SMTL ID : 3j94.1

Structure of ATP-bound N-ethylmaleimide sensitive factor determined by single particle cryoelectron microscopy

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 4.20 Å

Oligo State

homo-hexamer

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: Y.505, I.506, M.507, N.508, G.509, I.510, I.511, P.548, H.549, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 Chain F: K.634 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:N.508, A:G.509, A:I.511, A:H.549, A:G.551, A:T.553, A:T.553, A:T.553, A:A.554, A:L.555 Salt bridges: A:K.552, A:K.552, A:K.711, F:K.634, F:K.634 ATP.2: 12 residues within 4Å: Chain A: G.224, C.267, G.268, K.269, T.270, L.271, D.331, I.409, H.413, G.441, A.442, E.445 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.268, A:K.269, A:T.270, A:T.270, A:T.270, A:L.271 ATP.3: 19 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, H.549, S.550, G.551, K.552, T.553, A.554, L.555, D.607, I.710, K.711 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Y.505, B:M.507, B:N.508, B:G.509, B:I.511, B:W.513, B:H.549, B:S.550, B:K.552, B:T.553, B:A.554 Salt bridges: B:H.549, B:K.711, B:K.711, B:K.711 ATP.4: 14 residues within 4Å: Chain A: A.385 Chain B: G.224, P.265, G.266, C.267, G.268, K.269, T.270, L.271, I.409, S.440, G.441, A.442, E.445 8 PLIP interactions: 8 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 Salt bridges: B:K.269 ATP.5: 17 residues within 4Å: Chain C: 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 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:M.507, C:N.508, C:N.508, C:G.509, C:I.511, C:I.511, C:H.549, C:G.551, C:K.552, C:T.553, C:A.554 Salt bridges: C:K.552, C:K.552, C:K.711, C:K.711, C:K.711 ATP.6: 18 residues within 4Å: Chain B: A.385, R.388, R.391 Chain C: G.224, P.264, P.265, G.266, C.267, G.268, K.269, T.270, L.271, N.377, I.409, S.440, G.441, A.442, E.443 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain C Hydrogen bonds: B:A.385, C:G.224, C:G.266, C:C.267, C:G.268, C:K.269, C:T.270, C:N.377 Salt bridges: B:R.388, B:R.388, B:R.388, B:R.391, B:R.391, C:K.269, C:K.269, C:K.269 ATP.7: 18 residues within 4Å: Chain C: K.634 Chain D: Y.505, I.506, M.507, N.508, G.509, I.510, I.511, P.547, P.548, H.549, S.550, G.551, K.552, T.553, A.554, I.710, K.711 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Y.505, D:M.507, D:N.508, D:G.509, D:I.511, D:G.551, D:K.552, D:T.553, D:A.554 Salt bridges: D:H.549, D:K.552, D:K.552, C:K.634 ATP.8: 18 residues within 4Å: Chain C: R.388, R.391 Chain D: G.224, G.225, P.265, G.266, C.267, G.268, K.269, T.270, L.271, N.377, I.409, H.413, S.440, G.441, A.442, E.445 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.224, D:G.266, D:G.268, D:K.269, D:T.270, D:N.377, D:N.377, C:R.391 Salt bridges: D:K.269, D:K.269, C:R.388, C:R.388, C:R.388 ATP.9: 18 residues within 4Å: Chain D: K.634 Chain E: M.507, N.508, G.509, I.510, I.511, P.548, H.549, S.550, G.551, K.552, T.553, A.554, L.555, D.607, I.710, K.711, L.714 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain D Hydrogen bonds: 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.552, E:K.552, E:K.711, E:K.711, D:K.634, D:K.634 ATP.10: 17 residues within 4Å: Chain D: L.358, A.385, R.391 Chain E: P.264, P.265, G.266, C.267, G.268, K.269, T.270, L.271, N.377, I.409, S.440, G.441, A.442, E.445 14 PLIP interactions: 10 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:G.266, E:C.267, E:G.268, E:K.269, E:T.270, E:N.377, E:G.441, D:A.385 Salt bridges: E:K.269, E:K.269, E:K.269, D:R.391, D:R.391, D:R.391 ATP.11: 18 residues within 4Å: Chain E: K.634 Chain F: I.506, N.508, G.509, I.510, I.511, W.513, P.548, H.549, S.550, G.551, K.552, T.553, A.554, L.555, I.710, K.711, L.714 15 PLIP interactions: 12 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:N.508, F:G.509, F:I.511, F:I.511, F:K.552, F:T.553, F:T.553, F:T.553, F:A.554 Salt bridges: F:K.552, F:K.711, F:K.711, E:K.634, E:K.634, E:K.634

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, M. et al., Mechanistic insights into the recycling machine of the SNARE complex. Nature (2015)

Release Date

2015-01-28

Peptides

Vesicle-fusing ATPase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Vesicle-fusing ATPase

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