MolNFT v1 · #118170 · protein
S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with ampcpp and inhibitor at 1.72 ångström resolution
5ETV · 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine…: “S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with ampcpp and inhibitor at 1.72…”. X-ray diffraction, 4 ligands (APC, 5RZ, MG), 1 pocket (best…
- PDB
- 5ETV
- Type
- protein
- Length
- 158 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
- EC
- 2.7.6.3
- UniProt
- A0A0H1ZSM1
- Ligands
- APC, 5RZ, MG, NO3
- Pockets
- 1 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (EC 2.7.6.3) | protein | 158 | 29% helix, 30% strand | A0A0H1ZSM1 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A
- 5RZ · 2-azanyl-8-[2-(4-bromophenyl)-2-oxidanylidene-ethyl]sulfanyl-1,9-dihydropurin-6-one · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- NO3 · Nitrate ion · ion · 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 | 332 | 0.65 | 0.81 | 42 | APC, 5RZ, MG |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5ETV · 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 5ETV · PDBe 5ETV · UniProt A0A0H1ZSM1
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