MolNFT v1 · #67326 · protein
Crystal structure of putative zinc protease from bordetella pertussis tohama I
3IH6: “Crystal structure of putative zinc protease from bordetella pertussis tohama I”. X-ray diffraction, 13 pockets (best druggability 0.80). MolNFT v1 #67326 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3IH6
- Type
- protein
- Length
- 1,085 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative zinc protease
- UniProt
- Q7VVY4
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative zinc protease | protein | 180 | 48% helix, 17% strand | Q7VVY4 |
| B | Putative zinc protease | protein | 180 | 51% helix, 18% strand | Q7VVY4 |
| C, F | Putative zinc protease | protein | 181 | 49% helix, 18% strand | Q7VVY4 |
| D | Putative zinc protease | protein | 181 | 49% helix, 18% strand | Q7VVY4 |
| E | Putative zinc protease | protein | 182 | 52% helix, 17% strand | Q7VVY4 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, D, C, F
- ACT · Acetate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.80 | 0.86 | 68 | empty |
| 2 | 217 | 0.74 | 0.89 | 23 | empty |
| 3 | 716 | 0.74 | 0.79 | 59 | empty |
| 4 | 355 | 0.73 | 0.85 | 33 | empty |
| 5 | 207 | 0.72 | 0.88 | 36 | empty |
Interfaces
12 interfaces between chains.
- D–F · 788 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 776 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 762 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 755 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 722 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3IH6 · Crystal structure of putative zinc protease from Bordetella pertussis Tohama I · 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 Q7VVY4
- Elsewhere: RCSB PDB 3IH6 · PDBe 3IH6 · UniProt Q7VVY4
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