Research workbench
Unreduced cathepsin L in complex with stefin a
Analyse Unreduced cathepsin L in complex with stefin a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KSE
- Type
- protein
- Length
- 954 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin L1; Cystatin-a
- EC
- 3.4.22.15
- UniProt
- P07711, P01040
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cathepsin L1 (EC 3.4.22.15) | protein | 220 | 29% helix, 22% strand | P07711 |
| D, E, F | Cystatin-a | protein | 98 | 24% helix, 39% strand | P01040 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 573 | 0.77 | 0.83 | 53 | empty |
| 2 | 355 | 0.59 | 0.76 | 46 | empty |
| 3 | 107 | 0.57 | 0.85 | 23 | empty |
| 4 | 130 | 0.44 | 0.77 | 26 | empty |
| 5 | 121 | 0.44 | 0.77 | 26 | empty |
Interfaces
7 interfaces between chains.
- B–E · 916 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 908 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 880 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 558 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 444 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 3 modified (disulfide, methylation).
Compared structures
- 3KSE · Unreduced cathepsin L in complex with stefin A · the same entry in another collection · chain F against F, 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 0.98
- P01040 · AlphaFold monomer V2.0 prediction for cystatin-a (P01040) · a predicted model of the same protein · chain E against A, TM-score 0.93
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
- Every structure of UniProt P01040
- Elsewhere: RCSB PDB 3KSE · PDBe 3KSE · UniProt P07711 · UniProt P01040
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