Research workbench
Crystal structure of M1 zinc metallopeptidase E323A mutant from Deinococcus radiodurans
Analyse Crystal structure of M1 zinc metallopeptidase E323A mutant from Deinococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IFF
- Type
- protein
- Length
- 858 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.83
- Source
- Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 /…
- Molecule
- Zinc metalloprotease
- UniProt
- Q9RVZ5
- Ligands
- TYR, ZN, NA
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · resolution 1.83 · 1 distinct chain · 29% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Zinc metalloprotease | protein | 429 | 29% helix, 34% strand | Q9RVZ5 |
Ligands and binding sites
- TYR · Tyrosine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.63 | 0.82 | 28 | TYR |
| 2 | 204 | 0.59 | 0.81 | 28 | TYR |
| 3 | 57 | 0.43 | 0.83 | 15 | empty |
| 4 | 67 | 0.39 | 0.79 | 24 | empty |
| 5 | 92 | 0.36 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 412 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6IFF · Crystal structure of M1 zinc metallopeptidase E323A mutant from deinococcus radiodurans · 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 Q9RVZ5
- Elsewhere: RCSB PDB 6IFF · PDBe 6IFF · UniProt Q9RVZ5
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