MolNFT v1 · #161100 · protein
Engineered human HLA_A2 MHC class I molecule in complex with TCR and SV9 peptide
6Q3S · HLA class I histocompatibility antigen, a-2 alpha chain: “Engineered human HLA_A2 MHC class I molecule in complex with TCR and SV9 peptide”. X-ray diffraction, 9 pockets (best druggability 0.73). MolNFT v1 #161100 on GenesisL1: 3D…
- PDB
- 6Q3S
- Type
- protein
- Length
- 827 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin…
- UniProt
- P01892, P61769, A0A0B4J279, K7N5N2, A0A0K0K1A5, K7N5M4
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 274 | 26% helix, 39% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Ser-leu-leu-met-TRP-ile-thr-gln-val | protein | 9 | 0% helix, 0% strand | — |
| D | T cell receptor alpha variable 21,T-cell receptor, SP3.4 alpha chain | protein | 203 | 1% helix, 46% strand | A0A0B4J279, K7N5N2 |
| E | T cell receptor beta variable 6-5,HUMAN nkt TCR beta chain | protein | 241 | 6% helix, 46% strand | A0A0K0K1A5, K7N5M4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.73 | 0.76 | 98 | empty |
| 2 | 622 | 0.68 | 0.77 | 56 | empty |
| 3 | 53 | 0.54 | 0.89 | 16 | ACT |
| 4 | 118 | 0.49 | 0.80 | 30 | empty |
| 5 | 139 | 0.44 | 0.76 | 21 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2237 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1376 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 802 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 522 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 380 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 covalent (disulfide, additive adduct).
Compared structures
- 6Q3S · Engineered Human HLA_A2 MHC Class I molecule in complex with TCR and SV9 peptide · the same entry in another collection · chain A against A, 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 0.98
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 P01892
- Every structure of UniProt P61769
- Every structure of UniProt A0A0B4J279
- Every structure of UniProt K7N5N2
- Every structure of UniProt A0A0K0K1A5
- Every structure of UniProt K7N5M4
- Elsewhere: RCSB PDB 6Q3S · PDBe 6Q3S · UniProt P01892 · UniProt P61769 · UniProt A0A0B4J279 · UniProt K7N5N2 · UniProt A0A0K0K1A5 · UniProt K7N5M4
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