MolNFT v1 · #154870 · protein
Crystal structure of two domain M1 zinc metallopeptidase E323A mutant bound to L-arginine
6KP0 · Zinc metalloprotease, putative: “Crystal structure of two domain M1 zinc metallopeptidase E323A mutant bound to L-arginine”. X-ray diffraction, 3 ligands (ARG, ZN, NA), 6 pockets (best druggability 0.64). MolNFT v1 #154870 on…
- PDB
- 6KP0
- Type
- protein
- Length
- 865 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc metalloprotease, putative
- UniProt
- Q9RVZ5
- Ligands
- ARG, ZN, NA
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc metalloprotease, putative | protein | 432 | 28% helix, 34% strand | Q9RVZ5 |
| B | Zinc metalloprotease, putative | protein | 433 | 28% helix, 33% strand | Q9RVZ5 |
Ligands and binding sites
- ARG · Arginine · 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.64 | 0.82 | 32 | ZN, ARG |
| 2 | 199 | 0.64 | 0.83 | 28 | ZN, ARG |
| 3 | 314 | 0.55 | 0.76 | 58 | empty |
| 4 | 114 | 0.43 | 0.78 | 23 | empty |
| 5 | 140 | 0.39 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 474 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6KP0 · Crystal structure of two domain M1 zinc metallopeptidase E323A mutant bound to L-arginine · 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 6KP0 · PDBe 6KP0 · UniProt Q9RVZ5
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