Research workbench
Crystal structure of arabidopsis thaliana pii bound to malonate
Analyse Crystal structure of arabidopsis thaliana pii bound to malonate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O67
- Type
- protein
- Length
- 317 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pii protein
- UniProt
- Q9ZST4
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pii protein | protein | 105 | 27% helix, 37% strand | Q9ZST4 |
| B | Pii protein | protein | 108 | 30% helix, 35% strand | Q9ZST4 |
| C | Pii protein | protein | 104 | 29% helix, 37% strand | Q9ZST4 |
Ligands and binding sites
- MLI · Malonate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.64 | 0.84 | 36 | MLI |
| 2 | 293 | 0.60 | 0.78 | 39 | MLI |
| 3 | 208 | 0.56 | 0.79 | 33 | MLI |
| 4 | 60 | 0.29 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1391 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1269 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1254 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2O67 · Crystal structure of Arabidopsis thaliana PII bound to malonate · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ZST4 · AlphaFold monomer V2.0 prediction for nitrogen regulatory protein P-II homolog (Q9ZST4) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q9ZST4
- Elsewhere: RCSB PDB 2O67 · PDBe 2O67 · UniProt Q9ZST4
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