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Crystal structure of two domain M1 Zinc metallopeptidase E323A mutant bound to L-tryptophan amino acid
Analyse Crystal structure of two domain M1 Zinc metallopeptidase E323A mutant bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KOY
- Type
- protein
- Length
- 864 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 /…
- Molecule
- Zinc metalloprotease
- UniProt
- Q9RVZ5
- Ligands
- TRP, ZN
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.35 · 1 distinct chain · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Zinc metalloprotease | protein | 432 | 28% helix, 33% strand | Q9RVZ5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.65 | 0.83 | 35 | TRP |
| 2 | 234 | 0.62 | 0.81 | 31 | TRP |
| 3 | 153 | 0.46 | 0.76 | 35 | empty |
| 4 | 109 | 0.43 | 0.78 | 29 | empty |
| 5 | 52 | 0.42 | 0.82 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 414 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6KOY · Crystal structure of two domain M1 zinc metallopeptidase E323A mutant bound to… · 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 6KOY · PDBe 6KOY · UniProt Q9RVZ5
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