Research workbench
Structure of anti-HCXCR2 ABN48-2 in complex with its CXCR2 epitope
Analyse Structure of anti-HCXCR2 ABN48-2 in complex with its CXCR2 epitope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KVA
- Type
- protein
- Length
- 876 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
- 5 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain | protein | 213 | 8% helix, 53% strand | — |
| L, l | Light chain | protein | 217 | 9% helix, 52% strand | — |
| h | Heavy chain | protein | 216 | 9% helix, 53% 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 | 7 | 0% helix, 29% strand | P25025 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.75 | 0.85 | 56 | empty |
| 2 | 301 | 0.72 | 0.86 | 61 | empty |
| 3 | 96 | 0.50 | 0.83 | 28 | empty |
| 4 | 72 | 0.47 | 0.83 | 15 | empty |
| 5 | 149 | 0.42 | 0.74 | 36 | empty |
Interfaces
10 interfaces between chains.
- H–L · 1662 Ų buried · 16 hydrogen bonds · protein-protein
- h–l · 1589 Ų buried · 16 hydrogen bonds · protein-protein
- H–B · 516 Ų buried · 5 hydrogen bonds · protein-protein
- h–b · 500 Ų buried · 5 hydrogen bonds · protein-protein
- L–l · 423 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6KVA · Structure of anti-hCXCR2 abN48-2 in complex with its CXCR2 epitope · the same entry in another collection · chain b against b, 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 0.48
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 6KVA · PDBe 6KVA · UniProt P25025
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