MolNFT v1 · #49400 · protein
The crystal structure of the prephenate dehydratase (pdt) from staphylococcus aureus subsp. aureus MU50
2QMW: “The crystal structure of the prephenate dehydratase (pdt) from staphylococcus aureus subsp. aureus MU50”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.64). MolNFT v1 #49400 on GenesisL1: 3D structure, binding…
- PDB
- 2QMW
- Type
- protein
- Length
- 513 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prephenate dehydratase
- UniProt
- Q99SX2
- Ligands
- NA
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prephenate dehydratase | protein | 264 | 27% helix, 34% strand | Q99SX2 |
| B | Prephenate dehydratase | protein | 249 | 29% helix, 35% strand | Q99SX2 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.64 | 0.90 | 23 | EDO |
| 2 | 145 | 0.53 | 0.80 | 26 | empty |
| 3 | 83 | 0.47 | 0.81 | 14 | EDO |
| 4 | 52 | 0.34 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 368 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 2QMW · The crystal structure of the prephenate dehydratase (PDT) from Staphylococcus aureus… · the same entry in another collection · chain A against A, 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 Q99SX2
- Elsewhere: RCSB PDB 2QMW · PDBe 2QMW · UniProt Q99SX2
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