Research workbench
Structure of HLA-DR15 with bound ALPHA3(135-145) peptide
Analyse Structure of HLA-DR15 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
- 5V4M
- Type
- protein
- Length
- 1,512 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA-DRA1; ALPHA3(135-145)-HLA-DRB1*15:01
- UniProt
- P01903, P01911
- Ligands
- NAG, FUC
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, G, J | HLA-DRA1 | protein | 178 | 15% helix, 46% strand | P01903 |
| F, C, I, L | ALPHA3(135-145)-HLA-DRB1*15:01 | protein | 200 | 19% helix, 43% strand | P01911 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains D, A, C, G, I, F, J, L
- FUC · alpha-L-fucopyranose · sugar · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.72 | 0.76 | 74 | empty |
| 2 | 426 | 0.69 | 0.81 | 34 | empty |
| 3 | 642 | 0.62 | 0.73 | 78 | empty |
| 4 | 184 | 0.52 | 0.78 | 32 | empty |
| 5 | 222 | 0.50 | 0.75 | 28 | empty |
Interfaces
12 interfaces between chains.
- D–F · 2877 Ų buried · 48 hydrogen bonds · protein-protein
- G–I · 2869 Ų buried · 49 hydrogen bonds · protein-protein
- J–L · 2863 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 2832 Ų buried · 47 hydrogen bonds · protein-protein
- F–I · 524 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5V4M · Structure of HLA-DR15 with bound alpha3(135-145) peptide · the same entry in another collection · chain L against L, 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 G against A, TM-score 0.97
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 P01911
- Elsewhere: RCSB PDB 5V4M · PDBe 5V4M · UniProt P01903 · UniProt P01911
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