Research workbench
Crystal structure of HLA-DP2
Analyse Crystal structure of HLA-DP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LQZ
- Type
- protein
- Length
- 379 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dp alpha 1 chain; HLA-DP2 beta chain linked with…
- UniProt
- P20036, Q5EP54
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dp alpha 1 chain | protein | 181 | 13% helix, 44% strand | P20036 |
| B | HLA-DP2 beta chain linked with dra peptide | protein | 198 | 17% helix, 38% strand | Q5EP54 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.41 | 0.73 | 28 | empty |
| 2 | 81 | 0.33 | 0.74 | 16 | empty |
| 3 | 77 | 0.33 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3268 Ų buried · 60 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 P20036
- Every structure of UniProt Q5EP54
- Elsewhere: RCSB PDB 3LQZ · PDBe 3LQZ · UniProt P20036 · UniProt Q5EP54
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