SMTL ID : 9nm1.1

Y20S (Sec18-Sec17-Sec9-Sso1-Snc1) EDTA - All Merge (Class 9, focused on D1/D2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ADP.1: 12 residues within 4Å: Chain A: G.245, G.287, T.288, G.289, K.290, T.291, L.292, I.430, Q.434, G.462, A.463, E.466 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.245, A:G.245, A:G.287, A:T.288, A:G.289, A:K.290, A:T.291, A:T.291, A:L.292, A:Q.434 Salt bridges: A:K.290 ADP.9: 12 residues within 4Å: Chain D: D.383 Chain E: G.245, G.287, T.288, G.289, K.290, T.291, L.292, I.430, Q.434, G.462, A.463 14 PLIP interactions: 10 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:G.245, E:G.245, E:G.287, E:T.288, E:G.289, E:K.290, E:T.291, E:T.291, E:L.292, D:R.412 Salt bridges: E:K.290, D:R.409, D:R.409 Water bridges: D:D.383

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

ATP.2: 10 residues within 4Å: Chain A: G.529, G.530, M.532, V.538, G.570, S.571, G.572, K.573, T.574, A.575 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.529, A:M.532, A:M.532, A:G.570, A:G.572, A:K.573, A:T.574, A:A.575 Water bridges: A:T.574 Salt bridges: A:K.573, A:K.573, A:K.734, A:K.734 ATP.3: 17 residues within 4Å: Chain A: D.383, R.409, R.412 Chain B: G.245, P.286, G.287, T.288, G.289, K.290, T.291, L.292, N.398, I.430, I.433, Q.434, A.463, E.466 16 PLIP interactions: 4 interactions with chain A, 12 interactions with chain B Salt bridges: A:R.409, A:R.409, A:R.409, A:R.412, B:K.290, B:K.290 Hydrogen bonds: B:G.245, B:G.245, B:G.287, B:T.288, B:G.289, B:K.290, B:T.291, B:L.292, B:N.398, B:Q.434 ATP.4: 13 residues within 4Å: Chain B: G.529, G.530, M.531, M.532, G.570, S.571, G.572, K.573, T.574, A.575, I.733, K.734, L.737 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.529, B:M.532, B:M.532, B:G.570, B:G.572, B:K.573, B:T.574, B:T.574, B:A.575 Salt bridges: B:K.573, B:K.573, B:K.734, B:K.734, B:K.734 ATP.5: 17 residues within 4Å: Chain B: D.383, R.409, R.412 Chain C: V.244, G.245, P.286, G.287, T.288, G.289, K.290, T.291, L.292, N.398, Q.434, G.462, A.463, E.466 18 PLIP interactions: 14 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:G.245, C:G.245, C:G.287, C:T.288, C:G.289, C:G.289, C:K.290, C:T.291, C:L.292, C:N.398, C:Q.434 Water bridges: C:T.291 Salt bridges: C:K.290, C:K.290, B:R.409, B:R.409, B:R.409, B:R.412 ATP.6: 17 residues within 4Å: Chain B: K.655 Chain C: G.529, G.530, M.531, M.532, Y.534, V.538, G.570, S.571, G.572, K.573, T.574, A.575, L.576, I.733, K.734, L.737 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.529, C:M.532, C:G.570, C:S.571, C:G.572, C:K.573, C:T.574, C:T.574, C:T.574, C:A.575 Salt bridges: C:K.573, C:K.573, C:K.734, C:K.734, C:K.734, B:K.655 ATP.7: 18 residues within 4Å: Chain C: D.383, R.409, R.412 Chain D: V.244, G.245, P.286, G.287, T.288, G.289, K.290, T.291, L.292, N.398, I.430, Q.434, G.462, A.463, E.466 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.245, D:G.245, D:G.287, D:G.289, D:K.290, D:T.291, D:L.292, D:Q.434 Water bridges: D:T.291, D:T.291, D:E.353 Salt bridges: D:K.290, D:K.290, C:R.409, C:R.409, C:R.409, C:R.412 ATP.8: 12 residues within 4Å: Chain D: G.529, G.530, M.532, Y.534, G.570, S.571, G.572, K.573, T.574, A.575, I.733, K.734 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.529, D:G.530, D:M.532, D:M.532, D:G.570, D:G.572, D:K.573, D:T.574, D:T.574, D:A.575 Salt bridges: D:K.573, D:K.573, D:K.734, D:K.734 ATP.10: 14 residues within 4Å: Chain E: G.529, G.530, M.531, M.532, Y.534, V.538, G.570, S.571, G.572, K.573, T.574, A.575, I.733, K.734 14 PLIP interactions: 13 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.529, E:G.530, E:M.532, E:G.570, E:G.572, E:K.573, E:T.574, E:T.574, E:A.575 Salt bridges: E:K.573, E:K.573, E:K.734, E:K.734, D:K.655 ATP.11: 15 residues within 4Å: Chain E: K.655 Chain F: E.528, G.529, G.530, M.531, M.532, Y.534, G.570, S.571, G.572, K.573, T.574, A.575, L.576, I.733 17 PLIP interactions: 16 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:E.528, F:E.528, F:G.529, F:G.529, F:M.532, F:G.570, F:G.572, F:K.573, F:T.574, F:T.574, F:A.575 Salt bridges: F:K.573, F:K.573, F:K.734, F:K.734, F:K.734, E:K.655

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khan, Y.A. et al., SNARE disassembly requires Sec18/NSF side loading. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-10-01

Peptides

Vesicular-fusion protein SEC18: ABCDEF
Protein SSO1: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
K

Vesicular-fusion protein SEC18

Protein SSO1

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