Research workbench
Crystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS G12D peptide (vvvgadgvgk)
Analyse Crystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS G12D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OW6
- Type
- protein
- Length
- 811 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; KRAS G12D peptide (vvvgadgvgk); TCR alpha; TCR…
- EC
- 3.6.5.2
- UniProt
- A0A583ZB34, P61769, P01111
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 26% helix, 42% strand | A0A583ZB34 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | KRAS G12D peptide (vvvgadgvgk) (EC 3.6.5.2) | protein | 10 | 0% helix, 0% strand | P01111 |
| D | TCR alpha | protein | 181 | 2% helix, 47% strand | — |
| E | TCR beta | protein | 245 | 7% helix, 48% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.70 | 0.75 | 80 | empty |
| 2 | 644 | 0.69 | 0.77 | 54 | empty |
| 3 | 82 | 0.48 | 0.82 | 17 | empty |
| 4 | 94 | 0.43 | 0.79 | 22 | empty |
| 5 | 94 | 0.42 | 0.78 | 26 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1918 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1306 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 843 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 578 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 198 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7OW6 · Crystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS G12D peptide… · 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 0.97
- P01111 · AlphaFold monomer V2.0 prediction for GTPase NRAS (P01111) · a predicted model of the same protein · chain C against A, TM-score 0.36
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 A0A583ZB34
- Every structure of UniProt P61769
- Every structure of UniProt P01111
- Elsewhere: RCSB PDB 7OW6 · PDBe 7OW6 · UniProt A0A583ZB34 · UniProt P61769 · UniProt P01111
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