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Crystal structure of the 6-hyroxymethyl-7,8-dihydropterin pyrophosphokinase dihydropteroate synthase bifunctional enzyme from francisella tularensis
Analyse Crystal structure of the 6-hyroxymethyl-7,8-dihydropterin pyrophosphokinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MCO
- Type
- protein
- Length
- 783 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine PYROPHOSPHOKINASE/DIHYDROPTEROATE…
- UniProt
- Q2A2W3
- Ligands
- PH2, APC, MG
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine PYROPHOSPHOKINASE/DIHYDROPTEROATE synthase | protein | 397 | 41% helix, 20% strand | Q2A2W3 |
| B | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine PYROPHOSPHOKINASE/DIHYDROPTEROATE synthase | protein | 386 | 42% helix, 21% strand | Q2A2W3 |
Ligands and binding sites
- PH2 · 2-amino-6-hydroxymethyl-7,8-dihydro-3H-pteridin-4-one · ligand · 4 copies · chains A, B
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.67 | 0.81 | 39 | PH2 |
| 2 | 273 | 0.64 | 0.81 | 43 | PH2, APC, MG |
| 3 | 277 | 0.62 | 0.80 | 38 | PH2 |
| 4 | 186 | 0.54 | 0.79 | 19 | empty |
| 5 | 186 | 0.51 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3MCO · Crystal Structure of the 6-hyroxymethyl-7,8-dihydropterin pyrophosphokinase… · 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 Q2A2W3
- Elsewhere: RCSB PDB 3MCO · PDBe 3MCO · UniProt Q2A2W3
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