MolNFT v1 · #135506 · protein
E. COLI dihydropteroate synthase complexed with an 8-mercaptoguanine derivative: 2-azanyl-8-[(2-FLUOROPHENYL)METHYLSULFANYL]-1,9- dihydropurin-6-one
5U12: “E. COLI dihydropteroate synthase complexed with an 8-mercaptoguanine derivative…”. X-ray diffraction, 1 ligand (5RU), 4 pockets (best druggability 0.64). MolNFT v1 #135506 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5U12
- Type
- protein
- Length
- 537 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
- 5RU
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 264 | 48% helix, 17% strand | P0AC14 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 273 | 46% helix, 16% strand | P0AC14 |
Ligands and binding sites
- 5RU · 2-azanyl-8-[(2-fluorophenyl)methylsulfanyl]-1,9-dihydropurin-6-one · 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 | 268 | 0.64 | 0.82 | 44 | 5RU |
| 2 | 224 | 0.59 | 0.80 | 40 | 5RU |
| 3 | 93 | 0.42 | 0.78 | 20 | empty |
| 4 | 65 | 0.35 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1341 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5U12 · 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 0.97
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 5U12 · PDBe 5U12 · UniProt P0AC14
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