Research workbench
3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with phenylalanine bound in only one site
Analyse 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with phenylalanine bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YPO
- Type
- protein
- Length
- 915 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-2-dehydro-3-deoxyheptonate aldolase arog
- EC
- 2.5.1.54
- UniProt
- O53512
- Ligands
- PHE, MN, SO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-2-dehydro-3-deoxyheptonate aldolase arog (EC 2.5.1.54) | protein | 458 | 45% helix, 14% strand | O53512 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase arog (EC 2.5.1.54) | protein | 457 | 45% helix, 15% strand | O53512 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.78 | 0.80 | 84 | GOL |
| 2 | 106 | 0.71 | 0.93 | 20 | PHE |
| 3 | 559 | 0.68 | 0.78 | 65 | empty |
| 4 | 244 | 0.67 | 0.84 | 35 | PHE |
| 5 | 434 | 0.62 | 0.76 | 39 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1790 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2YPO · 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with phenylalanine bound in only one… · the same entry in another collection · chain A against A, TM-score 1.00
- O53512 · AlphaFold monomer V2.0 prediction for phospho-2-dehydro-3-deoxyheptonate aldolase arog… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O53512
- Elsewhere: RCSB PDB 2YPO · PDBe 2YPO · UniProt O53512
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