Research workbench
Crystal structure of cc chemokine receptor 5 (CCR5) in complex with high potency HIV entry inhibitor 5P7-CCL5
Analyse Crystal structure of cc chemokine receptor 5 (CCR5) in complex with high… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UIW
- Type
- protein
- Length
- 420 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-C chemokine receptor type 5,RUBREDOXIN chimera; C-C motif chemokine 5
- UniProt
- P51681, P00268, P13501
- Ligands
- OLA, ZN
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-C chemokine receptor type 5,RUBREDOXIN chimera | protein | 352 | 71% helix, 7% strand | P51681, P00268 |
| B | C-C motif chemokine 5 | protein | 68 | 25% helix, 24% strand | P13501 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.59 | 0.84 | 26 | empty |
| 2 | 99 | 0.38 | 0.76 | 17 | empty |
| 3 | 85 | 0.33 | 0.74 | 19 | empty |
| 4 | 55 | 0.29 | 0.75 | 11 | empty |
| 5 | 63 | 0.29 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1749 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 5UIW · Crystal Structure of CC Chemokine Receptor 5 (CCR5) in complex with high potency HIV… · the same entry in another collection · chain A against A, TM-score 1.00
- P13501 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 5 (P13501) · a predicted model of the same protein · chain B against A, TM-score 0.89
- P51681 · AlphaFold monomer V2.0 prediction for C-C chemokine receptor type 5 (P51681) · a predicted model of the same protein · chain A against A, TM-score 0.85
- P00268 · AlphaFold monomer V2.0 prediction for rubredoxin (P00268) · a predicted model of the same protein · chain A against A, TM-score 0.15
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 P51681
- Every structure of UniProt P00268
- Every structure of UniProt P13501
- Elsewhere: RCSB PDB 5UIW · PDBe 5UIW · UniProt P51681 · UniProt P00268 · UniProt P13501
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.