MolNFT v1 · #66135 · protein
Crystal structure of cathepsin B from T. brucei in complex with CA074
3HHI · Cathepsin B-like cysteine protease: “Crystal structure of cathepsin B from T. brucei in complex with CA074”. X-ray diffraction, 3 ligands (074, MG, LI), 5 pockets (best druggability 0.54). MolNFT v1 #66135 on GenesisL1: 3D…
- PDB
- 3HHI
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B-like cysteine protease
- EC
- 3.4.22.-
- UniProt
- Q6R7Z5
- Ligands
- 074, MG, LI
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin B-like cysteine protease (EC 3.4.22.-) | protein | 258 | 26% helix, 26% strand | Q6R7Z5 |
| B | Cathepsin B-like cysteine protease (EC 3.4.22.-) | protein | 260 | 25% helix, 25% strand | Q6R7Z5 |
Ligands and binding sites
- 074 · [propylamino-3-hydroxy-butan-1,4-dionyl]-isoleucyl-proline · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- LI · Lithium ion · metal · chains B
- GOL · Glycerol · additive · 6 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.54 | 0.82 | 24 | GOL |
| 2 | 153 | 0.54 | 0.80 | 24 | GOL |
| 3 | 116 | 0.41 | 0.76 | 18 | 074 |
| 4 | 134 | 0.40 | 0.74 | 22 | 074 |
| 5 | 61 | 0.27 | 0.73 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 664 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 3HHI · Crystal Structure of Cathepsin B from T. brucei in complex with CA074 · the same entry in another collection · chain A 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 Q6R7Z5
- Elsewhere: RCSB PDB 3HHI · PDBe 3HHI · UniProt Q6R7Z5
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