Research workbench
E. COLI 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with ampcpp and inhibitor at 1.46 ångström resolution
Analyse E. COLI 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
- 5ETM
- Type
- protein
- Length
- 159 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
- P26281
- Ligands
- 5RW, APC, CA, NA, CL
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (EC 2.7.6.3) | protein | 159 | 30% helix, 27% strand | P26281 |
Ligands and binding sites
- 5RW · 2-azanyl-8-[(4-fluorophenyl)methylsulfanyl]-1,7-dihydropurin-6-one · ligand · chains A
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · 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 | 334 | 0.63 | 0.79 | 40 | 5RW, APC, CA, CL |
| 2 | 52 | 0.30 | 0.76 | 13 | empty |
Compared structures
- 5ETM · E. coli 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 P26281
- Elsewhere: RCSB PDB 5ETM · PDBe 5ETM · UniProt P26281
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