Research workbench
Crystal structure of HLA DR52C
Analyse Crystal structure of HLA DR52C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C5J
- Type
- protein
- Length
- 373 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; MHC class II antigen; Elongation…
- UniProt
- P01903, Q6YJU6, Q05639
- Ligands
- NAG, SO4
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 45% 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 | MHC class II antigen | protein | 182 | 19% helix, 46% strand | Q6YJU6 |
| C | Elongation factor 1-alpha 2 | protein | 13 | 0% helix, 8% strand | Q05639 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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 | 119 | 0.40 | 0.76 | 16 | empty |
| 2 | 67 | 0.29 | 0.73 | 15 | empty |
| 3 | 57 | 0.27 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2376 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 619 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 556 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3C5J · Crystal structure of HLA DR52c · the same entry in another collection · chain A against A, TM-score 1.00
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q05639 · AlphaFold monomer V2.0 prediction for elongation factor 1-alpha 2 (Q05639) · a predicted model of the same protein · chain C against A, TM-score 0.34
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 Q6YJU6
- Every structure of UniProt Q05639
- Elsewhere: RCSB PDB 3C5J · PDBe 3C5J · UniProt P01903 · UniProt Q6YJU6 · UniProt Q05639
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