Research workbench
Crystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS peptide (vvvgaggvgk)
Analyse Crystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OW5
- Type
- protein
- Length
- 821 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; KRAS peptide (vvvgaggvgk); TCR alpha; TCR beta
- EC
- 3.6.5.2
- UniProt
- A0A583ZB34, P61769, P01111
- Ligands
- SO4
- Pockets
- 12 · 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 | 275 | 27% helix, 39% strand | A0A583ZB34 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 47% strand | P61769 |
| C | KRAS peptide (vvvgaggvgk) (EC 3.6.5.2) | protein | 10 | 0% helix, 0% strand | P01111 |
| D | TCR alpha | protein | 191 | 3% helix, 48% strand | — |
| E | TCR beta | protein | 246 | 7% helix, 49% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D, E
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 | 983 | 0.70 | 0.75 | 92 | empty |
| 2 | 589 | 0.68 | 0.77 | 52 | SO4 |
| 3 | 57 | 0.68 | 0.96 | 25 | empty |
| 4 | 80 | 0.53 | 0.85 | 18 | empty |
| 5 | 132 | 0.49 | 0.79 | 28 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2216 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1345 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 810 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 578 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 196 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7OW5 · Crystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS peptide (VVVGAGGVGK) · 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 0.37
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 7OW5 · PDBe 7OW5 · UniProt A0A583ZB34 · UniProt P61769 · UniProt P01111
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