MolNFT v1 · #103805 · protein
Crystal structure of TK3 TCR-HLA-B*35:01-hpvg-Q5 complex
4PRP · MHC class I antigen: “Crystal structure of TK3 TCR-HLA-B*35:01-hpvg-Q5 complex”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.73). MolNFT v1 #103805 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PRP
- Type
- protein
- Length
- 827 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Epstein-barr nuclear antigen 1; TK3 TCR alpha…
- UniProt
- C5MK56, P61769, P03211
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 25% helix, 40% strand | C5MK56 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Epstein-barr nuclear antigen 1 | protein | 11 | 0% helix, 0% strand | P03211 |
| D | TK3 TCR alpha chain | protein | 200 | 3% helix, 48% strand | — |
| E | TK3 TCR beta chain | protein | 241 | 6% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.73 | 0.80 | 58 | empty |
| 2 | 1062 | 0.69 | 0.74 | 89 | empty |
| 3 | 116 | 0.51 | 0.81 | 27 | empty |
| 4 | 173 | 0.46 | 0.76 | 26 | empty |
| 5 | 189 | 0.46 | 0.75 | 29 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2128 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1273 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 918 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 418 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 304 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
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 C5MK56
- Every structure of UniProt P61769
- Every structure of UniProt P03211
- Elsewhere: RCSB PDB 4PRP · PDBe 4PRP · UniProt C5MK56 · UniProt P61769 · UniProt P03211
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