SMTL ID : 9e0u.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

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

ADP.1: 19 residues within 4Å: Chain A: L.2076, V.2077, T.2079, T.2082, A.2105, G.2106, T.2107, G.2108, K.2109, T.2110, E.2111, D.2155, I.2246, L.2287, R.2288, K.2291, D.2518, R.2555 Ligands: MG.6 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:V.2077, A:V.2077, A:T.2079, A:T.2082, A:G.2106, A:G.2108, A:K.2109, A:T.2110, A:E.2111, A:K.2291, A:D.2517, A:D.2518 Salt bridges: A:K.2109, A:K.2109, A:R.2288, A:R.2288, A:R.2555 ADP.4: 15 residues within 4Å: Chain A: V.2765, V.2766, T.2768, T.2771, P.2794, G.2795, G.2797, K.2798, T.2799, M.2800, I.2944, Y.2945, P.2993, R.2994, T.2997 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:V.2766, A:V.2766, A:G.2795, A:S.2796, A:G.2797, A:K.2798, A:T.2799, A:M.2800, A:R.2994, A:T.2997 Salt bridges: A:K.2798 ADP.5: 16 residues within 4Å: Chain A: V.3104, P.3105, L.3106, V.3107, S.3136, G.3137, A.3138, G.3139, K.3140, T.3141, T.3142, W.3294, R.3371, L.3374, N.3847, R.3892 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.3107, A:V.3107, A:G.3137, A:G.3139, A:K.3140, A:T.3141, A:T.3142, A:T.3142, A:R.3371, A:N.3847, A:R.3892 Salt bridges: A:K.3140

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

ATP.2: 19 residues within 4Å: Chain A: L.2388, T.2389, W.2400, P.2422, S.2423, G.2424, S.2425, G.2426, K.2427, S.2428, M.2429, E.2541, L.2566, M.2570, N.2574, L.2649, R.2923, R.2926 Ligands: MG.3 15 PLIP interactions: 15 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:S.2428, A:M.2429 Salt bridges: A:K.2427, A:R.2923, A:R.2926, A:R.2926, A:R.2926

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.2428, E.2541, R.2926 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.2428, A:E.2541 MG.6: 4 residues within 4Å: Chain A: T.2110, D.2155, T.2214 Ligands: ADP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.2155, A:D.2155

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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