Research workbench
Crystal structure of HLA-B*08:01 in complex with elrsrywai viral peptide
Analyse Crystal structure of HLA-B*08:01 in complex with elrsrywai viral peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NUI
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA-B*08:01 heavy chain; Beta-2-microglobulin; Glu-leu-arg-ser-arg-tyr-TRP-ala-ile
- UniProt
- P61769
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA-B*08:01 heavy chain | protein | 276 | 28% helix, 38% strand | — |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 46% strand | P61769 |
| D | Glu-leu-arg-ser-arg-tyr-TRP-ala-ile | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, D, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.66 | 0.75 | 58 | empty |
| 2 | 77 | 0.44 | 0.81 | 17 | empty |
| 3 | 106 | 0.38 | 0.75 | 17 | empty |
| 4 | 63 | 0.36 | 0.78 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1323 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1005 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7NUI · Crystal structure of HLA-B*08:01 in complex with ELRSRYWAI viral peptide · 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 0.99
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 P61769
- Elsewhere: RCSB PDB 7NUI · PDBe 7NUI · UniProt P61769
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