Research workbench
High resolution crystal structure of HLA-B*1402 in complex with the latent membrane protein 2 peptide (LMP2) of epstein-barr virus
Analyse High resolution crystal structure of HLA-B*1402 in complex with the latent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BVN
- Type
- protein
- Length
- 770 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B*1402 alpha chain; Beta-2-microglobulin; Latent…
- UniProt
- Q56H30, P61769, P13285
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, B*1402 alpha chain | protein | 277 | 26% helix, 39% strand | Q56H30 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, F | Latent membrane protein 2 peptide | protein | 9 | 0% helix, 0% strand | P13285 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.73 | 0.78 | 73 | empty |
| 2 | 562 | 0.68 | 0.78 | 52 | empty |
| 3 | 73 | 0.47 | 0.83 | 17 | empty |
| 4 | 143 | 0.46 | 0.77 | 25 | empty |
| 5 | 97 | 0.45 | 0.80 | 23 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1393 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1338 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1018 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1011 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 188 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3BVN · High resolution crystal structure of HLA-B*1402 in complex with the latent membrane… · the same entry in another collection · chain F against F, 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 0.99
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 Q56H30
- Every structure of UniProt P61769
- Every structure of UniProt P13285
- Elsewhere: RCSB PDB 3BVN · PDBe 3BVN · UniProt Q56H30 · UniProt P61769 · UniProt P13285
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