Research workbench
Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation
Analyse Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UON
- Type
- protein
- Length
- 1,629 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TCR-V-alpha-12-02*01; TCR-V-beta-10-2*01; HLA class I antigen; Beta-2-microglobulin…
- UniProt
- C1K0Y1, P61769, P01111
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 7 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | TCR-V-alpha-12-02*01 | protein | 199 | 4% helix, 41% strand | — |
| H, J | TCR-V-beta-10-2*01 | protein | 238 | 6% helix, 47% strand | — |
| I | TCR-V-alpha-12-02*01 | protein | 193 | 5% helix, 35% strand | — |
| A, D | HLA class I antigen | protein | 273 | 27% helix, 40% strand | C1K0Y1 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 52% strand | P61769 |
| C, F | Gly-ala-asp-gly-val-gly-lys-ser-ala-leu | protein | 10 | 0% helix, 0% strand | P01111 |
| E | Beta-2-microglobulin | protein | 97 | 0% helix, 53% strand | P61769 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.76 | 0.78 | 84 | empty |
| 2 | 672 | 0.75 | 0.81 | 77 | empty |
| 3 | 426 | 0.72 | 0.83 | 50 | empty |
| 4 | 51 | 0.68 | 0.97 | 18 | empty |
| 5 | 579 | 0.68 | 0.77 | 49 | empty |
Interfaces
15 interfaces between chains.
- I–J · 2237 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 2216 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1335 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1297 Ų buried · 18 hydrogen bonds · protein-protein
- H–J · 1005 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6UON · Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation · 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 E 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 C1K0Y1
- Every structure of UniProt P61769
- Every structure of UniProt P01111
- Elsewhere: RCSB PDB 6UON · PDBe 6UON · UniProt C1K0Y1 · UniProt P61769 · UniProt P01111
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