MolNFT v1 · #127589 · protein
Crystal structure of tce treated rppep-1
5N12 · Pro-pro endopeptidase: “Crystal structure of tce treated rppep-1”. X-ray diffraction, 2 ligands (8FH, ZN), 3 pockets (best druggability 0.74). MolNFT v1 #127589 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5N12
- Type
- protein
- Length
- 391 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pro-pro endopeptidase
- EC
- 3.4.24.89
- UniProt
- Q183R7
- Ligands
- 8FH, ZN
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pro-pro endopeptidase (EC 3.4.24.89) | protein | 197 | 54% helix, 8% strand | Q183R7 |
| B | Pro-pro endopeptidase (EC 3.4.24.89) | protein | 194 | 54% helix, 8% strand | Q183R7 |
Ligands and binding sites
- 8FH · 2,2,2-tris-chloroethanol · ligand · 3 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.74 | 0.79 | 64 | ZN, TRS |
| 2 | 292 | 0.58 | 0.77 | 32 | ZN, TRS |
| 3 | 74 | 0.28 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 416 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 Q183R7
- Elsewhere: RCSB PDB 5N12 · PDBe 5N12 · UniProt Q183R7
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