SMTL ID : 5zkq.1

Crystal structure of the human platelet-activating factor receptor in complex with ABT-491

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

2 x 9EU: 4-ethynyl-3-{3-fluoro-4-[(2-methyl-1H-imidazo[4,5-c]pyridin-1-yl)methyl]benzene-1-carbonyl}-N,N-dimethyl-1H-indole-1-carboxamide(Non-covalent)

9EU.1: 18 residues within 4Å: Chain A: Y.24, W.75, Y.79, G.96, F.99, F.100, Y.104, F.154, C.175, F.176, E.177, Y.179, I.189, H.190, I.193, Q.366, L.393 Ligands: OLC.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.75, A:F.99, A:F.100, A:F.176, A:E.177, A:I.189, A:I.193 Hydrogen bonds: A:Y.24, A:Y.79, A:Q.366 pi-Stacking: A:W.75, A:W.75, A:W.75, A:F.99, A:F.99, A:F.154, A:F.154 pi-Cation interactions: A:H.190, A:H.190 9EU.7: 17 residues within 4Å: Chain B: Y.24, W.75, Y.79, G.96, F.99, F.100, F.154, C.175, F.176, E.177, Y.179, H.190, I.193, H.362, Q.366, L.393 Ligands: OLC.8 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:W.75, B:F.99, B:F.99, B:F.100, B:F.100, B:F.176, B:E.177, B:I.193 Hydrogen bonds: B:Y.24, B:Y.79, B:Y.179, B:Q.366 pi-Stacking: B:W.75, B:W.75, B:W.75, B:F.99, B:F.154, B:F.154 pi-Cation interactions: B:H.190, B:H.190

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

OLC.2: 13 residues within 4Å: Chain A: A.150, Y.153, F.154, L.157, E.180, P.185, V.186, I.189, F.192, I.193 Ligands: 9EU.1, OLC.3, OLC.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.150, A:Y.153, A:F.154, A:L.157, A:L.157, A:V.186, A:I.189, A:F.192, A:I.193 OLC.3: 5 residues within 4Å: Chain A: Y.153, I.156, L.157, D.158 Ligands: OLC.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.153, A:Y.153, A:L.157 Hydrogen bonds: A:D.158, A:D.158 OLC.4: 12 residues within 4Å: Chain A: Y.104, A.108, V.142, I.143, V.145, A.146, I.147, G.149, A.150, S.196, V.200 Ligands: OLC.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.108, A:V.142, A:I.143, A:A.146, A:I.147, A:V.200 OLC.5: 3 residues within 4Å: Chain A: L.155, I.156, L.157 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.155, A:I.156 OLC.8: 11 residues within 4Å: Chain B: F.100, A.150, Y.153, F.154, L.157, S.183, P.185, V.186, F.192 Ligands: 9EU.7, OLC.9 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.100, B:Y.153, B:L.157, B:V.186, B:F.192 OLC.9: 4 residues within 4Å: Chain B: Y.153, L.157, I.189 Ligands: OLC.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.153, B:L.157, B:I.189 OLC.10: 10 residues within 4Å: Chain B: N.60, M.63, L.67, V.94, L.98, I.101, R.133, I.137, L.141, W.144 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:M.63, B:L.67, B:V.94, B:L.98, B:I.101, B:L.141, B:W.144, B:W.144 Hydrogen bonds: B:N.60, B:R.133

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: H.6, H.10, E.373, H.382, N.386 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.6, A:E.373, A:H.382 ZN.11: 4 residues within 4Å: Chain B: H.10, E.373, H.382, N.386 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.373, B:H.382

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.12: 2 residues within 4Å: Chain B: M.282 Ligands: SO4.17 No protein-ligand interaction detected (PLIP) SO4.13: 3 residues within 4Å: Chain B: A.249, R.252, R.256 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.249 Salt bridges: B:R.252, B:R.256 SO4.14: 2 residues within 4Å: Chain B: R.295, R.301 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.299 Salt bridges: B:R.295, B:R.301 SO4.15: 3 residues within 4Å: Chain B: G.286, G.289 Ligands: SO4.17 No protein-ligand interaction detected (PLIP) SO4.16: 4 residues within 4Å: Chain B: T.318, P.319, N.320, R.321 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.318, B:N.320, B:N.320, B:R.321 SO4.17: 4 residues within 4Å: Chain B: T.285, G.286 Ligands: SO4.12, SO4.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, C. et al., Structural basis for signal recognition and transduction by platelet-activating-factor receptor. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-06-20

Peptides

Platelet-activating factor receptor,Endolysin,Endolysin,Platelet-activating factor receptor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Platelet-activating factor receptor,Endolysin,Endolysin,Platelet-activating factor receptor