SMTL ID : 5o2l.1

Myosin VI motor domain in the Pre-Transition State

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

ADP.1: 20 residues within 4Å: Chain A: I.82, N.94, P.95, Y.96, F.97, Y.103, E.148, S.149, G.150, A.151, G.152, K.153, T.154, E.155, F.159, N.196, N.198, L.306 Ligands: MG.2, BEF.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.94, A:Y.103, A:G.150, A:A.151, A:G.152, A:K.153, A:T.154, A:E.155, A:N.196 Water bridges: A:E.155, A:S.200, A:S.200, A:S.200 Salt bridges: A:K.153

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.154, S.200 Ligands: ADP.1, BEF.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.154, A:S.200, H2O.1, H2O.2

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.3: 9 residues within 4Å: Chain A: S.149, G.150, K.153, T.154, N.196, S.199, S.200 Ligands: ADP.1, MG.2 No protein-ligand interaction detected (PLIP)

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: I.144, S.146, N.473, L.476, Q.477, F.480, F.661, R.663 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.473, A:N.473, A:Q.477, A:R.663, A:R.663 GOL.5: 9 residues within 4Å: Chain A: I.144, S.146, F.480, F.661, I.662, R.663, S.688, M.690 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.144, A:S.146, A:I.662, A:R.663, A:S.688 GOL.6: 5 residues within 4Å: Chain A: K.192, N.197, L.302, K.303, M.671 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.197, A:N.197, A:K.303 Water bridges: A:K.192, A:K.192 GOL.7: 2 residues within 4Å: Chain A: D.523, K.644 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.523 Water bridges: A:N.641 GOL.8: 3 residues within 4Å: Chain A: H.503, Y.504, D.506 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.503, A:Y.504, A:Y.504, A:D.506 GOL.9: 5 residues within 4Å: Chain A: E.207, H.209, F.220, F.441, K.653 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.207, A:K.653 GOL.10: 2 residues within 4Å: Chain A: K.670, E.677 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.670, A:K.670 GOL.11: 6 residues within 4Å: Chain A: R.557, S.559, K.560, L.561, A.562, R.565 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blanc, F. et al., An intermediate along the recovery stroke of myosin VI revealed by X-ray crystallography and molecular dynamics. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-05-23

Peptides

Unconventional myosin-VI: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Unconventional myosin-VI