Research workbench
Crystal structure of the yersinia pestis dihydropteroate synthase with sulfonamide drug complex.
Analyse Crystal structure of the yersinia pestis dihydropteroate synthase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TZF
- Type
- protein
- Length
- 549 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7,8-dihydropteroate synthase
- EC
- 2.5.1.15
- UniProt
- Q7CKJ1
- Ligands
- HH2, 08D, MG
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7,8-dihydropteroate synthase (EC 2.5.1.15) | protein | 275 | 45% helix, 16% strand | Q7CKJ1 |
| B | 7,8-dihydropteroate synthase (EC 2.5.1.15) | protein | 274 | 45% helix, 16% strand | Q7CKJ1 |
Ligands and binding sites
- HH2 · 6-hydroxymethylpterin-diphosphate · ligand · 2 copies · chains A, B
- 08D · Sulfamethoxazole · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.74 | 0.91 | 33 | HH2, MG, 08D |
| 2 | 153 | 0.73 | 0.92 | 32 | HH2, MG |
| 3 | 56 | 0.32 | 0.77 | 14 | empty |
| 4 | 54 | 0.27 | 0.74 | 14 | empty |
| 5 | 57 | 0.26 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1151 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3TZF · Crystal Structure of the Yersinia pestis Dihydropteroate Synthase with Sulfonamide Drug… · 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 Q7CKJ1
- Elsewhere: RCSB PDB 3TZF · PDBe 3TZF · UniProt Q7CKJ1
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