SMTL ID : 9e0x.1

Cryo-EM structure of Phi dynein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: L.2076, V.2077, T.2082, P.2104, A.2105, G.2106, T.2107, G.2108, K.2109, T.2110, E.2111, I.2246, L.2287, R.2288, K.2291, D.2517 Ligands: MG.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.2077, A:V.2077, A:P.2104, A:G.2106, A:T.2107, A:G.2108, A:K.2109, A:T.2110, A:E.2111 Salt bridges: A:K.2109, A:R.2288, A:R.2288 ADP.3: 17 residues within 4Å: Chain A: V.2765, V.2766, T.2768, T.2771, P.2794, G.2795, S.2796, G.2797, K.2798, T.2799, M.2800, I.2944, Y.2945, F.2948, P.2993, R.2994, T.2997 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.2766, A:V.2766, A:G.2795, A:G.2797, A:K.2798, A:T.2799, A:T.2799, A:T.2799, A:M.2800 Salt bridges: A:K.2798, A:R.2994, A:R.2994 ADP.4: 15 residues within 4Å: Chain A: V.3104, P.3105, L.3106, V.3107, V.3135, S.3136, G.3137, A.3138, G.3139, K.3140, T.3141, T.3142, R.3371, L.3374, N.3847 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:V.3107, A:V.3107, A:G.3137, A:A.3138, A:G.3139, A:K.3140, A:T.3141, A:T.3142, A:N.3847 Salt bridges: A:K.3140 ADP.7: 19 residues within 4Å: Chain B: L.2076, V.2077, T.2079, T.2082, P.2104, G.2106, T.2107, G.2108, K.2109, T.2110, E.2111, I.2246, L.2287, R.2288, K.2291, D.2517, D.2518, R.2555 Ligands: MG.12 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:V.2077, B:V.2077, B:T.2082, B:P.2104, B:G.2106, B:T.2107, B:G.2108, B:K.2109, B:T.2110, B:E.2111, B:K.2291, B:D.2518, B:D.2518 Salt bridges: B:K.2109, B:R.2288, B:R.2288, B:R.2555 ADP.9: 16 residues within 4Å: Chain B: V.2765, V.2766, T.2771, P.2794, G.2795, S.2796, G.2797, K.2798, T.2799, M.2800, I.2944, Y.2945, F.2948, P.2993, R.2994, T.2997 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:V.2766, B:V.2766, B:T.2771, B:G.2795, B:S.2796, B:G.2797, B:K.2798, B:T.2799, B:T.2799, B:M.2800, B:T.2997 Salt bridges: B:K.2798, B:R.2994, B:R.2994 ADP.10: 17 residues within 4Å: Chain B: V.3104, P.3105, L.3106, V.3107, F.3109, V.3135, S.3136, G.3137, A.3138, G.3139, K.3140, T.3141, T.3142, W.3294, R.3371, L.3374, N.3847 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:V.3107, B:V.3107, B:G.3137, B:A.3138, B:G.3139, B:K.3140, B:T.3141, B:T.3142, B:N.3847 Salt bridges: B:K.3140

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, E.2541, L.2566, M.2570, N.2574, E.2885, R.2923, R.2926 Ligands: MG.6 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:M.2429 Salt bridges: A:K.2427, A:K.2427, A:R.2881, A:R.2923, A:R.2926, A:R.2926, A:R.2926 ATP.8: 19 residues within 4Å: Chain B: L.2388, T.2389, W.2400, 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.2881, R.2923, R.2926 Ligands: MG.11 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:T.2389, B:T.2389, B:T.2389, B:G.2424, B:S.2425, B:G.2426, B:K.2427, B:S.2428, B:M.2429 Salt bridges: B:K.2427, B:K.2427, B:R.2881, B:R.2923, B:R.2926, B:R.2926, B:R.2926

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: T.2110 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.2110 MG.6: 5 residues within 4Å: Chain A: S.2428, D.2501, E.2541, E.2885 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.2428, A:E.2541 MG.11: 5 residues within 4Å: Chain B: S.2428, D.2501, E.2541, E.2885 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.2428, B:E.2541 MG.12: 4 residues within 4Å: Chain B: T.2110, T.2214, R.2555 Ligands: ADP.7 No protein-ligand interaction detected (PLIP)

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytoplasmic dynein 1 heavy chain 1

Related Entries With Identical Sequence