Research workbench
Crystal structure of the mutant G226S of the tyrosine-regulated 3- deoxy-D-arabino-heptulosonate-7-phosphate synthase from saccharomyces cerevisiae complexed with phenylalanine and manganese
Analyse Crystal structure of the mutant G226S of the tyrosine-regulated 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OG0
- Type
- protein
- Length
- 2,750 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine- inhibited
- EC
- 2.5.1.54
- UniProt
- P32449
- Ligands
- PHE, MN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine- inhibited (EC 2.5.1.54) | protein | 344 | 38% helix, 20% strand | P32449 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine- inhibited (EC 2.5.1.54) | protein | 346 | 37% helix, 18% strand | P32449 |
| C | Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine- inhibited (EC 2.5.1.54) | protein | 346 | 38% helix, 18% strand | P32449 |
| D | Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine- inhibited (EC 2.5.1.54) | protein | 349 | 38% helix, 18% strand | P32449 |
| E | Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine- inhibited (EC 2.5.1.54) | protein | 335 | 38% helix, 20% strand | P32449 |
| F | Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine- inhibited (EC 2.5.1.54) | protein | 345 | 39% helix, 18% strand | P32449 |
| G | Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine- inhibited (EC 2.5.1.54) | protein | 342 | 38% helix, 18% strand | P32449 |
| H | Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine- inhibited (EC 2.5.1.54) | protein | 343 | 38% helix, 18% strand | P32449 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 7 copies · chains A, B, C, D, E, F, G, H
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.78 | 0.88 | 45 | empty |
| 2 | 477 | 0.77 | 0.85 | 75 | MN |
| 3 | 538 | 0.75 | 0.83 | 68 | empty |
| 4 | 803 | 0.74 | 0.79 | 80 | empty |
| 5 | 487 | 0.74 | 0.83 | 63 | empty |
Interfaces
14 interfaces between chains.
- C–D · 3121 Ų buried · 57 hydrogen bonds · protein-protein
- A–B · 3090 Ų buried · 59 hydrogen bonds · protein-protein
- G–H · 3039 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 2984 Ų buried · 52 hydrogen bonds · protein-protein
- E–G · 312 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1OG0 · Crystal structure of the mutant G226S of the tyrosine-regulated… · the same entry in another collection · chain H against H, 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 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 P32449
- Elsewhere: RCSB PDB 1OG0 · PDBe 1OG0 · UniProt P32449
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