MolNFT v1 · #46158 · protein
Crystal structure of HLA-B*3508 presenting EBV peptide eplpqgqltay at 1.7A
2NW3 · HLA class I histocompatibility antigen, B-35 alpha chain: “Crystal structure of HLA-B*3508 presenting EBV peptide eplpqgqltay at 1.7A”. X-ray diffraction, 4 pockets (best druggability 0.70). MolNFT v1 #46158 on GenesisL1: 3D…
- PDB
- 2NW3
- 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; EBV…
- UniProt
- P30685, P61769
- Pockets
- 4 · best druggability 0.70
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 | EBV peptide eplpqgqltay | protein | 11 | 0% helix, 0% strand | — |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.70 | 0.93 | 21 | empty |
| 2 | 578 | 0.68 | 0.78 | 47 | empty |
| 3 | 218 | 0.54 | 0.78 | 33 | empty |
| 4 | 102 | 0.43 | 0.78 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1314 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 952 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2NW3 · Crystal structure of HLA-B*3508 presenting EBV peptide EPLPQGQLTAY at 1.7A · 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 2NW3 · PDBe 2NW3 · UniProt P30685 · UniProt P61769
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