Research workbench
E. coli dihydropteroate synthase complexed with 6-methylamino-5-nitrosoisocytosine
Analyse E. coli dihydropteroate synthase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U0V
- Type
- protein
- Length
- 506 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
- Molecule
- Dihydropteroate synthase
- EC
- 2.5.1.15
- UniProt
- P0AC14
- Ligands
- 7VJ, NA
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · resolution 1.7 · 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 | P0AC14 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 249 | 51% helix, 18% strand | P0AC14 |
Ligands and binding sites
- 7VJ · 2-amino-6-(methylamino)-5-nitrosopyrimidin-4(3H)-one · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- ACY · Acetic acid · additive · chains B
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 | 234 | 0.58 | 0.79 | 33 | 7VJ |
| 2 | 161 | 0.53 | 0.80 | 32 | 7VJ |
| 3 | 71 | 0.46 | 0.83 | 19 | empty |
| 4 | 69 | 0.36 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1147 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5U0V · E. COLI dihydropteroate synthase complexed with 6-methylamino-5- nitrosoisocytosine · the same entry in another collection · chain A against A, TM-score 1.00
- P0AC14 · AlphaFold monomer V2.0 prediction for dihydropteroate synthase (P0AC14) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P0AC14
- Elsewhere: RCSB PDB 5U0V · PDBe 5U0V · UniProt P0AC14
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