MolNFT v1 · #178109 · protein
Complex structure of HLA2402 with recognizing SARS-cov-2 epitope PEP4
7F4W · MHC class I antigen: “Complex structure of HLA2402 with recognizing SARS-cov-2 epitope PEP4”. X-ray diffraction, 10 pockets (best druggability 0.72). MolNFT v1 #178109 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7F4W
- Type
- protein
- Length
- 778 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; SARS-cov-2 T-cell epitope PEP4
- UniProt
- D9UAY1, P61769
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | MHC class I antigen | protein | 280 | 24% helix, 37% strand | D9UAY1 |
| B, D | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| E, F | SARS-cov-2 T-cell epitope PEP4 | protein | 9 | 0% helix, 0% strand | — |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.72 | 0.77 | 71 | empty |
| 2 | 664 | 0.70 | 0.78 | 54 | empty |
| 3 | 486 | 0.61 | 0.75 | 37 | empty |
| 4 | 208 | 0.52 | 0.77 | 35 | empty |
| 5 | 184 | 0.48 | 0.76 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1414 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1371 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 1012 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1004 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 292 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7F4W · Complex structure of HLA2402 with recognizing SARS-CoV-2 epitope pep4 · 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 D 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 D9UAY1
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 7F4W · PDBe 7F4W · UniProt D9UAY1 · UniProt P61769
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