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Crystal structure of two domain M1 zinc metallopeptidase E323 mutant bound to L-leucine amino acid
Analyse Crystal structure of two domain M1 zinc metallopeptidase E323 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
- 6KOZ
- Type
- protein
- Length
- 869 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc metalloprotease, putative
- UniProt
- Q9RVZ5
- Ligands
- LEU, ZN, NA
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Zinc metalloprotease, putative | protein | 433 | 29% helix, 34% strand | Q9RVZ5 |
| A | Zinc metalloprotease, putative | protein | 436 | 29% helix, 34% strand | Q9RVZ5 |
Ligands and binding sites
- LEU · Leucine · ligand · 2 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, A
- NA · Sodium ion · metal · 2 copies · chains B, A
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 | 220 | 0.61 | 0.81 | 29 | LEU |
| 2 | 201 | 0.60 | 0.81 | 28 | ZN, LEU |
| 3 | 123 | 0.46 | 0.78 | 30 | empty |
| 4 | 136 | 0.44 | 0.76 | 34 | empty |
| 5 | 58 | 0.41 | 0.81 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 393 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6KOZ · Crystal structure of two domain M1 zinc metallopeptidase E323 mutant bound to L-Leucine… · the same entry in another collection · chain B against B, 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 6KOZ · PDBe 6KOZ · UniProt Q9RVZ5
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