SMTL ID : 5o9h.1

Crystal structure of thermostabilised human C5a anaphylatoxin chemotactic receptor 1 (C5aR) in complex with NDT9513727

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x 9P2: 1-(1,3-benzodioxol-5-yl)-~{N}-(1,3-benzodioxol-5-ylmethyl)-~{N}-[(3-butyl-2,5-diphenyl-imidazol-4-yl)methyl]methanamine(Non-covalent)

9P2.1: 18 residues within 4Å: Chain A: I.95, L.96, A.99, T.100, L.127, V.130, A.131, L.134, L.180, W.184, P.185, T.188 Chain B: A.129, V.130, G.133, L.134, L.137 Ligands: OLA.6 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.95, A:A.99, A:T.100, A:L.134, A:L.134, A:W.184, A:P.185, B:L.137 9P2.19: 17 residues within 4Å: Chain A: I.126, V.130 Chain B: I.95, L.96, A.99, T.100, L.127, V.130, A.131, L.134, L.180, W.184, P.185, T.188 Ligands: OLA.16, OLA.22, OLA.25 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.96, B:A.99, B:L.134, B:W.184, B:P.185, A:I.126, A:V.130

3 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.2: 9 residues within 4Å: Chain A: T.40, I.41, N.42, R.119, E.296, E.297, S.298, V.299, R.301 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:I.41, A:N.42, A:E.296, A:S.298, A:V.299, A:V.299 Salt bridges: A:R.119, A:R.301 TLA.3: 7 residues within 4Å: Chain A: T.200, W.201, A.203, R.204, T.206, R.207, S.208 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.200, A:S.208 Salt bridges: A:R.204 TLA.20: 8 residues within 4Å: Chain B: R.39, T.40, I.41, R.119, E.297, S.298, V.299, R.301 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:I.41, B:R.119, B:E.297, B:E.297, B:S.298, B:V.299, B:V.299 Salt bridges: B:R.119, B:R.301

32 x OLA: OLEIC ACID(Non-covalent)(Non-functional Binders)

OLA.4: 12 residues within 4Å: Chain A: W.45, A.103, D.104, L.107, W.114, R.119, G.120, L.123, A.124, L.127 Chain B: L.123, I.126 Ligand excluded by PLIP OLA.5: 6 residues within 4Å: Chain A: F.106, F.110, K.111, T.188 Chain B: I.126 Ligands: OLA.6 Ligand excluded by PLIP OLA.6: 4 residues within 4Å: Chain A: L.189 Ligands: 9P2.1, OLA.5, OLA.23 Ligand excluded by PLIP OLA.7: 1 residues within 4Å: Chain A: A.34 Ligand excluded by PLIP OLA.8: 3 residues within 4Å: Chain A: P.61, T.65, Q.69 Ligand excluded by PLIP OLA.9: 1 residues within 4Å: Chain A: V.13 Ligand excluded by PLIP OLA.10: 1 residues within 4Å: Chain A: I.175 Ligand excluded by PLIP OLA.11: 8 residues within 4Å: Chain A: L.187, T.190, I.191, T.194, F.195, L.198, R.199, S.202 Ligand excluded by PLIP OLA.12: 5 residues within 4Å: Chain A: T.190, T.194, L.197, W.201 Ligands: OLA.17 Ligand excluded by PLIP OLA.13: 7 residues within 4Å: Chain A: K.213, A.217, S.221, I.224, I.266 Ligands: OLA.14, OLA.17 Ligand excluded by PLIP OLA.14: 5 residues within 4Å: Chain A: V.17, I.262, I.270, V.273 Ligands: OLA.13 Ligand excluded by PLIP OLA.15: 4 residues within 4Å: Chain A: L.178, L.183, V.231, M.235 Ligand excluded by PLIP OLA.16: 8 residues within 4Å: Chain A: G.122, A.129, V.130, G.133, L.134 Ligands: OLA.18, 9P2.19, OLA.24 Ligand excluded by PLIP OLA.17: 6 residues within 4Å: Chain A: L.186, V.216, A.220, F.223 Ligands: OLA.12, OLA.13 Ligand excluded by PLIP OLA.18: 1 residues within 4Å: Ligands: OLA.16 Ligand excluded by PLIP OLA.21: 4 residues within 4Å: Chain B: F.106, W.114, C.192 Ligands: OLA.22 Ligand excluded by PLIP OLA.22: 6 residues within 4Å: Chain A: I.126 Chain B: A.99, W.184 Ligands: 9P2.19, OLA.21, OLA.24 Ligand excluded by PLIP OLA.23: 8 residues within 4Å: Chain B: G.122, W.125, I.126, A.129, W.132 Ligands: OLA.6, OLA.28, OLA.29 Ligand excluded by PLIP OLA.24: 4 residues within 4Å: Chain B: L.180, W.184 Ligands: OLA.16, OLA.22 Ligand excluded by PLIP OLA.25: 8 residues within 4Å: Chain B: W.45, T.100, A.103, D.104, L.107, L.127 Ligands: 9P2.19, OLA.26 Ligand excluded by PLIP OLA.26: 9 residues within 4Å: Chain A: W.114, F.118 Chain B: L.107, W.114, C.115, F.118, R.119, L.123 Ligands: OLA.25 Ligand excluded by PLIP OLA.27: 5 residues within 4Å: Chain B: I.82, L.86, I.140, A.143, L.144 Ligand excluded by PLIP OLA.28: 5 residues within 4Å: Chain B: K.38, W.125, W.132 Ligands: OLA.23, OLA.35 Ligand excluded by PLIP OLA.29: 1 residues within 4Å: Ligands: OLA.23 Ligand excluded by PLIP OLA.30: 7 residues within 4Å: Chain B: L.186, L.187, T.190, I.191, F.195, L.198 Ligands: OLA.32 Ligand excluded by PLIP OLA.31: 4 residues within 4Å: Chain B: T.194, L.197, L.198, W.201 Ligand excluded by PLIP OLA.32: 4 residues within 4Å: Chain B: L.183, L.186, I.234 Ligands: OLA.30 Ligand excluded by PLIP OLA.33: 7 residues within 4Å: Chain B: K.213, V.216, A.217, I.224, F.225, F.259 Ligands: OLA.34 Ligand excluded by PLIP OLA.34: 8 residues within 4Å: Chain B: K.210, K.213, I.266, I.269, I.270, V.273, A.274 Ligands: OLA.33 Ligand excluded by PLIP OLA.35: 5 residues within 4Å: Chain B: A.34, A.37, V.51, W.125 Ligands: OLA.28 Ligand excluded by PLIP OLA.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OLA.37: 8 residues within 4Å: Chain A: L.137, L.138, P.141 Chain B: L.137, P.141, Y.145, Y.163, V.173 Ligand excluded by PLIP

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.38: 2 residues within 4Å: Chain B: E.150, Y.152 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Robertson, N. et al., Structure of the complement C5a receptor bound to the extra-helical antagonist NDT9513727. Nature (2018)

Release Date

2018-01-10

Peptides

C5a anaphylatoxin chemotactic receptor 1: 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

C5a anaphylatoxin chemotactic receptor 1