SMTL ID : 7mi3.1

Signal subtracted reconstruction of AAA2, AAA3, and AAA4 domains of dynein in the presence of a pyrazolo-pyrimidinone-based compound, Model 4

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.50 Å

Oligo State

monomer

Ligands

2 x ZG7: (8S)-6-(3-bromophenoxy)-2-[1-(4-chlorophenyl)cyclopropyl]-7-hydroxypyrazolo[1,5-a]pyrimidine-3-carbonitrile(Non-covalent)

ZG7.1: 16 residues within 4Å: Chain A: V.1368, P.1369, M.1370, V.1371, H.1373, A.1399, S.1400, R.1401, T.1402, G.1403, K.1404, T.1405, I.1406, W.1558, I.1631, R.2069 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.1404, A:W.1558, A:I.1631 Hydrogen bonds: A:T.1402, A:G.1403, A:K.1404 pi-Cation interactions: A:R.2069 Halogen bonds: A:V.1371, A:K.1404 ZG7.2: 17 residues within 4Å: Chain A: V.1029, I.1030, T.1032, T.1035, P.1058, G.1059, S.1060, G.1061, K.1062, T.1063, M.1064, D.1125, I.1208, Y.1209, P.1257, R.1258, T.1261 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.1029, A:I.1208, A:Y.1209, A:P.1257 Hydrogen bonds: A:G.1061 Halogen bonds: A:I.1030, A:T.1032

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

ATP.3: 18 residues within 4Å: Chain A: F.685, S.686, F.691, A.714, G.715, C.716, G.717, K.718, T.719, A.720, E.833, V.857, C.858, S.862, H.866, R.1187, R.1190 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.686, A:S.686, A:G.715, A:G.717, A:K.718, A:T.719, A:T.719, A:A.720 Salt bridges: A:K.718, A:K.718, A:R.1187, A:R.1190, A:R.1190, A:R.1190

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: T.719, E.833, E.1149 Ligands: ATP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.719, A:E.833

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Santarossa, C.C. et al., Targeting allostery in the Dynein motor domain with small molecule inhibitors. Cell Chem Biol (2021)

Release Date

2021-05-26

Peptides

Fusion protein of Dynein and Endolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Fusion protein of Dynein and Endolysin

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