SMTL ID : 9dzy.1

Cryo-EM structure of Pre-Chi dynein bound to Lis1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: V.3104, P.3105, L.3106, V.3107, F.3109, V.3112, V.3135, G.3137, A.3138, G.3139, K.3140, T.3141, T.3142, R.3371, L.3374, N.3847 14 PLIP interactions: 14 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.3141, A:T.3141, A:T.3142, A:R.3371, A:N.3847, A:N.3847 Salt bridges: A:K.3140 ADP.5: 11 residues within 4Å: Chain A: V.2766, G.2795, S.2796, G.2797, K.2798, T.2799, M.2800, I.2944, Y.2945, R.2994, T.2997 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:V.2766, A:V.2766, A:P.2793, A:G.2795, A:S.2796, A:G.2797, A:K.2798, A:T.2799, A:T.2799, A:M.2800, A:R.2994, A:T.2997 Salt bridges: A:K.2798, A:R.2994, A:R.2994 ADP.6: 18 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, I.2246, L.2287, R.2288, K.2291, D.2517, R.2555 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:V.2077, A:V.2077, A:T.2079, A:T.2082, A:G.2106, A:T.2107, A:G.2108, A:K.2109, A:T.2110, A:E.2111, A:K.2291, A:R.2555 Salt bridges: A:K.2109, A:R.2288, A:R.2288 ADP.8: 18 residues within 4Å: Chain D: V.2764, 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 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:V.2766, D:V.2766, D:T.2768, D:G.2795, D:G.2797, D:K.2798, D:T.2799, D:T.2799, D:T.2799, D:M.2800 Salt bridges: D:K.2798, D:R.2994, D:R.2994 ADP.9: 17 residues within 4Å: Chain D: V.3104, P.3105, L.3106, V.3107, F.3109, V.3112, V.3135, S.3136, G.3137, A.3138, G.3139, K.3140, T.3141, T.3142, W.3294, L.3374, N.3847 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:V.3107, D:V.3107, D:G.3137, D:A.3138, D:G.3139, D:K.3140, D:T.3141, D:T.3142, D:N.3847, D:N.3847 Salt bridges: D:K.3140 ADP.12: 18 residues within 4Å: Chain D: L.2076, V.2077, T.2079, T.2082, A.2105, G.2106, T.2107, G.2108, K.2109, T.2110, E.2111, I.2246, L.2287, R.2288, K.2291, D.2517, D.2518 Ligands: MG.11 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:V.2077, D:V.2077, D:T.2079, D:G.2106, D:T.2107, D:G.2108, D:K.2109, D:T.2110, D:E.2111, D:D.2518 Salt bridges: D:K.2109, D:R.2288, D:R.2288

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

ATP.2: 19 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, L.2649, R.2881, 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:M.2429, A:R.2881 Salt bridges: A:K.2427, A:K.2427, A:R.2923, A:R.2926, A:R.2926, A:R.2926 ATP.7: 21 residues within 4Å: Chain D: 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.2881, E.2885, R.2923, R.2926 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:T.2389, D:G.2424, D:S.2425, D:G.2426, D:K.2427, D:S.2428, D:M.2429, D:R.2926 Salt bridges: D:K.2427, D:K.2427, D:R.2881, D:R.2923, D:R.2926, D:R.2926

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.2428, E.2541, E.2885 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.2428, A:E.2541 MG.4: 3 residues within 4Å: Chain A: T.2110, D.2155 Ligands: ADP.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.2110 MG.10: 6 residues within 4Å: Chain D: S.2428, D.2501, E.2541, R.2881, E.2885 Ligands: ATP.7 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:S.2428, D:D.2501, D:E.2541, D:E.2541, D:E.2885 MG.11: 3 residues within 4Å: Chain D: T.2110, D.2155 Ligands: ADP.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.2110

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: AD
Platelet-activating factor acetylhydrolase IB subunit beta: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
A

B
E

C
C

Cytoplasmic dynein 1 heavy chain 1

Platelet-activating factor acetylhydrolase IB subunit beta

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