Research workbench
Structure of cathb with covalently linked compound 28
Analyse Structure of cathb with covalently linked compound 28 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AY2
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin B
- EC
- 3.4.22.1
- UniProt
- P07858
- Ligands
- C1G
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin B (EC 3.4.22.1) | protein | 255 | 25% helix, 23% strand | P07858 |
| B | Cathepsin B (EC 3.4.22.1) | protein | 254 | 25% helix, 23% strand | P07858 |
Ligands and binding sites
- C1G · N~1~-[(2S)-1-amino-5-(carbamoylamino)pentan-2-yl]-N'~1~-[(1R)-1-(thiophen-3-yl)ethyl]cyclobutane-1,1-dicarboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.55 | 0.89 | 20 | empty |
| 2 | 240 | 0.52 | 0.76 | 32 | C1G |
| 3 | 204 | 0.51 | 0.77 | 35 | C1G |
| 4 | 53 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 552 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
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
- Elsewhere: RCSB PDB 6AY2 · PDBe 6AY2 · UniProt P07858
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