MolNFT v1 · #157762 · protein
X-ray structure of a secreted C11 cysteine protease from bacteroides thetaiotaomicron in complex with an irreversible peptide inhibitor
6N9J · Clostripain-related protein: “X-ray structure of a secreted C11 cysteine protease from bacteroides thetaiotaomicron in complex with an…”. X-ray diffraction, 2 ligands (ACE, CKC), 5 pockets (best druggability 0.66). MolNFT v1 #157762…
- PDB
- 6N9J
- Type
- protein
- Length
- 714 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clostripain-related protein; Covalently bound peptide inhibitor
- UniProt
- Q8A866
- Ligands
- ACE, CKC
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clostripain-related protein | protein | 352 | 35% helix, 26% strand | Q8A866 |
| C, D | Covalently bound peptide inhibitor | protein | 3 | 0% helix, 0% strand | — |
| B | Clostripain-related protein | protein | 356 | 35% helix, 25% strand | Q8A866 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- CKC · (3S)-3,7-diaminoheptan-2-one · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.66 | 0.75 | 76 | empty |
| 2 | 115 | 0.43 | 0.77 | 23 | empty |
| 3 | 64 | 0.42 | 0.81 | 14 | empty |
| 4 | 109 | 0.41 | 0.77 | 21 | empty |
| 5 | 64 | 0.34 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 347 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 346 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 249 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6N9J · X-ray structure of a secreted C11 cysteine protease from Bacteroides thetaiotaomicron in… · 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 Q8A866
- Elsewhere: RCSB PDB 6N9J · PDBe 6N9J · UniProt Q8A866
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