MolNFT v1 · #30071 · protein
Crystal structure of HLA-B*3501 presenting an 11-mer EBV antigen eplpqgqltay
1ZSD · HLA class I histocompatibility antigen, B-35 alpha chain: “Crystal structure of HLA-B*3501 presenting an 11-mer EBV antigen eplpqgqltay”. X-ray diffraction, 5 pockets (best druggability 0.74). MolNFT v1 #30071 on GenesisL1: 3D…
- PDB
- 1ZSD
- Type
- protein
- Length
- 386 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; BZLF1…
- UniProt
- P30685, P61769, P03206
- Pockets
- 5 · best druggability 0.74
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 | 27% helix, 39% strand | P30685 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | BZLF1 trans-activator protein | protein | 11 | 0% helix, 0% strand | P03206 |
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 | 92 | 0.74 | 0.96 | 19 | empty |
| 2 | 623 | 0.68 | 0.77 | 55 | empty |
| 3 | 134 | 0.46 | 0.77 | 22 | empty |
| 4 | 103 | 0.43 | 0.78 | 22 | empty |
| 5 | 59 | 0.32 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1341 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 945 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1ZSD · Crystal Structure Of HLA-B*3501 Presenting an 11-Mer EBV Antigen EPLPQGQLTAY · 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
- Every structure of UniProt P03206
- Elsewhere: RCSB PDB 1ZSD · PDBe 1ZSD · UniProt P30685 · UniProt P61769 · UniProt P03206
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