MolNFT v1 · #142820 · protein
Molecular basis for feedback inhibition of tyrosine-regulated 3-deoxy- D-arabino-heptulosonate-7-phosphate synthase from escherichia COLI
6AGM · Phospho-2-dehydro-3-deoxyheptonate aldolase, tyr-sensitive: “Molecular basis for feedback inhibition of tyrosine-regulated 3-deoxy- D-arabino-heptulosonate-7-phosphate…”. X-ray diffraction, 1 ligand (TYR), 18 pockets (best…
- PDB
- 6AGM
- Type
- protein
- Length
- 1,336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-2-dehydro-3-deoxyheptonate aldolase, tyr-sensitive
- EC
- 2.5.1.54
- UniProt
- P00888
- Ligands
- TYR
- Pockets
- 18 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phospho-2-dehydro-3-deoxyheptonate aldolase, tyr-sensitive (EC 2.5.1.54) | protein | 334 | 42% helix, 16% strand | P00888 |
Ligands and binding sites
- TYR · Tyrosine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.69 | 0.83 | 44 | TYR |
| 2 | 343 | 0.67 | 0.81 | 46 | TYR |
| 3 | 188 | 0.67 | 0.86 | 29 | empty |
| 4 | 261 | 0.64 | 0.81 | 46 | TYR |
| 5 | 476 | 0.63 | 0.77 | 45 | empty |
Interfaces
4 interfaces between chains.
- A–C · 389 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 343 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 343 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 149 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6AGM · Molecular basis for feedback inhibition of tyrosine-regulated… · the same entry in another collection · chain D against D, TM-score 1.00
- P00888 · 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 0.97
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 P00888
- Elsewhere: RCSB PDB 6AGM · PDBe 6AGM · UniProt P00888
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