Research workbench
Structure of HLA-DR1 with bound ALPHA3(135-145) peptide
Analyse Structure of HLA-DR1 with bound ALPHA3(135-145) peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V4N
- Type
- protein
- Length
- 755 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA-DRA1; ALPHA3(135-145)-HLA-DRB1*01:01
- UniProt
- P01903, P04229
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA-DRA1 | protein | 179 | 15% helix, 45% strand | P01903 |
| C | ALPHA3(135-145)-HLA-DRB1*01:01 | protein | 200 | 20% helix, 43% strand | P04229 |
| F | ALPHA3(135-145)-HLA-DRB1*01:01 | protein | 197 | 18% helix, 43% strand | P04229 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.73 | 0.78 | 71 | empty |
| 2 | 422 | 0.71 | 0.82 | 36 | empty |
| 3 | 246 | 0.50 | 0.74 | 28 | empty |
| 4 | 256 | 0.47 | 0.72 | 28 | empty |
| 5 | 146 | 0.40 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2936 Ų buried · 44 hydrogen bonds · protein-protein
- D–F · 2869 Ų buried · 46 hydrogen bonds · protein-protein
- C–F · 613 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5V4N · Structure of HLA-DR1 with bound alpha3(135-145) peptide · 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 D against A, TM-score 0.96
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 P04229
- Elsewhere: RCSB PDB 5V4N · PDBe 5V4N · UniProt P01903 · UniProt P04229
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