Research workbench
Crystal structure of HLA-DQ0602 in complex with a hypocretin peptide
Analyse Crystal structure of HLA-DQ0602 in complex with a hypocretin peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UVQ
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen; Orexin
- UniProt
- P01907, P03992, O43612
- Ligands
- GLY, NAG, BMA, FUC, ZN
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen | protein | 182 | 15% helix, 43% strand | P01907 |
| B | HLA class II histocompatibility antigen | protein | 181 | 20% helix, 45% strand | P03992 |
| C | Orexin | protein | 20 | 0% helix, 5% strand | O43612 |
Ligands and binding sites
- GLY · Glycine · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A, C
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains B
- ZN · Zinc ion · metal · chains B
- ACY · Acetic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.48 | 0.74 | 37 | GLY |
| 2 | 125 | 0.40 | 0.75 | 22 | empty |
| 3 | 109 | 0.36 | 0.74 | 19 | empty |
| 4 | 56 | 0.27 | 0.74 | 12 | empty |
| 5 | 57 | 0.26 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2721 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 870 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 605 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 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 P01907
- Every structure of UniProt P03992
- Every structure of UniProt O43612
- Elsewhere: RCSB PDB 1UVQ · PDBe 1UVQ · UniProt P01907 · UniProt P03992 · UniProt O43612
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