Research workbench
The crystal structure of L-phe inhibited prephenate dehydratase from chlorobium tepidum tls
Analyse The crystal structure of L-phe inhibited prephenate dehydratase from chlorobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QMX
- Type
- protein
- Length
- 556 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prephenate dehydratase
- EC
- 4.2.1.51
- UniProt
- Q8KBW6
- Ligands
- PHE
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prephenate dehydratase (EC 4.2.1.51) | protein | 278 | 27% helix, 36% strand | Q8KBW6 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.87 | 0.88 | 72 | ACT |
| 2 | 66 | 0.72 | 0.97 | 21 | PHE |
| 3 | 63 | 0.72 | 0.98 | 22 | PHE |
| 4 | 289 | 0.60 | 0.79 | 37 | empty |
| 5 | 237 | 0.59 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1955 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 2QMX · The crystal structure of L-Phe inhibited prephenate dehydratase from Chlorobium tepidum… · the same entry in another collection · chain B against B, 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 Q8KBW6
- Elsewhere: RCSB PDB 2QMX · PDBe 2QMX · UniProt Q8KBW6
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