MolNFT v1 · #161094 · protein
Engineered human HLA_A2 MHC class I molecule in complex with NV9 peptide
6Q3K · HLA class I histocompatibility antigen, a-2 alpha chain: “Engineered human HLA_A2 MHC class I molecule in complex with NV9 peptide”. X-ray diffraction, 1 ligand (CO), 5 pockets (best druggability 0.68). MolNFT v1 #161094 on…
- PDB
- 6Q3K
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- 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
- Ligands
- CO
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 26% helix, 41% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| P | Asn-leu-val-pro-met-val-ala-thr-val | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 7 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.68 | 0.76 | 58 | GOL |
| 2 | 60 | 0.50 | 0.85 | 16 | GOL |
| 3 | 129 | 0.44 | 0.76 | 18 | empty |
| 4 | 69 | 0.42 | 0.81 | 18 | empty |
| 5 | 67 | 0.34 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1293 Ų buried · 19 hydrogen bonds · protein-protein
- A–P · 784 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6Q3K · Engineered Human HLA_A2 MHC Class I molecule in complex with NV9 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
- Elsewhere: RCSB PDB 6Q3K · PDBe 6Q3K · UniProt P01892 · UniProt P61769
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