MolNFT v1 · #184999 · protein
Crystal structure of jdi TCR in complex with HLA-A*11:01 bound to KRAS G12D peptide (vvvgadgvgk)
7PB2 · MHC class I antigen: “Crystal structure of jdi TCR in complex with HLA-A*11:01 bound to KRAS G12D peptide (vvvgadgvgk)”. X-ray diffraction, 20 pockets (best druggability 0.72). MolNFT v1 #184999 on GenesisL1: 3D structure, binding…
- PDB
- 7PB2
- Type
- protein
- Length
- 1,593 residues
- Chains
- 10
- 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
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 7 distinct chains · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | MHC class I antigen | protein | 274 | 25% helix, 39% strand | A0A583ZB34 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 46% strand | P61769 |
| C, H | KRAS G12D peptide (vvvgadgvgk) (EC 3.6.5.2) | protein | 10 | 0% helix, 10% strand | P01111 |
| D | TCR alpha | protein | 163 | 2% helix, 53% strand | — |
| E, J | TCR beta | protein | 244 | 7% helix, 50% strand | — |
| G | Beta-2-microglobulin | protein | 97 | 0% helix, 46% strand | P61769 |
| I | TCR alpha | protein | 179 | 2% helix, 50% strand | — |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.72 | 0.76 | 88 | empty |
| 2 | 1007 | 0.71 | 0.75 | 78 | empty |
| 3 | 542 | 0.68 | 0.78 | 50 | empty |
| 4 | 538 | 0.66 | 0.77 | 48 | empty |
| 5 | 396 | 0.56 | 0.74 | 51 | empty |
Interfaces
17 interfaces between chains.
- I–J · 1881 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1766 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1389 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 1361 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 857 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 7PB2 · Crystal structure of JDI TCR in complex with HLA-A*11:01 bound to KRAS G12D peptide… · the same entry in another collection · chain J against J, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain G against A, TM-score 0.99
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 7PB2 · PDBe 7PB2 · UniProt A0A583ZB34 · UniProt P61769 · UniProt P01111
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