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Crystal structure of dihydropteroate synthase from anaplasma phagocytophilum with bound 6-hydroxymethylpterin-monophosphate
Analyse Crystal structure of dihydropteroate synthase from anaplasma phagocytophilum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UCZ
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropteroate synthase
- EC
- 2.5.1.15
- UniProt
- S5PWL8
- Ligands
- PMM, NA
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 254 | 46% helix, 15% strand | S5PWL8 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 265 | 49% helix, 14% strand | S5PWL8 |
Ligands and binding sites
- PMM · Pterin-6-yl-methyl-monophosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 5 copies · chains A, B
- CIT · Citric acid · additive · chains A
- ACT · Acetate ion · additive · chains A
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.69 | 0.76 | 84 | PMM, NA |
| 2 | 433 | 0.62 | 0.77 | 52 | empty |
| 3 | 251 | 0.61 | 0.80 | 34 | PMM, CIT |
Interfaces
1 interface between chains.
- A–B · 534 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6UCZ · Crystal structure of dihydropteroate synthase from Anaplasma phagocytophilum with bound… · 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
- Every structure of UniProt S5PWL8
- Elsewhere: RCSB PDB 6UCZ · PDBe 6UCZ · UniProt S5PWL8
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