6C1Q

Crystal structure of human C5a receptor in complex with an orthosteric antagonist PMX53 and an allosteric antagonist NDT9513727


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Orthosteric and allosteric action of the C5a receptor antagonists.

Liu, H.Kim, H.R.Deepak, R.N.V.K.Wang, L.Chung, K.Y.Fan, H.Wei, Z.Zhang, C.

(2018) Nat. Struct. Mol. Biol. 25: 472-481


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Soluble cytochrome b562, C5a anaphylatoxin chemotactic receptor 1 chimera
B
422Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: cybC, C5AR1 (C5AR, C5R1)
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P21730 (Homo sapiens)
Go to Gene View: C5AR1
Go to UniProtKB:  P21730
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PMX53
L
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9P2
Query on 9P2

Download SDF File 
Download CCD File 
B
1-(1,3-benzodioxol-5-yl)-~{N}-(1,3-benzodioxol-5-ylmethyl)-~{N}-[(3-butyl-2,5-diphenyl-imidazol-4-yl)methyl]methanamine
C36 H35 N3 O4
ITACCRHKSPSKKL-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002303
Query on PRD_002303
LPMX53Cyclic peptide / 

--

Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
B
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.369α = 90.00
b = 52.558β = 107.75
c = 84.503γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-06-20
    Type: Data collection, Database references