MolNFT v1 · #190314 · protein
Crystal structure of HLA-A*2402 complexed with 8-mer influenza PB1 peptide
7WT4 · MHC class I antigen: “Crystal structure of HLA-A*2402 complexed with 8-mer influenza PB1 peptide”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.71). MolNFT v1 #190314 on GenesisL1: 3D structure, binding sites…
- PDB
- 7WT4
- Type
- protein
- Length
- 715 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; PB1 peptide
- UniProt
- A0A411J078, P61769, Q9WLS3
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 277 | 27% helix, 40% strand | A0A411J078 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | PB1 peptide | protein | 8 | 0% helix, 0% strand | Q9WLS3 |
| D | MHC class I antigen | protein | 233 | 30% helix, 33% strand | A0A411J078 |
| E | Beta-2-microglobulin | protein | 89 | 0% helix, 42% strand | P61769 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 46 copies · chains A, B, C, D, F, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.71 | 0.78 | 60 | EDO, ACT |
| 2 | 660 | 0.68 | 0.77 | 57 | EDO |
| 3 | 205 | 0.50 | 0.76 | 36 | EDO |
| 4 | 127 | 0.43 | 0.77 | 23 | EDO |
| 5 | 74 | 0.42 | 0.80 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1295 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1156 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 942 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 929 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7WT4 · Crystal structure of HLA-A*2402 complexed with 8-mer Influenza PB1 peptide · 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 A0A411J078
- Every structure of UniProt P61769
- Every structure of UniProt Q9WLS3
- Elsewhere: RCSB PDB 7WT4 · PDBe 7WT4 · UniProt A0A411J078 · UniProt P61769 · UniProt Q9WLS3
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