Research workbench
Yersinia pestis dhps with pterine-sulfa conjugate compound 16
Analyse Yersinia pestis dhps with pterine-sulfa conjugate compound 16 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JQ9
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropteroate synthase
- EC
- 2.5.1.15
- UniProt
- A0A0J9WZK8
- Ligands
- 6MB
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 257 | 49% helix, 18% strand | A0A0J9WZK8 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 252 | 50% helix, 18% strand | A0A0J9WZK8 |
Ligands and binding sites
- 6MB · 4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl) methyl]amino}-N-(3,4-dimethyl-1,2-oxazol-5-yl)benzene-1-sulfonamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.70 | 0.93 | 38 | empty |
| 2 | 194 | 0.55 | 0.80 | 28 | 6MB |
| 3 | 148 | 0.54 | 0.81 | 32 | 6MB |
| 4 | 63 | 0.30 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1101 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5JQ9 · Yersinia pestis DHPS with pterine-sulfa conjugate Compound 16 · 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 A0A0J9WZK8
- Elsewhere: RCSB PDB 5JQ9 · PDBe 5JQ9 · UniProt A0A0J9WZK8
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