MolNFT v1 · #169462 · protein
Immune receptor complex
6XCP · MHC class II HLA-dq-alpha chain: “Immune receptor complex”. X-ray diffraction, 2 ligands (NAG, PO4), 10 pockets (best druggability 0.58). MolNFT v1 #169462 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XCP
- Type
- protein
- Length
- 809 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II HLA-dq-alpha chain; Hybrid insulin peptide, MHC class II HLA-DQ8-beta chain…
- UniProt
- Q30069, O19707
- Ligands
- NAG, PO4
- Pockets
- 10 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class II HLA-dq-alpha chain | protein | 182 | 13% helix, 41% strand | Q30069 |
| C | Hybrid insulin peptide, MHC class II HLA-DQ8-beta chain fusion | protein | 200 | 18% helix, 41% strand | O19707 |
| D | T-cell-receptor, A2.13-alpha chain | protein | 188 | 0% helix, 43% strand | — |
| E | T-cell-receptor, A2.13-beta chain | protein | 239 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C
- PO4 · Phosphate ion · ion · chains D, E
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.58 | 0.78 | 34 | empty |
| 2 | 382 | 0.55 | 0.73 | 45 | empty |
| 3 | 300 | 0.55 | 0.75 | 33 | PO4 |
| 4 | 226 | 0.50 | 0.75 | 33 | empty |
| 5 | 127 | 0.46 | 0.78 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3209 Ų buried · 59 hydrogen bonds · protein-protein
- D–E · 2019 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 507 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 418 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 339 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6XCP · Immune receptor complex · the same entry in another collection · chain A against A, TM-score 1.00
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 Q30069
- Every structure of UniProt O19707
- Elsewhere: RCSB PDB 6XCP · PDBe 6XCP · UniProt Q30069 · UniProt O19707
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