Research workbench
1.9 ångström resolution crystal structure of a plant cysteine protease ervatamin-C refinement with cdna derived amino acid sequence
Analyse 1.9 ångström resolution crystal structure of a plant cysteine protease… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PNS
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ervatamin-C, a papain-like plant cysteine protease
- EC
- 3.4.22.-
- UniProt
- P83654
- Ligands
- THJ, PO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ervatamin-C, a papain-like plant cysteine protease (EC 3.4.22.-) | protein | 208 | 27% helix, 21% strand | P83654 |
Ligands and binding sites
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 | 692 | 0.73 | 0.79 | 62 | empty |
| 2 | 109 | 0.51 | 0.81 | 25 | empty |
| 3 | 52 | 0.29 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 606 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 2PNS · 1.9 Angstrom resolution crystal structure of a plant cysteine protease Ervatamin-C… · 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 P83654
- Elsewhere: RCSB PDB 2PNS · PDBe 2PNS · UniProt P83654
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.