Research workbench
The high resolution crystal structure of HLA-B*1402 complexed with a cathepsin a signal sequence peptide, pcata
Analyse The high resolution crystal structure of HLA-B*1402 complexed with a cathepsin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BXN
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA-B*1402 extracellular domain; Beta-2-microglobulin; Cathepsin a signal sequence…
- UniProt
- Q56H30, P61769, P10619
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA-B*1402 extracellular domain | protein | 276 | 28% helix, 39% strand | Q56H30 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Cathepsin a signal sequence octapeptide | protein | 9 | 0% helix, 0% strand | P10619 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.69 | 0.78 | 57 | GOL |
| 2 | 174 | 0.52 | 0.79 | 23 | empty |
| 3 | 95 | 0.44 | 0.79 | 23 | empty |
| 4 | 53 | 0.28 | 0.75 | 14 | GOL |
Interfaces
2 interfaces between chains.
- A–B · 1298 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 918 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3BXN · The high resolution crystal structure of HLA-B*1402 complexed with a Cathepsin A signal… · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P10619 · AlphaFold monomer V2.0 prediction for lysosomal protective protein (P10619) · a predicted model of the same protein · chain C against A, TM-score 0.49
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 Q56H30
- Every structure of UniProt P61769
- Every structure of UniProt P10619
- Elsewhere: RCSB PDB 3BXN · PDBe 3BXN · UniProt Q56H30 · UniProt P61769 · UniProt P10619
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