Research workbench
Crystal structure of peruvianin-I (cysteine peptidase from thevetia peruviana latex)
Analyse Crystal structure of peruvianin-I (cysteine peptidase from thevetia peruviana… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ORM
- Type
- protein
- Length
- 486 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peruvianin-I
- EC
- 3.4.22.2
- Ligands
- NAG, BMA, FUC
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Peruvianin-I (EC 3.4.22.2) | protein | 163 | 8% helix, 36% strand | — |
| B | Peruvianin-I (EC 3.4.22.2) | protein | 160 | 8% helix, 34% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 4 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.69 | 0.80 | 60 | empty |
| 2 | 124 | 0.65 | 0.88 | 25 | empty |
| 3 | 198 | 0.64 | 0.84 | 32 | empty |
| 4 | 307 | 0.64 | 0.80 | 46 | empty |
| 5 | 231 | 0.56 | 0.78 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1983 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 626 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 566 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ORM · Crystal Structure of Peruvianin-I (Cysteine peptidase from Thevetia peruviana latex) · 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 6ORM · PDBe 6ORM
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