Research workbench
Mouse cathepsin S with covalent ligand (3S,4S)-N-[(2E)-2-iminoethyl]- 4-(morpholin-4-ylcarbonyl)-1-(PHENYLSULFONYL)PYRROLIDINE-3- carboxamide
Analyse Mouse cathepsin S with covalent ligand (3S,4S)-N-[(2E)-2-iminoethyl]… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MZO
- Type
- protein
- Length
- 1,746 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin S
- EC
- 3.4.22.27
- UniProt
- O70370
- Ligands
- 2EW
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, G, H | Cathepsin S (EC 3.4.22.27) | protein | 218 | 29% helix, 23% strand | O70370 |
| B, F | Cathepsin S (EC 3.4.22.27) | protein | 219 | 29% helix, 22% strand | O70370 |
Ligands and binding sites
- 2EW · (3S,4S)-N-[(2E)-2-iminoethyl]-4-(morpholin-4-ylcarbonyl)-1-(phenylsulfonyl)pyrrolidine-3-carboxamide · ligand · 8 copies · chains A, B, C, D, E, G, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.83 | 0.84 | 111 | 2EW |
| 2 | 758 | 0.81 | 0.84 | 81 | 2EW |
| 3 | 597 | 0.80 | 0.85 | 56 | empty |
| 4 | 745 | 0.79 | 0.83 | 73 | 2EW |
| 5 | 606 | 0.75 | 0.82 | 69 | 2EW |
Interfaces
13 interfaces between chains.
- B–C · 638 Ų buried · 5 hydrogen bonds · protein-protein
- E–G · 627 Ų buried · 4 hydrogen bonds · protein-protein
- F–H · 603 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 530 Ų buried · 3 hydrogen bonds · protein-protein
- E–H · 505 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 8 covalent (disulfide, covalent ligand).
Compared structures
- 4MZO · Mouse cathepsin s with covalent ligand (3S,4S)-N-[(2E)-2-IMINOETHYL]-4-(MORPHOLIN-4-YLCARB… · the same entry in another collection · chain H against H, TM-score 1.00
- O70370 · AlphaFold monomer V2.0 prediction for cathepsin S (O70370) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 O70370
- Elsewhere: RCSB PDB 4MZO · PDBe 4MZO · UniProt O70370
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