MolNFT v1 · #110586 · protein
Immune complex
4Y1A · HLA class II histocompatibility antigen, dr alpha chain: “Immune complex”. X-ray diffraction, 1 ligand (NAG), 12 pockets (best druggability 0.71). MolNFT v1 #110586 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4Y1A
- Type
- protein
- Length
- 821 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
- UniProt
- P01903, P13760, P01308
- Ligands
- NAG
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 178 | 15% helix, 47% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-4 beta chain | protein | 184 | 18% helix, 43% strand | P13760 |
| C | Insulin | protein | 14 | 0% helix, 14% strand | P01308 |
| D | FS17_ALPHA | protein | 205 | 3% helix, 46% strand | — |
| E | FS17_BETA | protein | 240 | 5% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.71 | 0.85 | 38 | empty |
| 2 | 923 | 0.70 | 0.75 | 79 | empty |
| 3 | 171 | 0.49 | 0.77 | 26 | empty |
| 4 | 96 | 0.47 | 0.80 | 16 | empty |
| 5 | 114 | 0.46 | 0.79 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2470 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 2171 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 654 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 644 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 280 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
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 P01903
- Every structure of UniProt P13760
- Every structure of UniProt P01308
- Elsewhere: RCSB PDB 4Y1A · PDBe 4Y1A · UniProt P01903 · UniProt P13760 · UniProt P01308
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