SMTL ID : 3vw7.1

Crystal structure of human protease-activated receptor 1 (PAR1) bound with antagonist vorapaxar at 2.2 angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x VPX: ethyl [(1R,3aR,4aR,6R,8aR,9S,9aS)-9-{(E)-2-[5-(3-fluorophenyl)pyridin-2-yl]ethenyl}-1-methyl-3-oxododecahydronaphtho[2,3-c]fur an-6-yl]carbamate(Non-covalent)

VPX.1: 22 residues within 4Å: Chain A: Y.101, Y.105, G.151, P.154, L.155, H.173, D.174, V.175, L.176, L.180, F.189, L.409, L.410, H.413, Y.414, L.417, S.421, A.426, Y.427, A.429, Y.430 Ligands: OLC.7 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.155, A:L.155, A:L.176, A:F.189, A:F.189, A:L.410, A:Y.427, A:Y.430, A:Y.430, A:Y.430 Hydrogen bonds: A:L.176, A:Y.414, A:A.426 Water bridges: A:H.413 pi-Stacking: A:Y.101

9 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.2: 6 residues within 4Å: Chain A: F.119, Y.124, I.202, V.206, R.213 Ligands: OLC.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.202, A:V.206 Hydrogen bonds: A:S.210, A:R.213, A:R.213 OLC.3: 10 residues within 4Å: Chain A: F.119, L.120, Y.124, A.194, F.198, V.199, I.202, I.203, V.206 Ligands: OLC.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.194, A:F.198, A:V.199, A:I.202, A:I.203 OLC.4: 7 residues within 4Å: Chain A: F.31, V.32, P.74, I.77, S.78, F.81, S.82 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.31, A:V.32, A:P.74, A:I.77 Hydrogen bonds: A:F.81 OLC.5: 11 residues within 4Å: Chain A: L.37, M.40, V.44, F.45, I.439, C.442, P.445, L.446, Y.448, Y.449, S.452 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.37, A:L.446 Hydrogen bonds: A:S.452, A:S.452 OLC.6: 8 residues within 4Å: Chain A: W.18, I.400, P.405, E.424, A.425, F.428, L.432, C.433 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.400, A:L.432 Hydrogen bonds: A:W.18 OLC.7: 10 residues within 4Å: Chain A: F.197, I.400, G.404, P.405, V.408, T.420, T.423, A.425, C.433 Ligands: VPX.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.197, A:I.400, A:V.408 Hydrogen bonds: A:T.420, A:T.420 OLC.8: 7 residues within 4Å: Chain A: V.57, H.61, S.138, L.142, W.145, A.146, V.153 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.142, A:A.146, A:V.153 Salt bridges: A:H.61 OLC.9: 10 residues within 4Å: Chain A: L.147, A.150, G.151, P.154, K.158, L.181, Y.185, Y.188, F.189, F.192 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.147, A:P.154, A:L.181, A:Y.188, A:F.189 Hydrogen bonds: A:K.158, A:K.158 OLC.10: 7 residues within 4Å: Chain A: Y.58, T.112, R.136, F.139, T.140, A.143, L.147 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.112, A:F.139, A:A.143, A:L.147 Hydrogen bonds: A:T.140

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 3 residues within 4Å: Chain A: K.53, R.118, K.384 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 4 residues within 4Å: Chain A: L.62, D.66, S.107, D.444 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.107, A:D.444

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, C. et al., High-resolution crystal structure of human protease-activated receptor 1. Nature (2012)

Release Date

2012-12-12

Peptides

Proteinase-activated receptor 1, Lysozyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Proteinase-activated receptor 1, Lysozyme