Research workbench
Crystal structure of the tyrosine regulated 3-deoxy-D-arabino- heptulosonate-7-phosphate synthase from saccharomyces cerevisiae in complex with 2-phosphoglycolate
Analyse Crystal structure of the tyrosine regulated 3-deoxy-D-arabino… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OFO
- Type
- protein
- Length
- 683 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-2-dehydro-3-deoxyheptonate aldolase
- EC
- 4.1.2.15
- UniProt
- P32449
- Ligands
- PGA
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 344 | 40% helix, 19% strand | P32449 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 339 | 40% helix, 19% strand | P32449 |
Ligands and binding sites
- PGA · 2-phosphoglycolic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.72 | 0.80 | 79 | PGA |
| 2 | 198 | 0.70 | 0.87 | 29 | empty |
| 3 | 156 | 0.68 | 0.88 | 28 | empty |
| 4 | 52 | 0.68 | 0.97 | 15 | empty |
| 5 | 56 | 0.46 | 0.84 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3089 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 1OFO · Crystal Structure of the Tyrosine Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate… · the same entry in another collection · chain A against A, TM-score 1.00
- P32449 · AlphaFold monomer V2.0 prediction for phospho-2-dehydro-3-deoxyheptonate aldolase… · a predicted model of the same protein · chain B 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 P32449
- Elsewhere: RCSB PDB 1OFO · PDBe 1OFO · UniProt P32449
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