SMTL ID : 9nud.1

Y20S after Mg2+ (Sec18) - Class 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.574, D.627 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.574 MG.4: 3 residues within 4Å: Chain B: T.574, D.627 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.574 MG.7: 3 residues within 4Å: Chain C: T.574, D.627 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.574 MG.10: 3 residues within 4Å: Chain D: T.574, D.627 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.574 MG.13: 3 residues within 4Å: Chain E: T.574, D.627 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.574 MG.16: 2 residues within 4Å: Chain F: T.574 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.574

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

ADP.2: 7 residues within 4Å: Chain A: G.245, G.287, T.288, G.289, K.290, T.291, Q.434 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.245, A:G.245, A:G.287, A:G.287, A:G.289, A:K.290, A:T.291, A:T.291, A:Q.434 Salt bridges: A:K.290 ADP.5: 11 residues within 4Å: Chain B: G.243, V.244, G.245, G.287, T.288, G.289, K.290, T.291, L.292, Q.434, E.466 10 PLIP interactions: 10 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:L.292, B:Q.434 Salt bridges: B:K.290 ADP.8: 10 residues within 4Å: Chain C: G.243, G.245, G.287, T.288, G.289, K.290, T.291, L.292, Q.434, E.466 10 PLIP interactions: 10 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:L.292, C:Q.434, C:E.466 ADP.11: 11 residues within 4Å: Chain D: V.244, G.245, G.287, T.288, G.289, K.290, T.291, L.292, Q.434, A.463, E.466 11 PLIP interactions: 11 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:L.292, D:Q.434 Salt bridges: D:K.290 ADP.14: 12 residues within 4Å: Chain E: G.245, P.286, G.287, T.288, G.289, K.290, T.291, L.292, I.430, Q.434, G.462, E.466 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.245, E:G.245, E:G.287, E:G.289, E:K.290, E:T.291, E:T.291, E:L.292, E:Q.434 Salt bridges: E:K.290 ADP.17: 10 residues within 4Å: Chain F: P.286, G.287, T.288, G.289, K.290, T.291, I.430, Q.434, G.462, E.466 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.287, F:G.289, F:K.290, F:T.291, F:T.291, F:Q.434 Salt bridges: F:K.290

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

ATP.3: 13 residues within 4Å: Chain A: V.527, G.529, G.530, M.531, M.532, G.570, S.571, G.572, K.573, T.574, A.575, K.734 Ligands: MG.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.527, A:G.529, A:M.532, A:M.532, A:G.570, A:G.572, A:K.573, A:T.574, A:A.575 Salt bridges: A:K.734, A:K.734, A:K.734 ATP.6: 14 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, S.671, K.734, L.737 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.529, B:G.530, B:M.532, B:M.532, B:G.570, B:G.572, B:K.573, B:T.574, B:T.574, B:A.575, B:S.671, B:S.671 Salt bridges: B:K.573, B:K.573, B:K.734, B:K.734, B:K.734 ATP.9: 15 residues within 4Å: Chain B: K.655 Chain C: G.529, G.530, M.531, M.532, G.570, S.571, G.572, K.573, T.574, A.575, S.671, K.734, L.737 Ligands: MG.7 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.529, 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:A.575, C:S.671, C:S.671 Salt bridges: C:K.573, C:K.573, C:K.734, C:K.734, C:K.734, B:K.655 ATP.12: 16 residues within 4Å: Chain C: K.655 Chain D: G.529, G.530, M.531, M.532, Y.534, G.570, S.571, G.572, K.573, T.574, A.575, S.671, K.734, L.737 Ligands: MG.10 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.529, 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:A.575, D:S.671, D:S.671 Salt bridges: D:K.573, D:K.734, D:K.734, D:K.734, C:K.655 ATP.15: 13 residues within 4Å: Chain D: K.655 Chain E: G.529, G.530, M.531, M.532, G.570, S.571, G.572, K.573, T.574, A.575, L.737 Ligands: MG.13 18 PLIP interactions: 1 interactions with chain D, 17 interactions with chain E Salt bridges: D:K.655, E:K.573, E:K.573, E:K.734, E:K.734, E:K.734 Hydrogen bonds: E:G.529, E:G.530, E:M.532, E:M.532, E:G.570, E:G.572, E:K.573, E:T.574, E:T.574, E:A.575, E:S.671, E:S.671 ATP.18: 15 residues within 4Å: Chain E: K.655 Chain F: G.529, G.530, M.531, M.532, A.569, G.570, S.571, G.572, K.573, T.574, A.575, K.734, L.737 Ligands: MG.16 15 PLIP interactions: 14 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.529, F:M.532, F:M.532, F:G.570, F:S.571, F:G.572, F:K.573, F:T.574, F:T.574 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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Vesicular-fusion protein SEC18

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