SMTL ID : 5n69.1

Cardiac muscle myosin S1 fragment in the pre-powerstroke state co-crystallized with the activator Omecamtiv Mecarbil

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-2-2-mer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: I.114, N.126, P.127, Y.128, K.129, W.130, 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 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.126, A:Y.134, A:G.181, A:A.182, A:G.183, A:K.184, A:T.185, A:V.186, A:N.238, A:S.242 Water bridges: A:T.185, A:N.240 Salt bridges: A:K.184 ADP.18: 19 residues within 4Å: Chain B: I.114, N.126, P.127, Y.128, K.129, W.130, Y.134, E.179, S.180, G.181, A.182, G.183, K.184, T.185, V.186, N.238, N.240 Ligands: VO4.19, MG.20 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.126, B:Y.134, B:Y.134, B:G.181, B:A.182, B:G.183, B:K.184, B:T.185, B:V.186, B:N.238, B:S.242 Water bridges: B:S.242 Salt bridges: B:K.184

2 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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.181, A:K.184, A:N.238, A:S.241, A:S.242, A:S.242, A:S.242, A:R.243, A:G.464 VO4.19: 11 residues within 4Å: Chain B: S.180, G.181, K.184, N.238, S.241, S.242, R.243, A.463, G.464 Ligands: ADP.18, MG.20 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:E.179, B:G.181, B:K.184, B:N.238, B:S.241, B:S.242, B:R.243, B:G.464 Water bridges: B:T.185, B:N.240

2 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.1 MG.20: 4 residues within 4Å: Chain B: T.185, S.242 Ligands: ADP.18, VO4.19 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.185, B:S.242, H2O.15, H2O.15

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

2OW.4: 17 residues within 4Å: Chain A: K.146, R.147, N.160, Q.163, 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 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.167, A:I.713, A:L.770 Hydrogen bonds: A:D.168, A:N.711, A:R.712, A:R.712 Salt bridges: A:E.774 pi-Stacking: A:H.666 2OW.21: 18 residues within 4Å: Chain B: K.146, R.147, N.160, Q.163, Y.164, T.167, D.168, H.492, H.666, P.710, N.711, R.712, I.713, R.721, Y.722, F.765, L.770, E.774 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.167, B:I.713, B:I.713, B:F.765, B:L.770 Hydrogen bonds: B:Y.164, B:D.168, B:N.711, B:R.712, B:R.712 pi-Stacking: B:H.666

25 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: N.361, M.362, K.363, D.376, G.377, T.378, E.379, E.380 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: F.494, Q.498, F.510, I.511, D.512, F.513, G.514, M.515 Ligand excluded by PLIP GOL.7: 10 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 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: E.269, S.271, R.272, F.275, E.474, Q.475 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: M.6, A.7, F.9, R.17, P.151 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: F.275, L.277, F.470, P.573 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain A: L.267, L.268, E.269, K.270, S.271, E.474, V.647 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: V.236, L.277, A.279, F.468, D.469, F.470 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain A: E.537, F.540, K.542, A.543, T.547, K.551 Ligand excluded by PLIP GOL.14: 3 residues within 4Å: Chain A: W.130, L.131, P.132 Ligand excluded by PLIP GOL.15: 2 residues within 4Å: Chain A: D.382, K.383 Ligand excluded by PLIP GOL.16: 2 residues within 4Å: Chain A: R.739, H.760 Ligand excluded by PLIP GOL.17: 3 residues within 4Å: Chain A: Q.498, K.502, F.510 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: D.382, A.385, Y.386, L.390, N.391, S.392 Ligand excluded by PLIP GOL.23: 9 residues within 4Å: Chain B: G.245, Y.266, L.267, I.462, A.463, C.477, I.478, T.481, H.651 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain B: V.236, L.277, K.278, A.279, F.468, D.469, F.470 Ligand excluded by PLIP GOL.25: 7 residues within 4Å: Chain B: F.494, Q.498, F.510, I.511, D.512, F.513, M.515 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain B: R.403, Y.410, E.603, T.604, D.607 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain A: G.253, A.254, P.452 Chain B: E.536 Ligand excluded by PLIP GOL.28: 9 residues within 4Å: Chain B: E.269, S.271, R.272, F.275, L.277, E.280, F.468, E.474, Q.475 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain B: E.64, Y.103, K.106, E.107, A.110 Ligand excluded by PLIP GOL.30: 3 residues within 4Å: Chain B: W.130, L.131, P.132 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain A: V.795, M.799 Chain D: L.176, A.178, G.179, H.195 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain A: R.793 Chain D: R.85, Q.93, K.167, E.172 Ligands: GOL.34 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain D: R.85, Q.93, V.96, L.108 Ligands: GOL.33 Ligand excluded by PLIP

1 x TCE: 3,3',3''-phosphanetriyltripropanoic acid(Non-covalent)

TCE.31: 8 residues within 4Å: Chain B: L.302, I.303, T.304, D.309, N.361, E.379, E.380, K.383 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.309 Hydrogen bonds: B:N.361 Salt bridges: B:K.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Planelles-Herrero, V.J. et al., Mechanistic and structural basis for activation of cardiac myosin force production by omecamtiv mecarbil. Nat Commun (2017)

Release Date

2017-08-16

Peptides

Myosin-7: AB
Myosin light chain 3: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
G

D
H

Myosin-7

Myosin light chain 3

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