SMTL ID : 7mgm.1

Structure of yeast cytoplasmic dynein with AAA3 Walker B mutation bound to Lis1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-mer

Ligands

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

ATP.1: 20 residues within 4Å: Chain A: L.552, I.553, A.581, G.582, T.583, G.584, K.585, T.586, E.587, D.631, E.632, N.682, I.712, L.753, R.754, K.757, R.761, D.955, R.992 Ligands: MG.5 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:I.553, A:I.553, A:G.582, A:T.583, A:G.584, A:G.584, A:K.585, A:T.586, A:E.587, A:E.632, A:E.632, A:N.682, A:K.757, A:R.761, A:D.955 Salt bridges: A:K.585, A:K.585, A:R.754, A:R.754, A:R.754, A:R.992 ATP.2: 17 residues within 4Å: Chain A: I.1175, T.1180, P.1203, G.1204, S.1205, G.1206, K.1207, T.1208, M.1209, Q.1271, N.1319, I.1353, Y.1357, P.1402, R.1403, T.1406, N.1693 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:I.1175, A:I.1175, A:G.1204, A:S.1205, A:G.1206, A:K.1207, A:T.1208, A:T.1208, A:M.1209, A:Q.1271, A:Y.1357, A:T.1406 Salt bridges: A:K.1207, A:K.1207, A:R.1403, A:R.1403 ATP.3: 20 residues within 4Å: Chain A: F.830, S.831, F.836, A.859, G.860, C.861, G.862, K.863, T.864, A.865, E.978, V.1002, C.1003, S.1007, K.1008, H.1011, E.1068, R.1332, R.1335 Ligands: MG.6 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.831, A:S.831, A:G.860, A:C.861, A:G.862, A:K.863, A:T.864, A:T.864, A:A.865, A:E.978, A:H.1011, A:R.1290 Salt bridges: A:K.863, A:K.863, A:R.1332, A:R.1335, A:R.1335, A:R.1335

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

ADP.4: 16 residues within 4Å: Chain A: P.1514, M.1515, V.1516, H.1518, M.1521, A.1544, S.1545, R.1546, T.1547, G.1548, K.1549, T.1550, I.1551, W.1703, R.1780, R.2295 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:V.1516, A:V.1516, A:A.1544, A:R.1546, A:R.1546, A:T.1547, A:G.1548, A:K.1549, A:T.1550, A:T.1550, A:I.1551, A:R.1780, A:R.1780 Salt bridges: A:K.1549, A:R.2295, A:R.2295

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: T.586, D.631 Ligands: ATP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.586, A:D.631, A:D.631 MG.6: 3 residues within 4Å: Chain A: T.864, E.978 Ligands: ATP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.864, A:E.978

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gillies, J.P. et al., Structural basis for cytoplasmic dynein-1 regulation by Lis1. Elife (2022)

Release Date

2022-01-19

Peptides

dynein AAA3-WalkerB mutant (E2488Q): A
Nuclear distribution protein PAC1: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

dynein AAA3-WalkerB mutant (E2488Q)

Nuclear distribution protein PAC1

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