MolNFT v1 · #141559 · protein
Crystal structure of asparaginyl endopeptidases from viola canadensis
5ZBI · Peptide asparaginyl ligase: “Crystal structure of asparaginyl endopeptidases from viola canadensis”. X-ray diffraction, 1 ligand (NA), 8 pockets (best druggability 0.59). MolNFT v1 #141559 on GenesisL1: 3D structure, binding sites…
- PDB
- 5ZBI
- Type
- protein
- Length
- 835 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide asparaginyl ligase
- Ligands
- NA
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide asparaginyl ligase | protein | 420 | 45% helix, 12% strand | — |
| B | Peptide asparaginyl ligase | protein | 415 | 45% helix, 13% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.59 | 0.81 | 37 | empty |
| 2 | 311 | 0.57 | 0.77 | 37 | empty |
| 3 | 154 | 0.50 | 0.79 | 26 | empty |
| 4 | 142 | 0.46 | 0.77 | 22 | empty |
| 5 | 75 | 0.38 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 148 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5ZBI · Crystal structure of asparaginyl endopeptidases from Viola Canadensis · 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
- Elsewhere: RCSB PDB 5ZBI · PDBe 5ZBI
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