SMTL ID : 9dgq.1

Structure of dynein-1 on microtubules

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

ADP.1: 8 residues within 4Å: Chain A: V.1880, A.1908, G.1909, T.1910, G.1911, K.1912, T.1913, E.1914 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:V.1880, A:V.1880, A:G.1909, A:T.1910, A:G.1911, A:G.1911, A:K.1912, A:T.1913, A:E.1914 ADP.6: 8 residues within 4Å: Chain B: V.1880, A.1908, G.1909, T.1910, G.1911, K.1912, T.1913, E.1914 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:V.1880, B:V.1880, B:G.1909, B:G.1909, B:T.1910, B:G.1911, B:G.1911, B:K.1912, B:T.1913, B:E.1914

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

ATP.2: 11 residues within 4Å: Chain A: L.2191, T.2192, S.2226, G.2227, S.2228, G.2229, K.2230, S.2231, M.2232, M.2373 Ligands: MG.3 8 PLIP interactions: 8 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 ATP.7: 12 residues within 4Å: Chain B: T.2192, S.2226, G.2227, S.2228, G.2229, K.2230, S.2231, M.2232, M.2373, I.2374, R.2726 Ligands: MG.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.2192, B:T.2192, B:G.2227, B:S.2228, B:G.2229, B:K.2230, B:S.2231, B:M.2232, B:R.2726

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 1 residues within 4Å: Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: ATP.7 No protein-ligand interaction detected (PLIP)

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

ANP.4: 8 residues within 4Å: Chain A: V.2569, G.2598, S.2599, G.2600, K.2601, T.2602, M.2603, R.2797 8 PLIP interactions: 8 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:T.2602, A:M.2603 ANP.5: 8 residues within 4Å: Chain A: P.2908, L.2909, V.2910, G.2940, G.2942, K.2943, T.2944, T.2945 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.2910, A:V.2910, A:G.2940, A:G.2942, A:K.2943 ANP.9: 10 residues within 4Å: Chain B: V.2569, P.2597, G.2598, S.2599, G.2600, K.2601, T.2602, M.2603, P.2796, R.2797 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:V.2569, B:V.2569, B:G.2598, B:S.2599, B:G.2600, B:K.2601, B:T.2602, B:M.2603 ANP.10: 8 residues within 4Å: Chain B: P.2908, L.2909, V.2910, G.2940, G.2942, K.2943, T.2944, T.2945 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.2910, B:V.2910, B:G.2940, B:G.2942, B:K.2943

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rao, Q. et al., Structure of dynein on microtubules. To Be Published

Release Date

2025-09-10

Peptides

Cytoplasmic dynein 1 heavy chain 1: AB
Dynein light intermediate chain: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
m

B
n

C
q

D
r

Cytoplasmic dynein 1 heavy chain 1

Dynein light intermediate chain

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