MolNFT v1 · #118165 · protein
S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with ampcpp and inhibitor at 1.96 ångström resolution
5ETQ · 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine…: “S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with ampcpp and inhibitor at 1.96…”. X-ray diffraction, 4 ligands (APC, YH2, MG), 2 pockets (best…
- PDB
- 5ETQ
- Type
- protein
- Length
- 314 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
- UniProt
- A0A0H1ZSM1
- Ligands
- APC, YH2, MG, NA
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase | protein | 157 | 29% helix, 31% strand | A0A0H1ZSM1 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- YH2 · 4-{[(2-amino-6-oxo-6,9-dihydro-1H-purin-8-yl)sulfanyl]methyl}benzonitrile · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.80 | 0.82 | 105 | MG, APC, YH2 |
| 2 | 262 | 0.55 | 0.77 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 1003 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5ETQ · S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and… · 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 A0A0H1ZSM1
- Elsewhere: RCSB PDB 5ETQ · PDBe 5ETQ · UniProt A0A0H1ZSM1
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