MolNFT v1 · #29725 · protein
Crystal structure of HLA-B*3508 presenting 13-mer EBV antigen lpeplpqgqltay
1ZHL · HLA class I histocompatibility antigen, B-35 alpha chain: “Crystal structure of HLA-B*3508 presenting 13-mer EBV antigen lpeplpqgqltay”. X-ray diffraction, 3 pockets (best druggability 0.68). MolNFT v1 #29725 on GenesisL1: 3D…
- PDB
- 1ZHL
- Type
- protein
- Length
- 388 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-35 alpha chain; Beta-2-microglobulin…
- UniProt
- P30685, P61769
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-35 alpha chain | protein | 276 | 26% helix, 39% strand | P30685 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | EBV-peptide lpeplpqgqltay | protein | 13 | 0% helix, 0% strand | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.68 | 0.77 | 53 | empty |
| 2 | 143 | 0.51 | 0.79 | 23 | empty |
| 3 | 109 | 0.42 | 0.77 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1316 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 947 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1ZHL · Crystal structure of HLA-B*3508 presenting 13-mer EBV antigen LPEPLPQGQLTAY · 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 B 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 P30685
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 1ZHL · PDBe 1ZHL · UniProt P30685 · UniProt P61769
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