SMTL ID : 8fd6.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

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

ATP.1: 20 residues within 4Å: Chain A: L.736, T.737, W.748, S.771, G.772, S.773, G.774, K.775, S.776, M.777, D.849, E.889, L.914, M.918, N.922, L.997, R.1229, E.1233, R.1271, R.1274 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.737, A:T.737, A:G.772, A:S.773, A:S.773, A:G.774, A:K.775, A:S.776, A:M.777, A:D.849 Salt bridges: A:K.775, A:K.775, A:R.1229, A:R.1271, A:R.1274, A:R.1274, A:R.1274

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

ADP.2: 17 residues within 4Å: Chain A: V.1112, V.1113, V.1114, T.1116, T.1119, P.1142, G.1143, S.1144, G.1145, K.1146, T.1147, M.1148, I.1292, Y.1293, P.1341, R.1342, T.1345 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:V.1114, A:V.1114, A:T.1116, A:T.1119, A:G.1143, A:G.1145, A:K.1146, A:T.1147, A:M.1148 Salt bridges: A:K.1146, A:R.1342 ADP.3: 17 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, N.2128 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:V.1455, A:V.1455, A:G.1485, A:A.1486, A:G.1487, A:K.1488, A:T.1489, A:T.1489, A:T.1489, A:T.1489, A:T.1490, A:N.2128 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.866 Ligands: VO4.5, MG.6 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:V.425, A:V.425, A:G.454, A:T.455, A:G.456, A:G.456, A:K.457, A:T.458, A:E.459, A:K.639, A:D.866, A:D.866 Salt bridges: A:K.457, A:R.636, A:R.636

1 x VO4: VANADATE ION(Non-covalent)

VO4.5: 13 residues within 4Å: Chain A: P.452, A.453, G.454, K.457, T.458, E.504, N.564, R.636, N.861, A.899, R.903 Ligands: ADP.4, MG.6 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.454, A:K.457, A:K.457, A:E.504, A:N.564, A:R.636, A:R.636, A:N.861, A:R.903, A:R.903

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: T.458 Ligands: ADP.4, VO4.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.458

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

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

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