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Crystal structure of dihydropteroate synthase from mycobacterium smegmatis with bound 6-hydroxymethylpterin-monophosphate
Analyse Crystal structure of dihydropteroate synthase from mycobacterium smegmatis with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OMZ
- Type
- protein
- Length
- 274 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropteroate synthase
- EC
- 2.5.1.15
- UniProt
- A0A2U9PYL8
- Ligands
- PMM
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 274 | 46% helix, 13% strand | A0A2U9PYL8 |
Ligands and binding sites
- PMM · Pterin-6-yl-methyl-monophosphate · ligand · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A
- CIT · Citric acid · additive · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.69 | 0.81 | 53 | CIT, PMM |
| 2 | 143 | 0.42 | 0.75 | 22 | DMS |
| 3 | 80 | 0.40 | 0.79 | 21 | EDO |
Compared structures
- 6OMZ · Crystal Structure of Dihydropteroate synthase from Mycobacterium smegmatis 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 A0A2U9PYL8
- Elsewhere: RCSB PDB 6OMZ · PDBe 6OMZ · UniProt A0A2U9PYL8
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