MolNFT v1 · #91254 · protein
Crystal structure of HLA-A*2402 complexed with a newly identified peptide from 2009H1N1 PB1 (496-505)
4F7P · HLA class I histocompatibility antigen, a-24 alpha chain: “Crystal structure of HLA-A*2402 complexed with a newly identified peptide from 2009H1N1 PB1 (496-505)”. X-ray diffraction, 5 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 4F7P
- Type
- protein
- Length
- 380 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-24 alpha chain; Beta-2-microglobulin…
- EC
- 2.7.7.48
- UniProt
- P05534, P61769, Q9YXL6
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-24 alpha chain | protein | 274 | 28% helix, 39% strand | P05534 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 7 | 0% helix, 0% strand | Q9YXL6 |
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 | 619 | 0.71 | 0.79 | 62 | empty |
| 2 | 176 | 0.49 | 0.77 | 35 | empty |
| 3 | 68 | 0.37 | 0.78 | 15 | empty |
| 4 | 51 | 0.36 | 0.80 | 13 | empty |
| 5 | 50 | 0.26 | 0.74 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1267 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 951 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4F7P · Crystal Structure of HLA-A*2402 Complexed with a Newly Identified Peptide from 2009H1N1… · 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 P05534
- Every structure of UniProt P61769
- Every structure of UniProt Q9YXL6
- Elsewhere: RCSB PDB 4F7P · PDBe 4F7P · UniProt P05534 · UniProt P61769 · UniProt Q9YXL6
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