MolNFT v1 · #135507 · protein
E. COLI dihydropteroate synthase complexed with an 8-mercaptoguanine derivative: 2-amino-8-{[2-(4-methoxyphenyl)-2-OXOETHYL]SULFANYL}-1,7- dihydro-6H-purin-6-one
5U13: “E. COLI dihydropteroate synthase complexed with an 8-mercaptoguanine derivative…”. X-ray diffraction, 1 ligand (YH5), 4 pockets (best druggability 0.67). MolNFT v1 #135507 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5U13
- Type
- protein
- Length
- 532 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
- YH5
- Pockets
- 4 · best druggability 0.67
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 | 272 | 45% helix, 17% strand | P0AC14 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 260 | 48% helix, 16% strand | P0AC14 |
Ligands and binding sites
- YH5 · 2-amino-8-{[2-(4-methoxyphenyl)-2-oxoethyl]sulfanyl}-1,9-dihydro-6H-purin-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 | 287 | 0.67 | 0.83 | 42 | YH5 |
| 2 | 262 | 0.63 | 0.81 | 40 | YH5 |
| 3 | 85 | 0.43 | 0.80 | 19 | empty |
| 4 | 77 | 0.40 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1335 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5U13 · 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 5U13 · PDBe 5U13 · UniProt P0AC14
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