SMTL ID : 6ip2.1

NSF-D1D2 part in the whole 20S complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: G.244, I.245, G.246, L.248, G.288, C.289, G.290, K.291, T.292, L.293, I.431, H.435, A.464, E.467 Chain F: R.410, R.413 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:G.246, A:G.288, A:C.289, A:C.289, A:G.290, A:K.291, A:T.292, A:T.292, A:T.292, A:L.293, F:R.413 Salt bridges: A:K.291, A:K.291, F:R.410 ATP.2: 18 residues within 4Å: Chain A: I.528, M.529, N.530, G.531, I.532, I.533, V.539, P.570, H.571, G.573, K.574, T.575, A.576, L.577, S.672, I.732, K.733, L.736 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:M.529, A:N.530, A:I.533, A:I.533, A:H.571, A:S.572, A:G.573, A:K.574, A:T.575, A:T.575, A:T.575, A:A.576, A:S.672 Salt bridges: A:K.574, A:K.574, A:K.733, A:K.733, A:K.733 ATP.3: 22 residues within 4Å: Chain A: K.276, L.380, S.381, D.384, R.410, R.413 Chain B: I.245, G.246, L.248, G.288, C.289, G.290, K.291, T.292, L.293, R.296, D.353, I.431, H.435, G.463, A.464, E.467 19 PLIP interactions: 5 interactions with chain A, 14 interactions with chain B Hydrogen bonds: A:S.381, B:G.246, B:G.246, B:G.288, B:C.289, B:G.290, B:K.291, B:T.292, B:T.292, B:T.292, B:L.293, B:D.353 Salt bridges: A:R.410, A:R.410, A:R.413, A:R.413, B:K.291, B:K.291, B:K.291 ATP.4: 19 residues within 4Å: Chain A: K.656 Chain B: M.529, N.530, G.531, I.532, I.533, W.535, V.539, H.571, S.572, G.573, K.574, T.575, A.576, L.577, S.672, I.732, K.733, L.736 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:M.529, B:N.530, B:I.533, B:I.533, B:H.571, B:S.572, B:G.573, B:K.574, B:T.575, B:T.575, B:T.575, B:A.576, B:S.672 Salt bridges: B:K.574, B:K.574, B:K.733, B:K.733, B:K.733, A:K.656, A:K.656 ATP.5: 22 residues within 4Å: Chain B: D.384, R.410, R.413 Chain C: G.244, I.245, G.246, L.248, P.287, G.288, C.289, G.290, K.291, T.292, L.293, R.296, D.353, N.399, I.431, H.435, G.463, A.464, E.467 19 PLIP interactions: 15 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:G.246, C:G.246, C:G.288, C:C.289, C:G.290, C:K.291, C:T.292, C:T.292, C:T.292, C:L.293, C:R.296, C:D.353, C:N.399 Salt bridges: C:K.291, C:K.291, B:R.410, B:R.410, B:R.410, B:R.413 ATP.6: 20 residues within 4Å: Chain B: K.656 Chain C: Y.527, I.528, M.529, N.530, G.531, I.532, I.533, W.535, V.539, H.571, S.572, G.573, K.574, T.575, A.576, L.577, S.672, K.733, L.736 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:M.529, C:N.530, C:I.533, C:I.533, C:H.571, C:S.572, C:G.573, C:K.574, C:T.575, C:T.575, C:A.576, C:S.672 Salt bridges: C:K.574, C:K.574, C:K.733, C:K.733, C:K.733 ATP.7: 16 residues within 4Å: Chain C: R.410, R.413 Chain D: P.287, G.288, C.289, G.290, K.291, T.292, L.293, R.296, E.354, N.399, I.431, H.435, A.464, E.467 19 PLIP interactions: 14 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:G.288, D:C.289, D:G.290, D:K.291, D:T.292, D:T.292, D:L.293, D:R.296, D:N.399, D:N.399, D:N.399, D:A.464, C:R.410 Salt bridges: D:K.291, D:K.291, C:R.410, C:R.410, C:R.413, C:R.413 ATP.8: 18 residues within 4Å: Chain C: K.656 Chain D: M.529, N.530, G.531, I.532, I.533, W.535, P.570, H.571, S.572, G.573, K.574, T.575, A.576, D.629, S.672, I.732, K.733 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:M.529, D:N.530, D:I.533, D:H.571, D:S.572, D:G.573, D:K.574, D:T.575, D:T.575, D:T.575, D:A.576, D:D.629, D:S.672 Salt bridges: D:H.571, D:K.574, D:K.574, D:K.733, D:K.733, D:K.733 ATP.9: 11 residues within 4Å: Chain E: I.245, G.246, G.290, K.291, T.292, L.293, L.294, L.422, P.423, D.424, I.431 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:G.246, E:K.291, E:T.292, E:T.292, E:L.293, E:L.294, E:D.424, E:D.424 ATP.10: 19 residues within 4Å: Chain D: K.656 Chain E: M.529, N.530, G.531, I.532, I.533, W.535, V.539, H.571, S.572, G.573, K.574, T.575, A.576, L.577, S.672, I.732, K.733, L.736 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:M.529, E:N.530, E:I.533, E:H.571, E:S.572, E:G.573, E:K.574, E:T.575, E:T.575, E:T.575, E:A.576 Salt bridges: E:K.574, E:K.574, E:K.733, E:K.733, E:K.733 ATP.11: 14 residues within 4Å: Chain F: G.244, P.286, P.287, G.288, C.289, G.290, K.291, T.292, L.293, D.353, I.431, G.463, A.464, E.467 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:G.288, F:C.289, F:C.289, F:G.290, F:K.291, F:T.292, F:T.292, F:T.292, F:L.293, F:D.353, F:N.399 Salt bridges: F:K.291, F:K.291 ATP.12: 16 residues within 4Å: Chain F: M.529, N.530, G.531, I.532, I.533, V.539, H.571, S.572, G.573, K.574, T.575, A.576, L.577, S.672, I.732, K.733 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:M.529, F:N.530, F:I.533, F:I.533, F:H.571, F:S.572, F:G.573, F:K.574, F:T.575, F:T.575, F:T.575, F:A.576 Salt bridges: F:K.574, F:K.574, F:K.733

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, X. et al., Mechanistic insights into the SNARE complex disassembly. Sci Adv (2019)

Release Date

2019-04-24

Peptides

Vesicle-fusing ATPase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

E
F

F
A

Vesicle-fusing ATPase