Research workbench
S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with ampcpp and inhibitor at 1.95 ångström resolution
Analyse S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ETS
- 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
- EC
- 2.7.6.3
- UniProt
- A0A0H1ZSM1
- Ligands
- APC, 5RX, MG, NA
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (EC 2.7.6.3) | protein | 157 | 29% helix, 31% strand | A0A0H1ZSM1 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains B, A
- 5RX · 2-azanyl-8-[(4-chlorophenyl)methylsulfanyl]-1,9-dihydropurin-6-one · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 4 copies · chains B, A
- NA · Sodium ion · metal · 3 copies · chains B, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.79 | 0.81 | 98 | APC, 5RX, MG |
| 2 | 260 | 0.55 | 0.77 | 40 | empty |
Interfaces
1 interface between chains.
- B–A · 972 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5ETS · S. aureus 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with AMPCPP and… · the same entry in another collection · chain B against B, 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 5ETS · PDBe 5ETS · UniProt A0A0H1ZSM1
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