SMTL ID : 9bmd.1

Motor domain from full-length human dynein-1 bound to microtubules in 5mM AMPPNP condition

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: L.1879, V.1880, T.1882, T.1885, A.1908, G.1909, T.1910, G.1911, K.1912, T.1913, E.1914, I.2049, L.2090, R.2091, K.2094 Ligands: MG.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:V.1880, A:V.1880, A:G.1909, A:T.1910, A:G.1911, A:K.1912, A:T.1913, A:E.1914, A:E.1914, A:R.2091, A:K.2094 Salt bridges: A:K.1912, A:R.2091

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

ATP.2: 19 residues within 4Å: Chain A: L.2191, T.2192, W.2203, S.2226, G.2227, S.2228, G.2229, K.2230, S.2231, M.2232, E.2344, L.2369, M.2373, N.2377, L.2452, E.2688, R.2726, R.2729 Ligands: MG.6 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:T.2192, A:T.2192, A:G.2227, A:S.2228, A:G.2229, A:K.2230, A:S.2231, A:M.2232, A:N.2377, A:R.2729 Salt bridges: A:K.2230, A:K.2230, A:R.2726, A:R.2729, A:R.2729, A:R.2729

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.3: 20 residues within 4Å: Chain A: V.2567, V.2568, V.2569, T.2574, P.2597, G.2598, S.2599, G.2600, K.2601, T.2602, M.2603, N.2713, I.2747, Y.2748, F.2751, P.2796, R.2797, T.2800, R.3088 Ligands: MG.7 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:V.2569, A:V.2569, A:G.2598, A:S.2599, A:G.2600, A:K.2601, A:K.2601, A:K.2601, A:K.2601, A:T.2602, A:M.2603, A:N.2713, A:N.2713, A:R.2797, A:R.2797, A:T.2800, A:R.3088, A:R.3088 Salt bridges: A:R.2797 ANP.4: 24 residues within 4Å: Chain A: V.2907, P.2908, L.2909, V.2910, F.2912, V.2915, V.2938, S.2939, G.2940, A.2941, G.2942, K.2943, T.2944, T.2945, N.3069, W.3097, R.3174, L.3177, N.3650, E.3652, D.3691, S.3694, R.3695 Ligands: MG.8 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:V.2910, A:V.2910, A:S.2939, A:G.2940, A:A.2941, A:G.2942, A:K.2943, A:K.2943, A:T.2944, A:T.2945, A:T.2945, A:N.3069, A:N.3069, A:N.3650, A:E.3652, A:D.3691, A:D.3691, A:S.3694 pi-Stacking: A:W.3097, A:W.3097

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.5: 1 residues within 4Å: Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain A: S.2231, D.2304, E.2344, E.2688 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.2231, A:E.2344 MG.7: 3 residues within 4Å: Chain A: T.2602, D.2664 Ligands: ANP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.2602 MG.8: 3 residues within 4Å: Chain A: T.2944, R.3695 Ligands: ANP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.2944

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chai, P. et al., Cryo-EM Reveals the Mechanochemical Cycle of Reactive Full-length Human Dynein-1. To Be Published

Release Date

2025-04-23

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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