Research workbench
E. COLI dihydropteroate synthase complexed with an 8-mercaptoguanine derivative
Analyse E. COLI dihydropteroate synthase complexed with an 8-mercaptoguanine derivative in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U0Z
- Type
- protein
- Length
- 536 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropteroate synthase
- EC
- 2.5.1.15
- UniProt
- P0AC14
- Ligands
- 7PM
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 272 | 46% helix, 16% strand | P0AC14 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 264 | 49% helix, 17% strand | P0AC14 |
Ligands and binding sites
- 7PM · (2R)-[(2-amino-6-oxo-6,9-dihydro-1H-purin-8-yl)sulfanyl](phenyl)acetic acid · ligand · 2 copies · chains A, 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 | 321 | 0.66 | 0.81 | 45 | 7PM |
| 2 | 264 | 0.59 | 0.79 | 33 | 7PM |
| 3 | 78 | 0.38 | 0.77 | 17 | empty |
| 4 | 61 | 0.35 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1381 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5U0Z · E. coli dihydropteroate synthase complexed with an 8-mercaptoguanine derivative · 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 A against A, TM-score 0.98
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 5U0Z · PDBe 5U0Z · UniProt P0AC14
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