SMTL ID : 4pjm.1

Myosin VI motor domain in the Pi release state, space group P212121 - soaked with PO4 - located in the active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 10 residues within 4Å: Chain A: S.152, G.153, K.156, N.199, S.202, S.203, R.204, A.457 Ligands: MG.2, ADP.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.152, A:G.153, A:N.199, A:S.203, A:S.203, A:R.204 Water bridges: A:S.152, A:K.156, A:S.203, A:S.203, A:A.457, A:G.458 Salt bridges: A:K.156

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.157, S.203 Ligands: PO4.1, ADP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.157, A:S.203, H2O.1, H2O.2

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

ADP.3: 21 residues within 4Å: Chain A: I.85, N.97, P.98, Y.99, F.100, D.101, Y.106, E.151, S.152, G.153, A.154, G.155, K.156, T.157, E.158, F.162, N.199, N.201, L.309 Ligands: PO4.1, MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:N.97, A:Y.106, A:Y.106, A:G.153, A:A.154, A:G.155, A:K.156, A:T.157, A:E.158, A:N.199 Water bridges: A:D.101, A:T.157, A:N.159, A:N.201, A:N.201, A:S.203, A:S.203, A:S.203, A:D.307 Salt bridges: A:K.156

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: D.287, K.288, I.290, Q.292, K.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.288, A:Q.292, A:K.295 GOL.5: 9 residues within 4Å: Chain A: A.252, G.253, A.254, S.255, Q.289, I.290, L.291, R.294, H.313 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.291 Water bridges: A:E.256, A:Q.289, A:H.313 GOL.6: 8 residues within 4Å: Chain A: I.92, F.483, F.664, R.666, S.691, M.693, V.696 Ligands: GOL.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.149, A:I.665, A:R.666 Water bridges: A:S.149, A:S.691 GOL.9: 2 residues within 4Å: Chain A: Q.16, F.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.16 GOL.10: 10 residues within 4Å: Chain A: Q.480, F.483, N.484, L.488, S.691, G.692, M.693, S.695, V.696 Ligands: GOL.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.480, A:N.484, A:S.691, A:G.692 Water bridges: A:R.666 GOL.11: 5 residues within 4Å: Chain A: E.210, H.212, F.223, F.444, K.656 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.656, A:K.656 GOL.12: 7 residues within 4Å: Chain A: S.388, T.391, R.392, L.410, H.601, S.603, L.604 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.388, A:S.603 Water bridges: A:V.393

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.7: 6 residues within 4Å: Chain A: N.283, D.287, Y.299, G.303, S.304, K.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.306, A:K.306 IPA.8: 4 residues within 4Å: Chain A: N.476, L.479, Q.480, F.483 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.479, A:F.483 Water bridges: A:G.150, A:F.459, A:N.476

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Llinas, P. et al., How actin initiates the motor activity of Myosin. Dev.Cell (2015)

Release Date

2015-04-29

Peptides

Unconventional myosin-VI: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Unconventional myosin-VI

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