Research workbench
Crystal structure of the tyrosine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from saccharomyces cerevisiae in complex with phosphoenolpyruvate and COBALT(II)
Analyse Crystal structure of the tyrosine-regulated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OFA
- Type
- protein
- Length
- 681 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
- PEP, CO
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 343 | 38% helix, 20% strand | P32449 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) | protein | 338 | 40% helix, 19% strand | P32449 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains B, A
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.80 | 0.88 | 64 | GOL |
| 2 | 588 | 0.72 | 0.80 | 82 | PEP, GOL |
| 3 | 58 | 0.50 | 0.86 | 18 | empty |
| 4 | 79 | 0.48 | 0.83 | 18 | empty |
| 5 | 60 | 0.39 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3066 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 1OFA · 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 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 P32449
- Elsewhere: RCSB PDB 1OFA · PDBe 1OFA · UniProt P32449
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