MolNFT v1 · #4772 · protein
Ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from escherichia COLI with ATP and a substrate analogue.
1DY3 · 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase: “Ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from escherichia COLI with ATP and a…”. X-ray diffraction, 3 ligands (ATP, 87Y, MG), 1 pocket (best…
- PDB
- 1DY3
- Type
- protein
- Length
- 158 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase
- EC
- 2.7.6.3
- UniProt
- P26281
- Ligands
- ATP, 87Y, MG
- Pockets
- 1 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (EC 2.7.6.3) | protein | 158 | 30% helix, 27% strand | P26281 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- 87Y · 7,8-dihydro-6-hydroxymethyl-7-methyl-7-[2-phenylethyl]-pterin · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.65 | 0.80 | 45 | ATP, 87Y, MG |
Compared structures
- 1DY3 · Ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from Escherichia… · 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 1DY3 · PDBe 1DY3 · UniProt P26281
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