: 22 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 Ligands: MG.21 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:N.508, E:I.511, E:I.511, E:H.549, E:S.550, E:G.551, E:K.552, E:T.553, E:T.553, E:A.554 Salt bridges: E:K.552, E:K.711, E:K.711 ATP.22: 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.24 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:N.508, 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:K.552, F:K.552, F:K.711, E:K.634

10 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.553, D.606, D.607, T.648 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: T.553, D.606, T.648 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.553 MG.7: 2 residues within 4Å: Chain B: T.270 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain C: T.270, D.331, E.332 Ligands: ADP.9, PO4.12 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain C: T.553, D.606 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.553 MG.15: 4 residues within 4Å: Chain D: T.553, D.607, T.648 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.553 MG.16: 5 residues within 4Å: Chain C: R.391 Chain D: T.270, E.332 Ligands: ADP.14, PO4.17 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain D: R.391 Chain E: T.270, E.332 Ligands: ATP.18 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain E: T.553, D.607 Ligands: ATP.19 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.553 MG.24: 2 residues within 4Å: Chain F: T.553 Ligands: ATP.22 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.553

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

PO4.12: 10 residues within 4Å: Chain B: R.340, A.385, R.388, R.391 Chain C: P.265, K.269, E.332, N.377 Ligands: ADP.9, MG.10 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Salt bridges: B:R.391, C:K.269 Hydrogen bonds: C:E.332, C:N.377 PO4.17: 9 residues within 4Å: Chain C: A.385, R.388, R.391 Chain D: P.265, K.269, E.332, N.377 Ligands: ADP.14, MG.16 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Salt bridges: C:R.391 Hydrogen bonds: D:E.332, D:N.377

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
SNAP-25 or syntaxin N-: 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

SNAP-25 or syntaxin N-

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