SMTL ID : 8qyu.2 (1 other biounit)

Beta-cardiac myosin S1 fragment in the pre-powerstroke state complexed to Omecamtiv mecarbil

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

hetero-1-1-mer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: I.114, N.126, P.127, Y.128, K.129, Y.134, E.179, S.180, G.181, A.182, G.183, K.184, T.185, V.186, N.238, N.240 Ligands: VO4.2, MG.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.126, A:Y.134, A:Y.134, A:G.181, A:A.182, A:G.183, A:K.184, A:T.185, A:V.186, A:N.238 Water bridges: A:N.187, A:S.242, A:S.242, A:S.242 Salt bridges: A:K.184

1 x VO4: VANADATE ION(Non-covalent)

VO4.2: 11 residues within 4Å: Chain A: S.180, G.181, K.184, N.238, S.241, S.242, R.243, A.463, G.464 Ligands: ADP.1, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.181, A:K.184, A:N.238, A:S.241, A:S.242, A:R.243, A:G.464 Water bridges: A:T.185, A:N.240, A:S.242, A:I.462

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: T.185, S.242 Ligands: ADP.1, VO4.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.185, A:S.242, H2O.1, H2O.2

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 7 residues within 4Å: Chain A: Y.266, T.481, H.651, N.654, L.655, L.658 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.654 Water bridges: A:H.651, A:N.654 FMT.5: 4 residues within 4Å: Chain A: E.264, T.265, N.437, V.440 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.263, A:T.265 Water bridges: A:E.264

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 5 residues within 4Å: Chain A: H.492, M.493, E.497, P.710 Ligands: 2OW.10 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.497

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 11 residues within 4Å: Chain A: F.244, G.245, Y.266, L.267, I.462, A.463, C.477, I.478, T.481, H.651 Ligands: FMT.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.245, A:L.267, A:A.463, A:A.463, A:C.477 GOL.8: 7 residues within 4Å: Chain A: D.168, E.170, R.712, I.713, L.714, K.762 Ligands: 2OW.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.168, A:R.712 Water bridges: A:E.170, A:K.762, A:K.762

1 x MLA: MALONIC ACID(Non-covalent)

MLA.9: 9 residues within 4Å: Chain A: E.269, S.271, R.272, F.275, L.277, E.280, F.468, E.474, Q.475 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.474 Hydrogen bonds: A:E.269, A:S.271, A:Q.475 Salt bridges: A:R.272, A:R.272

1 x 2OW: methyl 4-(2-fluoro-3-{[(6-methylpyridin-3-yl)carbamoyl]amino}benzyl)piperazine-1-carboxylate(Non-covalent)

2OW.10: 18 residues within 4Å: Chain A: K.146, R.147, N.160, Y.164, T.167, D.168, H.492, H.666, P.710, N.711, R.712, I.713, R.721, Y.722, L.770, E.774 Ligands: DMS.6, GOL.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.167, A:I.713, A:L.770 Hydrogen bonds: A:D.168, A:D.168, A:N.711, A:R.712 Water bridges: A:Y.164 Salt bridges: A:E.774 pi-Stacking: A:H.666

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Auguin, D. et al., Omecamtiv mecarbil and Mavacamten target the same myosin pocket despite antagonistic effects in heart contraction. Biorxiv (2023)

Release Date

2023-12-13

Peptides

Myosin-7: A
Myosin light chain 3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
G

Myosin-7

Myosin light chain 3

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