MolNFT v1 · #118164 · protein
E. COLI 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with ampcpp and inhibitor at 1.05 ångström resolution
5ETP · 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine…: “E. COLI 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase complexed with ampcpp and inhibitor at 1.05…”. X-ray diffraction, 5 ligands (APC, 5RZ, CA), 2 pockets (best…
- PDB
- 5ETP
- Type
- protein
- Length
- 160 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
- APC, 5RZ, CA, NA, CL
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 29% 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 | 160 | 29% helix, 27% strand | P26281 |
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
- CA · Calcium ion · metal · 4 copies · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- CL · Chloride ion · ion · 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 | 291 | 0.60 | 0.78 | 37 | APC, CA, 5RZ |
| 2 | 55 | 0.33 | 0.77 | 15 | empty |
Compared structures
- 5ETP · 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 5ETP · PDBe 5ETP · UniProt P26281
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