Research workbench
Crystal structure of the putative protease I from bacteroides thetaiotaomicron
Analyse Crystal structure of the putative protease I from bacteroides thetaiotaomicron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CNE
- Type
- protein
- Length
- 695 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative protease I
- UniProt
- Q8A8A4
- Ligands
- FMN, ZN, CA
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Putative protease I | protein | 174 | 39% helix, 26% strand | Q8A8A4 |
| B | Putative protease I | protein | 173 | 38% helix, 27% strand | Q8A8A4 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains B, C, A, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, D, B, C
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 | 905 | 0.80 | 0.82 | 86 | empty |
| 2 | 1029 | 0.75 | 0.78 | 100 | ZN, FMN |
| 3 | 83 | 0.35 | 0.75 | 21 | ZN |
| 4 | 68 | 0.32 | 0.75 | 19 | ZN |
| 5 | 52 | 0.30 | 0.76 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–C · 901 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 899 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 470 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 332 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 321 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 3CNE · Crystal structure of the putative protease I from Bacteroides thetaiotaomicron · 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 Q8A8A4
- Elsewhere: RCSB PDB 3CNE · PDBe 3CNE · UniProt Q8A8A4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.