SMTL ID : 6c1r.1

Crystal structure of human C5a receptor in complex with an orthosteric antagonist PMX53 and an allosteric antagonist avacopan

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x ACE- PHE- ORN- PRO- ZAL- TRP- ARG: PMX53(Non-covalent)

ACE-PHE-ORN-PRO-ZAL-TRP-ARG.1: 25 residues within 4Å: Chain A: L.178, S.181, I.182, H.186, P.199, I.202, R.261, V.262, R.264, L.273, C.274, G.275, V.276, D.277, Y.278, S.279, Y.344, T.347, G.348, M.351, K.365, D.368, S.369, C.371, V.372 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:L.178, A:L.178, A:I.182, A:V.262, A:R.264, A:L.273, A:V.276, A:K.365, A:V.372, A:V.372 Hydrogen bonds: A:R.261, A:R.261, A:C.274, A:V.276, A:V.276, A:D.277, A:Y.278, A:Y.344, A:T.347, A:D.368, A:D.368 Water bridges: A:L.203, A:R.292, A:R.292, A:D.368, A:D.368 Salt bridges: A:D.368

1 x EFD: avacopan(Non-covalent)

EFD.2: 19 residues within 4Å: Chain A: L.211, A.214, T.215, S.217, A.218, F.221, A.242, V.245, A.246, L.249, L.295, W.299, P.300, T.303, L.304, C.307 Ligands: PGE.6, OLA.10, OLA.12 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.211, A:A.214, A:F.221, A:F.221, A:V.245, A:A.246, A:P.300 Hydrogen bonds: A:T.215, A:T.303 Water bridges: A:T.303

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

MLI.3: 8 residues within 4Å: Chain A: N.157, R.220, S.323, K.325, T.326, E.411, E.412, S.413 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.411 Hydrogen bonds: A:N.157, A:N.157, A:T.326, A:T.326, A:T.326 Salt bridges: A:R.220 MLI.4: 7 residues within 4Å: Chain A: Y.207, L.253, P.256, V.288, V.291, R.292 Ligands: OLC.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.292

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

NA.5: 3 residues within 4Å: Chain A: D.168, N.378, N.382 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.168, A:N.382 Water bridges: A:N.382

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 8 residues within 4Å: Chain A: T.215, A.218, C.230, R.234, G.235, L.238, A.239 Ligands: EFD.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.235, A:A.239

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

OLC.7: 4 residues within 4Å: Chain A: P.256, R.284, V.288 Ligands: MLI.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.284 OLC.8: 8 residues within 4Å: Chain A: W.316, K.328, V.331, A.332, A.335, I.339, F.340, F.374 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.335, A:I.339, A:F.340, A:F.340, A:F.374 Hydrogen bonds: A:A.332

4 x OLA: OLEIC ACID(Non-covalent)

OLA.9: 4 residues within 4Å: Chain A: I.290, L.298, L.301, L.302 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.290, A:I.290, A:L.298, A:L.301, A:L.302 OLA.10: 4 residues within 4Å: Chain A: V.294, L.295, W.299 Ligands: EFD.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.294, A:L.295, A:W.299 OLA.11: 4 residues within 4Å: Chain A: W.240, A.244, W.247, L.251 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.240, A:W.240, A:A.244, A:L.251 Salt bridges: A:K.153 OLA.12: 7 residues within 4Å: Chain A: F.221, F.225, K.226, W.299, I.306, F.310 Ligands: EFD.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.221, A:F.221, A:W.299, A:I.306, A:F.310 Salt bridges: A:K.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H. et al., Orthosteric and allosteric action of the C5a receptor antagonists. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-05-30

Peptides

Soluble cytochrome b562, C5a anaphylatoxin chemotactic receptor 1 chimera: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Membrane

We predict this structure to be a membrane protein.
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Soluble cytochrome b562, C5a anaphylatoxin chemotactic receptor 1 chimera

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