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
- 6ULK
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I antigen; Beta-2-microglobulin; Gly-ala-asp-gly-val-gly-lys-ser-ala-leu
- UniProt
- C1K0Y1, P61769, P01111
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I antigen | protein | 273 | 27% helix, 39% strand | C1K0Y1 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Gly-ala-asp-gly-val-gly-lys-ser-ala-leu | protein | 10 | 0% helix, 0% strand | P01111 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.67 | 0.77 | 54 | empty |
| 2 | 124 | 0.50 | 0.80 | 24 | empty |
| 3 | 94 | 0.43 | 0.79 | 16 | empty |
| 4 | 112 | 0.43 | 0.77 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1440 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 814 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6ULK · Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation · 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 0.97
- P01111 · AlphaFold monomer V2.0 prediction for GTPase NRAS (P01111) · a predicted model of the same protein · chain C against A, TM-score 0.32
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 6ULK · PDBe 6ULK · UniProt C1K0Y1 · UniProt P61769 · UniProt P01111
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