MolNFT v1 · #28419 · protein
1.9A crystal structure of HLA-G
1YDP · MHC class I antigen: “1.9A crystal structure of HLA-G”. X-ray diffraction, 2 ligands (CO, CL), 5 pockets (best druggability 0.68). MolNFT v1 #28419 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1YDP
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Histone 2A peptide
- UniProt
- P17693, P61769
- Ligands
- CO, CL
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 275 | 28% helix, 39% strand | P17693 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| P | Histone 2A peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
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 | 652 | 0.68 | 0.77 | 59 | empty |
| 2 | 60 | 0.42 | 0.82 | 16 | empty |
| 3 | 118 | 0.40 | 0.76 | 35 | empty |
| 4 | 54 | 0.31 | 0.76 | 14 | empty |
| 5 | 53 | 0.27 | 0.74 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1333 Ų buried · 22 hydrogen bonds · protein-protein
- A–P · 999 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1YDP · 1.9A crystal structure of HLA-G · the same entry in another collection · chain A against A, TM-score 1.00
- P17693 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, alpha chain… · a predicted model of the same protein · chain A against A, TM-score 0.98
- 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 P17693
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 1YDP · PDBe 1YDP · UniProt P17693 · UniProt P61769
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