MolNFT v1 · #155052 · protein
Structure of anti-HCXCR2 ABN48 in complex with its CXCR2 epitope
6KVF · Heavy chain: “Structure of anti-HCXCR2 ABN48 in complex with its CXCR2 epitope”. X-ray diffraction, 11 pockets (best druggability 0.51). MolNFT v1 #155052 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KVF
- Type
- protein
- Length
- 862 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain; Light chain; Peptide from C-X-C chemokine receptor type 2
- UniProt
- P25025
- Pockets
- 11 · best druggability 0.51
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain | protein | 212 | 4% helix, 53% strand | — |
| A | Heavy chain | protein | 208 | 3% helix, 53% strand | — |
| L | Light chain | protein | 217 | 8% helix, 51% strand | — |
| C | Light chain | protein | 217 | 8% helix, 52% strand | — |
| b | Peptide from C-X-C chemokine receptor type 2 | protein | 6 | 0% helix, 33% strand | P25025 |
| B | Peptide from C-X-C chemokine receptor type 2 | protein | 2 | 0% helix, 0% strand | P25025 |
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.51 | 0.78 | 30 | empty |
| 2 | 273 | 0.48 | 0.73 | 41 | empty |
| 3 | 228 | 0.46 | 0.73 | 28 | empty |
| 4 | 216 | 0.45 | 0.73 | 33 | empty |
| 5 | 80 | 0.43 | 0.80 | 23 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1656 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1551 Ų buried · 15 hydrogen bonds · protein-protein
- H–b · 502 Ų buried · 6 hydrogen bonds · protein-protein
- H–A · 349 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 264 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6KVF · Structure of anti-hCXCR2 abN48 in complex with its CXCR2 epitope · the same entry in another collection · chain H against H, TM-score 1.00
- P25025 · AlphaFold monomer V2.0 prediction for C-X-C chemokine receptor type 2 (P25025) · a predicted model of the same protein · chain b against A, TM-score 0.44
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 P25025
- Elsewhere: RCSB PDB 6KVF · PDBe 6KVF · UniProt P25025
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