MolNFT v1 · #67815 · protein
The crystal structure of the inactive peptidase domain of a putative zinc protease from bordetella parapertussis to 2.2A
3IVL: “The crystal structure of the inactive peptidase domain of a putative zinc protease from bordetella…”. X-ray diffraction, 4 pockets (best druggability 0.55). MolNFT v1 #67815 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3IVL
- Type
- protein
- Length
- 370 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative zinc protease
- UniProt
- Q7W521
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative zinc protease | protein | 187 | 47% helix, 14% strand | Q7W521 |
| B | Putative zinc protease | protein | 183 | 48% helix, 15% strand | Q7W521 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.55 | 0.76 | 26 | empty |
| 2 | 242 | 0.55 | 0.77 | 31 | empty |
| 3 | 97 | 0.37 | 0.75 | 20 | empty |
| 4 | 101 | 0.37 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 328 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3IVL · The Crystal Structure of the Inactive Peptidase Domain of a Putative Zinc Protease from… · 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 Q7W521
- Elsewhere: RCSB PDB 3IVL · PDBe 3IVL · UniProt Q7W521
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