MolNFT v1 · #91257 · protein
Crystal structure of HLA-A*2402 complexed with a newly identified peptide from 2009 H1N1 PB1 (498-505)
4F7T · HLA class I histocompatibility antigen, a-24 alpha chain: “Crystal structure of HLA-A*2402 complexed with a newly identified peptide from 2009 H1N1 PB1 (498-505)”. X-ray diffraction, 6 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 4F7T
- Type
- protein
- Length
- 762 residues
- Chains
- 6
- 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
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a-24 alpha chain | protein | 274 | 27% helix, 39% strand | P05534 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, F | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 8 | 0% helix, 0% strand | Q9YXL6 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.75 | 0.78 | 110 | empty |
| 2 | 716 | 0.70 | 0.77 | 58 | empty |
| 3 | 573 | 0.69 | 0.78 | 59 | empty |
| 4 | 261 | 0.51 | 0.75 | 32 | empty |
| 5 | 80 | 0.48 | 0.83 | 17 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1324 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1291 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 950 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 927 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 232 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4F7T · Crystal Structure of HLA-A*2402 Complexed with a Newly Identified Peptide from 2009 H1N1… · 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 0.98
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 4F7T · PDBe 4F7T · UniProt P05534 · UniProt P61769 · UniProt Q9YXL6
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