Research workbench
Crystal structure of the CXCR4 chemokine receptor in complex with a cyclic peptide antagonist CVX15
Analyse Crystal structure of the CXCR4 chemokine receptor in complex with a cyclic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OE0
- Type
- protein
- Length
- 448 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-X-C chemokine receptor type 4, lysozyme chimera; Polyphemusin analog, cxc chemokine…
- EC
- 3.2.1.17
- UniProt
- P61073, P00720
- Ligands
- CIR
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-X-C chemokine receptor type 4, lysozyme chimera (EC 3.2.1.17) | protein | 433 | 73% helix, 7% strand | P61073, P00720 |
| I | Polyphemusin analog, cxc chemokine receptor antagonist | protein | 15 | 0% helix, 27% strand | — |
Ligands and binding sites
- CIR · Citrulline · ligand · chains A, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.74 | 0.87 | 31 | empty |
| 2 | 373 | 0.61 | 0.77 | 37 | CIR |
| 3 | 273 | 0.60 | 0.78 | 30 | empty |
| 4 | 231 | 0.58 | 0.79 | 35 | empty |
| 5 | 55 | 0.31 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–I · 1085 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 covalent, 2 d-amino, 1 modified (disulfide, covalent ligand, D-amino acid, nonstandard).
Compared structures
- 3OE0 · Crystal structure of the CXCR4 chemokine receptor in complex with a cyclic peptide… · the same entry in another collection · chain A against A, TM-score 1.00
- P61073 · AlphaFold monomer V2.0 prediction for C-X-C chemokine receptor type 4 (P61073) · a predicted model of the same protein · chain A against A, TM-score 0.62
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 P61073
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 3OE0 · PDBe 3OE0 · UniProt P61073 · UniProt P00720
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