MolNFT v1 · #66086 · protein
Germline-governed recognition of a cancer epitope by an immunodominant human T cell receptor
3HG1 · MHC class I antigen: “Germline-governed recognition of a cancer epitope by an immunodominant human T cell receptor”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.68). MolNFT v1 #66086 on GenesisL1: 3D…
- PDB
- 3HG1
- Type
- protein
- Length
- 824 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; CANCER/MART-1; T-cell receptor, alpha chain…
- UniProt
- Q8WLS4, P61769
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 24% helix, 36% strand | Q8WLS4 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | CANCER/MART-1 | protein | 10 | 0% helix, 10% strand | — |
| D | T-cell receptor, alpha chain | protein | 194 | 2% helix, 44% strand | — |
| E | T-cell receptor, beta chain | protein | 244 | 5% helix, 48% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.68 | 0.74 | 70 | empty |
| 2 | 671 | 0.68 | 0.76 | 59 | SO4 |
| 3 | 68 | 0.54 | 0.87 | 21 | empty |
| 4 | 115 | 0.53 | 0.82 | 27 | empty |
| 5 | 102 | 0.48 | 0.81 | 20 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2130 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1356 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 883 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 479 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 461 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3HG1 · Germline-governed recognition of a cancer epitope by an immunodominant human T cell… · 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 Q8WLS4
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 3HG1 · PDBe 3HG1 · UniProt Q8WLS4 · UniProt P61769
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