Research workbench
Crystal structure of mature apo-cathepsin L C25A mutant in complex with gln-leu-ala peptide
Analyse Crystal structure of mature apo-cathepsin L C25A mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K24
- Type
- protein
- Length
- 446 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin L1; H3 peptide
- EC
- 3.4.22.15
- UniProt
- P07711
- Ligands
- NAG, NDG, MAN, BMA
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cathepsin L1 (EC 3.4.22.15) | protein | 220 | 30% helix, 21% strand | P07711 |
| C, D | H3 peptide | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, A
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.74 | 0.80 | 75 | empty |
| 2 | 72 | 0.36 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 548 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 337 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 333 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3K24 · Crystal structure of mature apo-Cathepsin L C25A mutant in complex with Gln-Leu-Ala… · the same entry in another collection · chain A against A, TM-score 1.00
- P07711 · AlphaFold monomer V2.0 prediction for procathepsin L (P07711) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P07711
- Elsewhere: RCSB PDB 3K24 · PDBe 3K24 · UniProt P07711
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