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
- 6ULN
- Type
- protein
- Length
- 810 residues
- Chains
- 5
- 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…
- UniProt
- C1K0Y1, P61769, P01111
- Ligands
- MG, SO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I antigen | protein | 273 | 29% helix, 38% strand | C1K0Y1 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Gly-ala-asp-gly-val-gly-lys-ser-ala | protein | 9 | 0% helix, 0% strand | P01111 |
| D | TCR-V-alpha-4*01 | protein | 189 | 3% helix, 44% strand | — |
| E | TCR-V-beta-5-6*01 | protein | 240 | 7% helix, 50% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, E
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, D, E
- GOL · Glycerol · additive · 6 copies · chains A, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.75 | 0.79 | 89 | SO4, GOL, MG |
| 2 | 696 | 0.71 | 0.78 | 76 | empty |
| 3 | 184 | 0.49 | 0.76 | 27 | empty |
| 4 | 144 | 0.44 | 0.75 | 18 | empty |
| 5 | 135 | 0.41 | 0.75 | 22 | empty |
Interfaces
5 interfaces between chains.
- D–E · 2133 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1234 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 719 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 489 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 6ULN · Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation · the same entry in another collection · chain B against B, 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 0.99
- P01111 · AlphaFold monomer V2.0 prediction for GTPase NRAS (P01111) · a predicted model of the same protein · chain C against A, TM-score 0.31
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 6ULN · PDBe 6ULN · UniProt C1K0Y1 · UniProt P61769 · UniProt P01111
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