Research workbench
Crystal structure of MHC class I HLA-A2 molecule complexed with EBV BMLF1-280-288 nonapeptide
Analyse Crystal structure of MHC class I HLA-A2 molecule complexed with EBV… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MRE
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; 9-meric…
- UniProt
- P01892, P61769, Q3KSU1
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 274 | 27% helix, 41% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| P | 9-meric peptide from mRNA export factor EB2 | protein | 9 | 0% helix, 0% strand | Q3KSU1 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.67 | 0.76 | 65 | empty |
| 2 | 85 | 0.44 | 0.80 | 19 | empty |
| 3 | 52 | 0.35 | 0.79 | 15 | empty |
| 4 | 56 | 0.34 | 0.78 | 14 | empty |
| 5 | 62 | 0.32 | 0.75 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1311 Ų buried · 19 hydrogen bonds · protein-protein
- A–P · 771 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3MRE · Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288… · 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 P01892
- Every structure of UniProt P61769
- Every structure of UniProt Q3KSU1
- Elsewhere: RCSB PDB 3MRE · PDBe 3MRE · UniProt P01892 · UniProt P61769 · UniProt Q3KSU1
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