MolNFT v1 · #96683 · protein
HLA-B*18:01 in complex with epstein-barr virus BZLF1-derived peptide (residues 173-180)
4JQV · HLA class I histocompatibility antigen, B-18 alpha chain: “HLA-B*18:01 in complex with epstein-barr virus BZLF1-derived peptide (residues 173-180)”. X-ray diffraction, 5 pockets (best druggability 0.68). MolNFT v1 #96683 on…
- PDB
- 4JQV
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-18 alpha chain; Beta-2-microglobulin…
- UniProt
- P30466, P61769, Q3KSS8
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-18 alpha chain | protein | 276 | 26% helix, 40% strand | P30466 |
| C | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| B | Trans-activator protein BZLF1 | protein | 8 | 0% helix, 0% strand | Q3KSS8 |
Ligands and binding sites
- ACT · Acetate ion · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.68 | 0.78 | 51 | empty |
| 2 | 200 | 0.53 | 0.78 | 39 | empty |
| 3 | 115 | 0.45 | 0.78 | 26 | ACT |
| 4 | 77 | 0.38 | 0.78 | 16 | empty |
| 5 | 52 | 0.28 | 0.75 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1296 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 960 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4JQV · HLA-B*18:01 in complex with Epstein-Barr virus BZLF1-derived peptide (residues 173-180) · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P30466
- Every structure of UniProt P61769
- Every structure of UniProt Q3KSS8
- Elsewhere: RCSB PDB 4JQV · PDBe 4JQV · UniProt P30466 · UniProt P61769 · UniProt Q3KSS8
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