Research workbench
Crystal structure of B. anthracis dhps with compound 21
Analyse Crystal structure of B. anthracis dhps with compound 21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D8A
- Type
- protein
- Length
- 515 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropteroate synthase
- EC
- 2.5.1.15
- UniProt
- C3P9L8
- Ligands
- 0HY, LYS, SO4
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 263 | 49% helix, 14% strand | C3P9L8 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 252 | 52% helix, 15% strand | C3P9L8 |
Ligands and binding sites
- 0HY · methyl (3R)-3-(7-amino-4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazin-3-yl)butanoate · ligand · 2 copies · chains A, B
- LYS · Lysine · ligand · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.48 | 0.77 | 38 | 0HY |
| 2 | 52 | 0.35 | 0.79 | 17 | 0HY |
| 3 | 68 | 0.34 | 0.77 | 14 | LYS |
Interfaces
1 interface between chains.
- A–B · 309 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4D8A · Crystal structure of B. anthracis DHPS with compound 21 · 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 C3P9L8
- Elsewhere: RCSB PDB 4D8A · PDBe 4D8A · UniProt C3P9L8
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