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Crystal structure of thermostabilised human C5A anaphylatoxin chemotactic receptor 1 (C5AR) in complex with NDT9513727
Analyse Crystal structure of thermostabilised human C5A anaphylatoxin chemotactic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O9H
- Type
- protein
- Length
- 589 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C5A anaphylatoxin chemotactic receptor 1
- UniProt
- P21730
- Ligands
- OLA, 9P2
- Pockets
- 6 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C5A anaphylatoxin chemotactic receptor 1 | protein | 294 | 78% helix, 4% strand | P21730 |
| B | C5A anaphylatoxin chemotactic receptor 1 | protein | 295 | 73% helix, 5% strand | P21730 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 32 copies · chains A, B
- 9P2 · 1-(1,3-benzodioxol-5-yl)-~{N}-(1,3-benzodioxol-5-ylmethyl)-~{N}-[(3-butyl-2,5-diphenyl-imidazol-4-yl) methyl]methanamine · ligand · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 3 copies · chains A, B
- CIT · Citric acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.88 | 0.89 | 110 | OLA |
| 2 | 1198 | 0.74 | 0.76 | 69 | 9P2, OLA |
| 3 | 91 | 0.42 | 0.78 | 19 | empty |
| 4 | 71 | 0.40 | 0.79 | 14 | TLA |
| 5 | 103 | 0.38 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 853 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5O9H · Crystal structure of thermostabilised human C5a anaphylatoxin chemotactic receptor 1… · the same entry in another collection · chain A against A, TM-score 1.00
- P21730 · AlphaFold monomer V2.0 prediction for C5A anaphylatoxin chemotactic receptor 1 (P21730) · a predicted model of the same protein · chain B against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P21730
- Elsewhere: RCSB PDB 5O9H · PDBe 5O9H · UniProt P21730
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