SMTL ID : 8pqz.1

Cytoplasmic dynein-1 A1/A2 motor domains bound to LIS1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-6-2-2-mer

Ligands

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

ADP.1: 9 residues within 4Å: Chain A: L.1879, V.1880, A.1908, G.1909, T.1910, G.1911, K.1912, T.1913 Ligands: MG.2 7 PLIP interactions: 7 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 ADP.5: 13 residues within 4Å: Chain A: V.2567, V.2568, V.2569, P.2597, G.2598, S.2599, G.2600, K.2601, T.2602, M.2603, P.2796, R.2797, T.2800 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 ADP.6: 12 residues within 4Å: Chain A: P.2908, L.2909, V.2910, V.2938, S.2939, G.2940, A.2941, G.2942, K.2943, T.2944, T.2945, N.3650 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:V.2910, A:V.2910, A:G.2940, A:A.2941, A:G.2942, A:K.2943, A:T.2944, A:T.2945, A:N.3650 ADP.7: 9 residues within 4Å: Chain J: L.1879, V.1880, A.1908, G.1909, T.1910, G.1911, K.1912, T.1913 Ligands: MG.8 7 PLIP interactions: 7 interactions with chain J Hydrogen bonds: J:V.1880, J:V.1880, J:G.1909, J:T.1910, J:G.1911, J:K.1912, J:T.1913 ADP.11: 10 residues within 4Å: Chain J: V.2569, P.2597, G.2598, G.2600, K.2601, T.2602, M.2603, P.2796, R.2797, T.2800 7 PLIP interactions: 7 interactions with chain J Hydrogen bonds: J:V.2569, J:V.2569, J:G.2598, J:G.2600, J:K.2601, J:T.2602, J:M.2603 ADP.12: 12 residues within 4Å: Chain J: P.2908, L.2909, V.2910, V.2938, S.2939, G.2940, A.2941, G.2942, K.2943, T.2944, T.2945, N.3650 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:V.2910, J:V.2910, J:V.2938, J:G.2940, J:A.2941, J:G.2942, J:K.2943, J:T.2944, J:T.2945, J:N.3650

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.1913, D.1958 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: S.2231 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain J: T.1913, D.1958 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain J: S.2231 Ligands: ATP.9 No protein-ligand interaction detected (PLIP)

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

ATP.3: 11 residues within 4Å: Chain A: T.2192, S.2226, G.2227, S.2228, G.2229, K.2230, S.2231, M.2232, M.2373, N.2377 Ligands: MG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.2192, A:G.2227, A:S.2228, A:G.2229, A:K.2230, A:S.2231, A:M.2232 ATP.9: 12 residues within 4Å: Chain J: T.2192, S.2226, G.2227, S.2228, G.2229, K.2230, S.2231, M.2232, E.2344, M.2373, N.2377 Ligands: MG.10 8 PLIP interactions: 8 interactions with chain J Hydrogen bonds: J:T.2192, J:T.2192, J:G.2227, J:S.2228, J:G.2229, J:K.2230, J:S.2231, J:M.2232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, K. et al., Molecular mechanism of dynein-dynactin complex assembly by LIS1. Science (2024)

Release Date

2024-03-27

Peptides

Cytoplasmic dynein 1 heavy chain 1: AJ
Platelet-activating factor acetylhydrolase IB subunit beta: BCDEKL
Dynactin subunit 1: FG
Cytoplasmic dynein 1 intermediate chain 2: HI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

J
J

B
B

C
C

D
D

E
E

K
K

L
L

F
F

G
G

H
H

I
I

Cytoplasmic dynein 1 heavy chain 1

Platelet-activating factor acetylhydrolase IB subunit beta

Dynactin subunit 1

Cytoplasmic dynein 1 intermediate chain 2

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