SMTL ID : 6mdp.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 2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: I.244, G.245, L.247, 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.245, A:C.288, A:G.289, A:K.290, A:T.291 ADP.10: 22 residues within 4Å: Chain D: K.275, D.383, R.409, R.412 Chain E: G.243, I.244, G.246, P.286, G.287, C.288, G.289, K.290, T.291, L.292, R.295, N.398, I.430, H.434, G.462, A.463, E.466, R.470 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:G.287, E:G.289, E:K.290, E:T.291, E:N.398, E:N.398, D:K.275 Salt bridges: E:K.290, D:R.412

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

ATP.2: 19 residues within 4Å: Chain A: I.527, M.528, N.529, G.530, I.531, I.532, W.534, V.538, P.569, H.570, G.572, K.573, T.574, A.575, L.576, S.671, I.731, K.732, L.735 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.529, A:N.529, A:N.529, A:N.529, A:I.532, A:W.534, A:G.572, A:K.573, A:A.575, A:S.671, A:S.671, A:S.671 Salt bridges: A:H.570, A:K.573, A:K.573, A:K.732, A:K.732, A:K.732 ATP.3: 23 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, I.731, K.732, L.735 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:N.529, B:N.529, B:G.530, B:I.532, B:H.570, 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, B:K.732, B:K.732 ATP.4: 25 residues within 4Å: Chain A: D.383, Q.387, R.409, R.412 Chain B: I.244, G.245, G.246, 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, H.434, G.462, A.463, L.465, E.466 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:G.245, B:G.287, B:G.287, B:G.289, B:N.398, A:D.383, A:R.409 Salt bridges: B:K.290, B:K.290, A:R.409, A:R.409, A:R.409, A:R.412 pi-Cation interactions: B:H.434 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, D.628, I.731, K.732, L.735 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.529, C:N.529, C:I.532, C:I.532, C:H.570, C:G.572, C:T.574, C:T.574, C:A.575, C:D.628 Salt bridges: C:H.570, C:K.573, C:K.573, C:K.732, C:K.732, B:K.655 ATP.6: 26 residues within 4Å: Chain B: K.275, L.379, D.383, A.406, 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, H.434, G.462, A.463, E.466 19 PLIP interactions: 6 interactions with chain B, 13 interactions with chain C Hydrogen bonds: B:K.275, 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:E.353, C:E.353, C:N.398 Salt bridges: B:R.409, B:R.409, B:R.409, B:R.412, B:R.412, C:K.290, C:K.290 ATP.7: 22 residues within 4Å: Chain C: K.655 Chain D: 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: 1 interactions with chain C, 16 interactions with chain D Salt bridges: C:K.655, D:H.570, D:K.573, D:K.573, D:K.732, D:K.732, D:K.732 Hydrogen bonds: D:M.528, D:N.529, D:N.529, D:I.532, D:W.534, D:H.570, D:G.572, D:K.573, D:T.574, D:A.575 ATP.8: 28 residues within 4Å: Chain C: K.275, L.379, S.380, D.383, A.406, R.409, R.412 Chain D: G.243, I.244, G.245, P.286, G.287, C.288, G.289, K.290, T.291, L.292, D.352, E.353, M.396, N.398, I.430, I.433, H.434, G.462, A.463, E.466, R.470 19 PLIP interactions: 13 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:G.243, D:G.245, D:G.287, D:G.287, D:G.289, D:K.290, D:T.291, D:E.353, D:E.353, D:N.398, C:D.383, C:R.409 Salt bridges: D:K.290, D:K.290, D:K.290, C:R.409, C:R.409, C:R.412, C:R.412 ATP.9: 22 residues within 4Å: Chain D: K.655 Chain E: Y.526, 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 15 PLIP interactions: 1 interactions with chain D, 14 interactions with chain E Salt bridges: D:K.655, E:K.573, E:K.573, E:K.732 Hydrogen bonds: E:M.528, E:N.529, E:I.532, E:I.532, E:W.534, E:H.570, E:K.573, E:T.574, E:T.574, E:T.574, E:A.575 ATP.11: 23 residues within 4Å: Chain E: K.655 Chain F: Y.526, I.527, M.528, N.529, G.530, I.531, I.532, K.533, W.534, V.538, P.569, H.570, G.572, K.573, T.574, A.575, L.576, D.628, S.671, I.731, K.732, L.735 11 PLIP interactions: 9 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:N.529, F:G.530, F:I.532, F:G.572, F:T.574, F:T.574, F:S.671 Salt bridges: F:K.732, F:K.732, E:K.655, E:K.655

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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