SMTL ID : 9nv1.1

Sec18 Mg2+ class 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.99 Å

Oligo State

homo-heptamer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: G.243, V.244, G.245, L.247, P.286, G.287, T.288, G.289, K.290, T.291, L.292, M.396, I.430, I.433, Q.434, G.462, A.463, E.466 10 PLIP interactions: 10 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:L.292, A:Q.434 Salt bridges: A:K.290 ADP.3: 17 residues within 4Å: Chain B: G.243, V.244, G.245, L.247, P.286, G.287, T.288, G.289, K.290, T.291, L.292, I.430, I.433, Q.434, G.462, A.463, E.466 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.245, B:G.245, B:G.287, B:T.288, B:G.289, B:K.290, B:T.291, B:T.291, B:L.292, B:Q.434 Salt bridges: B:K.290 ADP.5: 18 residues within 4Å: Chain C: G.243, V.244, G.245, L.247, P.286, G.287, T.288, G.289, K.290, T.291, L.292, M.396, I.430, I.433, Q.434, G.462, A.463, E.466 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.245, C:G.245, C:G.287, C:T.288, C:G.289, C:K.290, C:T.291, C:T.291, C:L.292, C:Q.434 Salt bridges: C:K.290 ADP.7: 17 residues within 4Å: Chain D: G.243, V.244, G.245, L.247, P.286, G.287, T.288, G.289, K.290, T.291, L.292, I.430, I.433, Q.434, G.462, A.463, E.466 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.245, D:G.245, D:G.287, D:T.288, D:G.289, D:K.290, D:T.291, D:T.291, D:Q.434 Salt bridges: D:K.290 ADP.9: 17 residues within 4Å: Chain E: G.243, V.244, G.245, L.247, P.286, G.287, T.288, G.289, K.290, T.291, L.292, I.430, I.433, Q.434, G.462, A.463, E.466 11 PLIP interactions: 11 interactions with chain E 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:Q.434, E:E.466 Salt bridges: E:K.290 ADP.11: 16 residues within 4Å: Chain F: G.243, V.244, G.245, P.286, G.287, T.288, G.289, K.290, T.291, L.292, I.430, I.433, Q.434, G.462, A.463, E.466 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:G.245, F:G.245, F:G.287, F:T.288, F:G.289, F:K.290, F:T.291, F:T.291, F:L.292, F:Q.434, F:E.466 ADP.13: 17 residues within 4Å: Chain G: G.243, V.244, G.245, L.247, P.286, G.287, T.288, G.289, K.290, T.291, L.292, I.430, I.433, Q.434, G.462, A.463, E.466 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:G.245, G:G.245, G:G.287, G:T.288, G:G.289, G:K.290, G:T.291, G:T.291, G:Q.434 Salt bridges: G:K.290

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

ATP.2: 22 residues within 4Å: Chain A: V.527, E.528, G.529, G.530, M.531, M.532, L.533, Y.534, V.538, A.569, G.570, S.571, G.572, K.573, T.574, A.575, L.576, S.671, I.733, K.734, L.737 Chain G: K.655 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain G Hydrogen bonds: A:G.529, A:M.532, A:M.532, A:G.570, A:S.571, A:G.572, A:K.573, A:T.574, A:T.574, A:T.574, A:A.575 Salt bridges: A:K.573, A:K.734, A:K.734, G:K.655 ATP.4: 20 residues within 4Å: Chain A: K.655 Chain B: E.528, G.529, G.530, M.531, M.532, Y.534, V.538, A.569, G.570, S.571, G.572, K.573, T.574, A.575, L.576, S.671, I.733, K.734, L.737 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.529, B:G.529, B:M.532, B:M.532, B:G.570, B:S.571, B:G.572, B:K.573, B:T.574, B:T.574, B:T.574, B:A.575, B:S.671 Water bridges: B:Y.534 Salt bridges: B:K.573, B:K.573, B:K.734, B:K.734, A:K.655 ATP.6: 20 residues within 4Å: Chain B: K.655 Chain C: E.528, G.529, G.530, M.531, M.532, Y.534, V.538, A.569, G.570, S.571, G.572, K.573, T.574, A.575, L.576, S.671, I.733, K.734, L.737 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.529, C:G.530, C:M.532, 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, C:S.671 Salt bridges: C:K.573, C:K.573, C:K.734, C:K.734, B:K.655 ATP.8: 21 residues within 4Å: Chain C: K.655 Chain D: V.527, E.528, G.529, G.530, M.531, M.532, Y.534, V.538, A.569, G.570, S.571, G.572, K.573, T.574, A.575, L.576, S.671, I.733, K.734, L.737 23 PLIP interactions: 22 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.529, D:G.530, D:M.532, D:M.532, D:G.570, D:S.571, D:G.572, D:K.573, D:T.574, D:T.574, D:T.574, D:A.575, D:S.671, D:S.671 Water bridges: D:K.573, D:K.734, D:K.734 Salt bridges: D:K.573, D:K.573, D:K.734, D:K.734, D:K.734, C:K.655 ATP.10: 20 residues within 4Å: Chain D: K.655 Chain E: V.527, E.528, G.529, G.530, M.531, M.532, Y.534, V.538, A.569, G.570, S.571, G.572, K.573, T.574, A.575, L.576, I.733, K.734, L.737 18 PLIP interactions: 17 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.529, E:G.530, E:M.532, E:M.532, E:G.570, E:S.571, E:G.572, E:K.573, E:T.574, E:T.574, E:T.574, E:A.575 Salt bridges: E:K.573, E:K.573, E:K.734, E:K.734, E:K.734, D:K.655 ATP.12: 21 residues within 4Å: Chain E: K.655 Chain F: V.527, E.528, G.529, G.530, M.531, M.532, Y.534, V.538, A.569, G.570, S.571, G.572, K.573, T.574, A.575, L.576, S.671, I.733, K.734, L.737 17 PLIP interactions: 16 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.529, F:G.530, F:M.532, F:M.532, F:G.570, F:S.571, 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 ATP.14: 20 residues within 4Å: Chain F: K.655 Chain G: E.528, G.529, G.530, M.531, M.532, Y.534, V.538, A.569, G.570, S.571, G.572, K.573, T.574, A.575, L.576, S.671, I.733, K.734, L.737 18 PLIP interactions: 17 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:G.529, G:G.530, G:M.532, G:M.532, G:G.570, G:S.571, G:G.572, G:K.573, G:T.574, G:T.574, G:A.575, G:S.671 Water bridges: G:Y.534 Salt bridges: G:K.573, G:K.573, G:K.734, G:K.734, F: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: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Vesicular-fusion protein SEC18

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