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Crystal structure of HLA-A*11:01 in complex with KRAS G12D peptide (vvvgadgvgk)
Analyse Crystal structure of HLA-A*11:01 in complex with KRAS G12D peptide (vvvgadgvgk) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OW4
- Type
- protein
- Length
- 1,532 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; KRAS G12D peptide (vvvgadgvgk)
- EC
- 3.6.5.2
- UniProt
- A0A583ZB34, P61769, P01111
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MHC class I antigen | protein | 276 | 26% helix, 39% strand | A0A583ZB34 |
| B, E, H, K | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| C, F, I, L | KRAS G12D peptide (vvvgadgvgk) (EC 3.6.5.2) | protein | 8 | 0% helix, 0% strand | P01111 |
| G, J | MHC class I antigen | protein | 274 | 26% helix, 40% strand | A0A583ZB34 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains D, K, B, G, H, E, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.82 | 0.83 | 115 | SO4 |
| 2 | 656 | 0.78 | 0.83 | 80 | SO4 |
| 3 | 646 | 0.68 | 0.77 | 58 | empty |
| 4 | 626 | 0.67 | 0.76 | 63 | empty |
| 5 | 577 | 0.67 | 0.77 | 56 | empty |
Interfaces
24 interfaces between chains.
- G–H · 1392 Ų buried · 24 hydrogen bonds · protein-protein
- J–K · 1385 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1382 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1373 Ų buried · 24 hydrogen bonds · protein-protein
- G–I · 791 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7OW4 · Crystal structure of HLA-A*11:01 in complex with KRAS G12D peptide (VVVGADGVGK) · the same entry in another collection · chain L against L, TM-score 1.00
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 7OW4 · PDBe 7OW4 · UniProt A0A583ZB34 · UniProt P61769 · UniProt P01111
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