SMTL ID : 9pdd.1

22bin20S complex (NSF-alphaSNAP-2:2 syntaxin-1a:SNAP-25), hydrolyzing, class 29

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-4-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: 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 A Hydrogen bonds: A:I.223, A:G.225, A:G.268, A:K.269, A:T.270, A:T.270, A:T.270, A:H.413 Salt bridges: A:K.269 ADP.4: 18 residues within 4Å: Chain A: D.362 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: PO4.6 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:L.271, B:H.413 Salt bridges: B:K.269 ADP.8: 19 residues within 4Å: Chain B: K.254, R.388, R.391 Chain C: G.222, I.223, G.224, 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: PO4.5 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:G.224, C:G.266, C:C.267, C:G.268, C:K.269, C:T.270, C:T.270, C:L.271, C:H.413, B:R.391 Salt bridges: B:R.388 ADP.11: 22 residues within 4Å: Chain C: K.254, D.362, R.388 Chain D: G.222, I.223, G.224, L.226, P.265, 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.9 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:G.268, D:K.269, D:T.270, D:T.270, D:T.270, D:L.271, D:H.413 Salt bridges: C:R.388, C:R.388 ADP.15: 15 residues within 4Å: Chain E: R.388 Chain F: G.222, 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 10 PLIP interactions: 9 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.222, F:G.224, F:G.266, F:C.267, F:G.268, F:K.269, F:T.270, E:R.388 Salt bridges: F:K.269, F:K.269

7 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, W.513, V.517, H.549, S.550, G.551, K.552, T.553, A.554, L.555, D.607, S.650, I.710, K.711, L.714 Chain F: K.634 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:M.507, A:N.508, 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:T.553, A:A.554, A:D.607, A:S.650 Salt bridges: A:K.711, F:K.634 ATP.3: 20 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, D.607, I.710, K.711 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.507, B:N.508, B:G.509, B:I.511, B:I.511, B:H.549, B:G.551, B:K.552, B:T.553, B:A.554 Salt bridges: B:K.552, B:K.552, B:K.711, B:K.711, A:K.634 ATP.7: 21 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, 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:G.509, C:I.511, C:I.511, C:W.513, C:H.549, C:G.551, C:K.552, C:T.553, C:T.553, C:T.553, C:A.554, C:D.607 Salt bridges: C:H.549, C:K.711 ATP.10: 19 residues within 4Å: Chain C: K.634 Chain D: 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 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: 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:T.553, D:A.554 Salt bridges: D:K.711 ATP.12: 18 residues within 4Å: Chain D: R.388, R.391 Chain E: G.222, I.223, G.224, P.265, G.266, C.267, G.268, K.269, T.270, L.271, N.377, I.409, H.413, G.441, A.442, E.445 15 PLIP interactions: 11 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:G.224, E:G.266, E:G.268, E:T.270, E:T.270, E:L.271, E:N.377, E:H.413, E:G.441, E:A.442, E:E.445 Salt bridges: D:R.388, D:R.388, D:R.391, D:R.391 ATP.13: 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, 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: 15 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:M.507, 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.711, D:K.634 ATP.14: 19 residues within 4Å: Chain F: 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 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:M.507, F:N.508, F:G.509, F:I.511, F:I.511, F:H.549, F:S.550, F:G.551, F:K.552, F:T.553, F:T.553, F:A.554, F:D.607, F:K.711 Salt bridges: F:K.552, F:K.552, F:K.711

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

PO4.5: 6 residues within 4Å: Chain B: R.388, R.391 Chain C: K.269, T.270, E.332 Ligands: ADP.8 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.270, C:E.332 Salt bridges: B:R.391 PO4.6: 6 residues within 4Å: Chain B: P.265, G.266, K.269, T.270, M.375 Ligands: ADP.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.266, B:T.270, B:T.270, B:T.270 Salt bridges: B:K.269

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain C: R.388, R.391 Chain D: T.270 Ligands: ADP.11 No protein-ligand interaction detected (PLIP)

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

2025-08-06

Peptides

Vesicle-fusing ATPase: ABCDEF
Unknown SNARE protein: G
Alpha-soluble NSF attachment protein: HIJK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
I

I
J

J
K

K
L

Vesicle-fusing ATPase

Unknown SNARE protein

Alpha-soluble NSF attachment protein

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