MolNFT v1 · #68895 · protein
Cathepsin B in complex with stefin a
3K9M: “Cathepsin B in complex with stefin a”. X-ray diffraction, 3 pockets (best druggability 0.77). MolNFT v1 #68895 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3K9M
- Type
- protein
- Length
- 704 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B; Cystatin-a
- EC
- 3.4.22.1
- UniProt
- P07858, P01040
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cathepsin B (EC 3.4.22.1) | protein | 254 | 26% helix, 26% strand | P07858 |
| C, D | Cystatin-a | protein | 98 | 17% helix, 35% strand | P01040 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.77 | 0.83 | 80 | empty |
| 2 | 99 | 0.53 | 0.84 | 32 | empty |
| 3 | 83 | 0.40 | 0.78 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1302 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1276 Ų buried · 16 hydrogen bonds · protein-protein
- C–B · 556 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 341 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3K9M · Cathepsin B in complex with stefin A · the same entry in another collection · chain D against D, TM-score 1.00
- P07858 · AlphaFold monomer V2.0 prediction for cathepsin B (P07858) · a predicted model of the same protein · chain B against A, TM-score 0.94
- P01040 · AlphaFold monomer V2.0 prediction for cystatin-a (P01040) · a predicted model of the same protein · chain D 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 P07858
- Every structure of UniProt P01040
- Elsewhere: RCSB PDB 3K9M · PDBe 3K9M · UniProt P07858 · UniProt P01040
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