MolNFT v1 · #19567 · protein
Complex between nk cell receptor LY49A and its MHC class I ligand H-2DD
1QO3 · MHC class I H-2DD heavy chain: “Complex between nk cell receptor LY49A and its MHC class I ligand H-2DD”. X-ray diffraction, 6 pockets (best druggability 0.63). MolNFT v1 #19567 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1QO3
- Type
- protein
- Length
- 633 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I H-2DD heavy chain; Beta-2-microglobulin; LY49A; HIV envelope glycoprotein 120…
- UniProt
- P01900, P01887, P20937, P04582
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 20% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I H-2DD heavy chain | protein | 274 | 27% helix, 38% strand | P01900 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P01887 |
| C | LY49A | protein | 128 | 20% helix, 36% strand | P20937 |
| D | LY49A | protein | 121 | 21% helix, 38% strand | P20937 |
| P | HIV envelope glycoprotein 120 peptide | protein | 10 | 0% helix, 0% strand | P04582 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C, P, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.63 | 0.75 | 48 | empty |
| 2 | 167 | 0.56 | 0.80 | 22 | empty |
| 3 | 262 | 0.54 | 0.77 | 33 | EDO |
| 4 | 148 | 0.46 | 0.77 | 21 | empty |
| 5 | 72 | 0.32 | 0.75 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1454 Ų buried · 21 hydrogen bonds · protein-protein
- A–P · 937 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 549 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 502 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 1QO3 · Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd · the same entry in another collection · chain P against P, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P20937 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein YE1/48 (P20937) · a predicted model of the same protein · chain D against A, TM-score 0.97
- P01900 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, D-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P01900
- Every structure of UniProt P01887
- Every structure of UniProt P20937
- Every structure of UniProt P04582
- Elsewhere: RCSB PDB 1QO3 · PDBe 1QO3 · UniProt P01900 · UniProt P01887 · UniProt P20937 · UniProt P04582
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