SMTL ID : 9e0y.1

Cryo-EM structure of human cytoplasmic dynein-1 in the presence of ATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: L.2076, V.2077, T.2079, A.2105, G.2106, T.2107, G.2108, K.2109, T.2110, E.2111, D.2155, E.2156, I.2246, L.2287, R.2288, K.2291 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:V.2077, A:V.2077, A:G.2106, A:T.2107, A:T.2107, A:G.2108, A:K.2109, A:T.2110, A:E.2111, A:E.2111, A:E.2111, A:R.2288, A:R.2288 Salt bridges: A:K.2109 ADP.4: 15 residues within 4Å: Chain A: P.3105, L.3106, V.3107, F.3109, G.3137, A.3138, G.3139, K.3140, T.3141, T.3142, W.3294, L.3374, N.3847, E.3849, R.3892 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.3107, A:V.3107, A:N.3847, A:E.3849, A:E.3849 Salt bridges: A:R.3892, A:R.3892

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

ATP.2: 18 residues within 4Å: Chain A: L.2388, T.2389, W.2400, S.2423, G.2424, S.2425, G.2426, K.2427, S.2428, M.2429, D.2501, E.2541, L.2566, M.2570, I.2571, N.2574, R.2923, R.2926 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:T.2389, A:T.2389, A:G.2424, A:S.2425, A:G.2426, A:K.2427, A:S.2428, A:S.2428, A:M.2429, A:D.2501, A:E.2541, A:E.2541, A:N.2574, A:R.2926 Salt bridges: A:K.2427, A:R.2923, A:R.2926 pi-Stacking: A:W.2400 ATP.3: 15 residues within 4Å: Chain A: P.2762, P.2794, G.2795, S.2796, G.2797, K.2798, T.2799, M.2800, E.2862, P.2936, I.2944, P.2993, R.2994, T.2997, R.3285 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.2795, A:G.2797, A:K.2798, A:T.2799, A:T.2799, A:M.2800, A:E.2862, A:E.2862, A:T.2997 Salt bridges: A:K.2798, A:R.2994, A:R.2994, A:R.3285, A:R.3285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, K.H.V. et al., Cryo-EM structure of Pre-Chi dynein bound to Lis1. To Be Published

Release Date

2025-07-09

Peptides

Cytoplasmic dynein 1 heavy chain 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytoplasmic dynein 1 heavy chain 1

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