SMTL ID : 6mdo.1

The D1 and D2 domain rings of NSF engaging the SNAP-25 N-terminus within the 20S supercomplex (focused refinement on D1/D2 rings, class 1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ATP.1: 24 residues within 4Å: Chain A: Y.526, I.527, M.528, N.529, G.530, I.531, I.532, K.533, W.534, V.538, P.569, H.570, S.571, G.572, K.573, T.574, A.575, L.576, D.628, S.671, I.731, K.732, L.735 Chain F: K.655 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.529, A:N.529, A:G.530, A:I.532, A:W.534, A:H.570, A:S.571, A:G.572, A:T.574 Salt bridges: A:H.570, A:K.573, A:K.573, A:K.732, A:K.732 ATP.3: 25 residues within 4Å: Chain A: K.275, L.379, D.383, A.406, R.409, R.412 Chain B: I.244, G.245, L.247, P.285, P.286, G.287, C.288, G.289, K.290, T.291, L.292, E.353, N.398, I.430, I.433, H.434, G.462, A.463, E.466 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:G.245, B:G.245, B:P.286, B:G.289, B:K.290, B:T.291, B:T.291, B:L.292, B:N.398, B:H.434, B:E.466, A:R.409 Salt bridges: B:K.290, B:K.290, B:K.290, A:R.409, A:R.409, A:R.412, A:R.412 ATP.4: 25 residues within 4Å: Chain A: K.655 Chain B: Y.526, I.527, M.528, N.529, G.530, I.531, I.532, K.533, W.534, V.538, P.569, H.570, S.571, G.572, K.573, T.574, A.575, L.576, D.628, S.671, L.707, I.731, K.732, L.735 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.529, B:G.530, B:I.532, B:I.532, B:W.534, B:S.571, B:G.572, B:K.573, B:T.574, B:T.574, B:T.574, B:A.575, B:D.628 Salt bridges: B:K.573, B:K.573, B:K.732, A:K.655, A:K.655 ATP.5: 22 residues within 4Å: Chain B: K.655 Chain C: Y.526, I.527, M.528, N.529, G.530, I.531, I.532, W.534, V.538, P.569, H.570, S.571, G.572, K.573, T.574, A.575, L.576, S.671, I.731, K.732, L.735 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.526, C:N.529, C:N.529, C:I.532, C:I.532, C:H.570, C:S.571, C:G.572, C:K.573, C:T.574, C:T.574 Salt bridges: C:K.573, C:K.573, C:K.732, C:K.732, C:K.732, B:K.655 ATP.6: 26 residues within 4Å: Chain B: K.275, D.383, R.409, R.412 Chain C: G.243, I.244, G.245, L.247, P.285, P.286, G.287, C.288, G.289, K.290, T.291, L.292, R.295, E.353, N.398, I.430, I.433, H.434, S.461, G.462, A.463, E.466 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:G.245, C:G.245, C:G.287, C:C.288, C:G.289, C:K.290, C:T.291, C:L.292, C:N.398, C:N.398 Salt bridges: C:K.290, B:R.409, B:R.409, B:R.409, B:R.412, B:R.412 ATP.7: 23 residues within 4Å: Chain C: K.655 Chain D: Y.526, I.527, M.528, N.529, G.530, I.531, I.532, K.533, W.534, V.538, P.569, H.570, S.571, G.572, K.573, T.574, A.575, L.576, D.628, S.671, I.731, K.732 17 PLIP interactions: 1 interactions with chain C, 16 interactions with chain D Salt bridges: C:K.655, D:H.570, D:K.573, D:K.732, D:K.732, D:K.732 Hydrogen bonds: D:M.528, D:N.529, D:N.529, D:G.530, D:I.532, D:I.532, D:W.534, D:H.570, D:S.571, D:G.572, D:K.573 ATP.8: 22 residues within 4Å: Chain C: D.383, R.409, R.412 Chain D: G.243, I.244, G.246, P.286, G.287, C.288, G.289, K.290, T.291, L.292, R.295, E.353, N.398, I.430, I.433, H.434, G.462, A.463, E.466 20 PLIP interactions: 14 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:I.244, D:G.287, D:C.288, D:G.289, D:K.290, D:T.291, D:L.292, D:R.295, D:N.398, D:N.398, D:N.398, D:H.434, C:D.383 Salt bridges: D:K.290, D:K.290, C:R.409, C:R.409, C:R.409, C:R.412, C:R.412 ATP.9: 23 residues within 4Å: Chain D: K.655 Chain E: Y.526, I.527, M.528, N.529, G.530, I.531, I.532, W.534, V.538, P.569, H.570, S.571, G.572, K.573, T.574, A.575, L.576, D.628, S.671, I.731, K.732, L.735 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:M.528, E:N.529, E:N.529, E:I.532, E:H.570, E:G.572, E:K.573, E:T.574, E:A.575, E:S.671, E:S.671 Salt bridges: E:K.573, E:K.573, E:K.732, E:K.732, E:K.732 ATP.11: 20 residues within 4Å: Chain E: K.655 Chain F: I.527, M.528, N.529, I.531, I.532, W.534, V.538, P.569, H.570, S.571, G.572, K.573, T.574, A.575, L.576, D.628, I.731, K.732, L.735 20 PLIP interactions: 18 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:N.529, F:N.529, F:N.529, F:I.532, F:I.532, F:H.570, F:S.571, F:G.572, F:K.573, F:T.574, F:T.574, F:T.574, F:A.575 Salt bridges: F:K.573, F:K.573, F:K.732, F:K.732, F:K.732, E:K.655, E:K.655

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

ADP.2: 16 residues within 4Å: Chain A: G.243, I.244, G.245, P.286, G.287, C.288, G.289, K.290, T.291, L.292, I.430, I.433, H.434, G.462, A.463, E.466 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.245, A:G.245, A:P.286, A:P.286, A:G.289, A:K.290, A:T.291, A:T.291, A:H.434 Salt bridges: A:K.290 ADP.10: 21 residues within 4Å: Chain D: K.275, D.383, Q.387, R.409, R.412 Chain E: I.244, G.246, P.286, G.287, C.288, G.289, K.290, T.291, L.292, N.398, I.430, I.433, H.434, G.462, A.463, E.466 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain E Hydrogen bonds: D:K.275, D:Q.387, D:R.409, E:I.244, E:G.289, E:K.290, E:T.291, E:N.398, E:N.398 Salt bridges: D:R.409, D:R.409, D:R.412

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

White, K.I. et al., Structural principles of SNARE complex recognition by the AAA+ protein NSF. Elife (2018)

Release Date

2018-09-19

Peptides

Vesicle-fusing ATPase: ABCDEF
Synaptosomal-associated protein 25: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

Vesicle-fusing ATPase

Synaptosomal-associated protein 25

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