SMTL ID : 5lwe.1 (1 other biounit)

Crystal structure of the human CC chemokine receptor type 9 (CCR9) in complex with vercirnon

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x 79K: Vercirnon(Non-covalent)

79K.1: 21 residues within 4Å: Chain A: V.47, V.50, Y.51, R.56, T.59, T.61, D.62, L.65, I.118, R.122, A.230, A.233, T.234, V.237, Y.295, G.299, E.300, R.301, F.302, D.305 Ligands: MLI.18 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.47, A:V.50, A:T.61, A:L.65, A:L.65, A:L.65, A:V.237, A:Y.295, A:R.301, A:F.302 Hydrogen bonds: A:R.56, A:R.301, A:F.302 Water bridges: A:R.122, A:E.300, A:R.301 pi-Stacking: A:Y.295

15 x OLA: OLEIC ACID(Non-covalent)

OLA.2: 8 residues within 4Å: Chain A: I.235, T.236, T.239, V.240, L.243, F.286 Ligands: OLA.3, CLR.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.239, A:V.240, A:L.243, A:F.286 OLA.3: 6 residues within 4Å: Chain A: Y.212, L.219, H.228, I.235 Ligands: OLA.2, OLA.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.212, A:I.235 Salt bridges: A:H.228 OLA.4: 6 residues within 4Å: Chain A: Y.212, T.213, I.216, L.219, I.235 Ligands: OLA.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.212, A:Y.212, A:Y.212, A:I.216, A:I.235 OLA.5: 2 residues within 4Å: Chain A: Y.123, H.217 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.217 OLA.6: 6 residues within 4Å: Chain A: I.48, W.52, I.70, L.73, L.74 Ligands: OLA.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.48, A:L.73, A:L.74 Hydrogen bonds: A:W.52 OLA.7: 5 residues within 4Å: Chain A: P.30, W.34, P.80, A.83, I.84 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.34, A:W.34, A:W.34, A:P.80, A:A.83, A:I.84 OLA.8: 6 residues within 4Å: Chain A: L.66, N.67, L.74, W.151 Ligands: OLA.6, OLA.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.151 Hydrogen bonds: A:N.67 OLA.9: 5 residues within 4Å: Chain A: I.38, A.41, L.42 Ligands: OLA.10, OLA.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.38, A:A.41 Hydrogen bonds: A:S.45 OLA.10: 6 residues within 4Å: Chain A: L.42, L.46, S.317 Ligands: OLA.9, OLA.12, OLA.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.42, A:L.46 Hydrogen bonds: A:S.317 OLA.11: 2 residues within 4Å: Chain A: Y.142, M.145 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.142 Hydrogen bonds: A:Y.142, A:Y.142 OLA.12: 4 residues within 4Å: Chain A: V.293, F.297 Ligands: OLA.10, CLR.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.293, A:F.297 OLA.13: 9 residues within 4Å: Chain A: K.144, C.147, F.148, W.151, V.152, A.155, A.156, I.159 Ligands: OLA.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.148, A:W.151, A:V.152, A:A.155, A:A.156, A:I.159 OLA.14: 7 residues within 4Å: Chain A: M.116, C.117, V.120, D.121, I.124, R.139, V.146 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.120, A:V.146 OLA.15: 5 residues within 4Å: Chain A: F.37, S.45, I.48, L.49 Ligands: OLA.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.37, A:I.48 OLA.16: 6 residues within 4Å: Chain A: L.46, L.306, L.310, L.313, G.314 Ligands: OLA.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.46, A:L.310 Hydrogen bonds: A:S.317

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.17: 6 residues within 4Å: Chain A: F.286, L.290, L.294, V.298 Ligands: OLA.2, OLA.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.286, A:F.286, A:L.290, A:V.298

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.18: 7 residues within 4Å: Chain A: T.59, D.121, R.122, A.125, R.139, R.301 Ligands: 79K.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.59 Hydrogen bonds: A:D.121 Water bridges: A:R.301 Salt bridges: A:R.122, A:R.122, A:R.139, A:R.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oswald, C. et al., Intracellular allosteric antagonism of the CCR9 receptor. Nature (2016)

Release Date

2016-12-07

Peptides

C-C chemokine receptor type 9: 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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C-C chemokine receptor type 9

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