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Crystal structure of francisella tularensis hppk-dhps in complex with bisubstrate analog hppk inhibitor J1D
Analyse Crystal structure of francisella tularensis hppk-dhps in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PZV
- Type
- protein
- Length
- 413 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine PYROPHOSPHOKINASE/DIHYDROPTEROATE…
- EC
- 2.5.1.15, 2.7.6.3
- UniProt
- Q5NGA7
- Ligands
- J1D
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine PYROPHOSPHOKINASE/DIHYDROPTEROATE synthase (EC 2.5.1.15, 2.7.6.3) | protein | 413 | 42% helix, 20% strand | Q5NGA7 |
Ligands and binding sites
- J1D · 5'-{[2-({N-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)carbonyl]glycyl}amino)ethyl]sulfonyl}-5'-deoxyadenosine · ligand · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.62 | 0.79 | 38 | J1D |
| 2 | 166 | 0.59 | 0.83 | 28 | EDO |
| 3 | 211 | 0.53 | 0.77 | 18 | empty |
| 4 | 77 | 0.37 | 0.77 | 10 | empty |
Compared structures
- 4PZV · Crystal structure of Francisella tularensis HPPK-DHPS in complex with bisubstrate analog… · 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 Q5NGA7
- Elsewhere: RCSB PDB 4PZV · PDBe 4PZV · UniProt Q5NGA7
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