SMTL ID : 8fdt.1

Engineered human dynein motor domain in the microtubule-unbound state with LIS1 complex in the buffer containing ATP-Vi

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-mer

Ligands

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

ATP.1: 20 residues within 4Å: Chain A: L.736, T.737, W.748, P.770, S.771, G.772, S.773, G.774, K.775, S.776, M.777, E.889, L.914, M.918, N.922, L.997, R.1229, E.1233, R.1271, R.1274 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:T.737, A:T.737, A:G.772, A:S.773, A:G.774, A:K.775, A:S.776, A:S.776, A:S.776, A:M.777, A:E.889, A:N.922 Salt bridges: A:K.775, A:K.775, A:R.1229, A:R.1271, A:R.1274, A:R.1274, A:R.1274 pi-Stacking: A:W.748

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

ADP.2: 17 residues within 4Å: Chain A: V.1112, V.1113, V.1114, P.1141, P.1142, G.1143, S.1144, G.1145, K.1146, T.1147, M.1148, I.1292, Y.1293, F.1296, P.1341, R.1342, T.1345 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:V.1114, A:V.1114, A:G.1143, A:S.1144, A:G.1145, A:K.1146, A:T.1147, A:T.1147, A:T.1147, A:M.1148 Salt bridges: A:K.1146, A:R.1342, A:R.1342 ADP.3: 16 residues within 4Å: Chain A: V.1452, P.1453, L.1454, V.1455, F.1457, V.1483, S.1484, G.1485, A.1486, G.1487, K.1488, T.1489, T.1490, W.1642, R.1719, L.1722 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:V.1455, A:V.1455, A:G.1485, A:G.1487, A:K.1488, A:T.1489, A:T.1489, A:T.1489, A:T.1490, A:R.1719 Salt bridges: A:K.1488 ADP.4: 18 residues within 4Å: Chain A: L.424, V.425, T.427, T.430, A.453, G.454, T.455, G.456, K.457, T.458, E.459, I.594, L.635, R.636, K.639, D.865, D.866 Ligands: VO4.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:V.425, A:V.425, A:G.454, A:T.455, A:T.455, A:G.456, A:K.457, A:T.458, A:T.458, A:E.459, A:K.639, A:D.865, A:D.866 Salt bridges: A:K.457, A:R.636, A:R.636

1 x VO4: VANADATE ION(Non-covalent)

VO4.5: 9 residues within 4Å: Chain A: K.457, T.458, D.503, E.504, N.564, R.636, N.861, R.903 Ligands: ADP.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.457, A:T.458, A:D.503, A:D.503, A:E.504, A:N.564, A:R.636, A:R.636, A:N.861, A:R.903, A:R.903

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ton, W.D. et al., Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-06-21

Peptides

Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligase: A
Platelet-activating factor acetylhydrolase IB subunit beta: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligase

Platelet-activating factor acetylhydrolase IB subunit beta

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