Research workbench
Petal death protein PSR132 with cysteine-linked glutaraldehyde forming a thiohemiacetal adduct
Analyse Petal death protein PSR132 with cysteine-linked glutaraldehyde forming a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZLP
- Type
- protein
- Length
- 569 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Petal death protein
- EC
- 4.1.3.-
- UniProt
- Q05957
- Ligands
- GAQ, MG
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Petal death protein (EC 4.1.3.-) | protein | 284 | 51% helix, 15% strand | Q05957 |
| B | Petal death protein (EC 4.1.3.-) | protein | 285 | 49% helix, 14% strand | Q05957 |
Ligands and binding sites
- GAQ · 5-hydroxypentanal · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.56 | 0.75 | 33 | empty |
| 2 | 62 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 769 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1ZLP · Petal death protein PSR132 with cysteine-linked glutaraldehyde forming a thiohemiacetal… · the same entry in another collection · chain A against A, TM-score 1.00
- Q05957 · AlphaFold monomer V2.0 prediction for petal death protein (Q05957) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q05957
- Elsewhere: RCSB PDB 1ZLP · PDBe 1ZLP · UniProt Q05957
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