Research workbench
Crystal structure of human Cathepsin L in complex with covalently bound MG132
Analyse Crystal structure of human Cathepsin L in complex with covalently bound MG132 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QKD
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Homo sapiens
- Molecule
- Cathepsin L
- UniProt
- P07711
- Ligands
- ALD
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.5 · 2 distinct chains · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Cathepsin L | protein | 220 | 29% helix, 22% strand | P07711 |
| C | Cathepsin L | protein | 216 | 29% helix, 22% strand | P07711 |
Ligands and binding sites
- ALD · N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide · ligand · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.84 | 0.85 | 111 | ACT |
| 2 | 342 | 0.75 | 0.86 | 51 | empty |
| 3 | 430 | 0.68 | 0.80 | 54 | PEG, ALD |
| 4 | 82 | 0.44 | 0.80 | 20 | empty |
| 5 | 72 | 0.33 | 0.75 | 23 | empty |
Interfaces
6 interfaces between chains.
- C–D · 564 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 554 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 495 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 441 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 384 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
- P07711 · AlphaFold monomer V2.0 prediction for procathepsin L (P07711) · a predicted model of the same protein · chain C against A, TM-score 1.00
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 7QKD · PDBe 7QKD · UniProt P07711
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