MolNFT v1 · #191321 · protein
Crystal structure of dihydropteroate synthase (folp-SMZ_B27) from soil uncultured bacterium in complex with 6-hydroxymethyl-7,8- dihydropterin
8D5H: “Crystal structure of dihydropteroate synthase (folp-SMZ_B27) from soil uncultured bacterium in complex with…”. X-ray diffraction, 3 ligands (HHR, SO4, CL), 2 pockets (best druggability 0.85). MolNFT v1 #191321 on GenesisL1: 3D…
- PDB
- 8D5H
- Type
- protein
- Length
- 541 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Folp-SMZ_B27
- Ligands
- HHR, SO4, CL
- Pockets
- 2 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Folp-SMZ_B27 | protein | 267 | 46% helix, 15% strand | — |
| B | Folp-SMZ_B27 | protein | 274 | 46% helix, 14% strand | — |
Ligands and binding sites
- HHR · 6-hydroxymethylpterin · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.85 | 0.86 | 95 | HHR, SO4 |
| 2 | 112 | 0.57 | 0.85 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 655 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 8D5H · Crystal structure of dihydropteroate synthase (folP-SMZ_B27) from soil uncultured… · 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
- Elsewhere: RCSB PDB 8D5H · PDBe 8D5H
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