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Crystal structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with HP4A, the two-substrate- mimicking inhibitor
Analyse Crystal structure of 6-hydroxymethyl-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
- 1EX8
- Type
- protein
- Length
- 158 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
- EC
- 2.7.6.3
- UniProt
- P26281
- Ligands
- A4P, MG, CL
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (EC 2.7.6.3) | protein | 158 | 28% helix, 27% strand | P26281 |
Ligands and binding sites
- A4P · 6-(adenosine tetraphosphate-methyl)-7,8-dihydropterin · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.65 | 0.80 | 38 | MG, A4P |
| 2 | 51 | 0.27 | 0.74 | 15 | empty |
Compared structures
- 1EX8 · Crystal structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P26281 · AlphaFold monomer V2.0 prediction for 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P26281
- Elsewhere: RCSB PDB 1EX8 · PDBe 1EX8 · UniProt P26281
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