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Crystal structure of a ternary complex of E. COLI HPPK(V83G/DEL84-89) with mgampcpp and 6-hydroxymethyl-7,8-dihydropterin at 1.40 ångström resolution (monoclinic form)
Analyse Crystal structure of a ternary complex of E. COLI HPPK(V83G/DEL84-89) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RU1
- Type
- protein
- Length
- 295 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
- P26281
- Ligands
- APC, PH2, MG, CL
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (EC 2.7.6.3) | protein | 143 | 34% helix, 29% strand | P26281 |
| B | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (EC 2.7.6.3) | protein | 152 | 33% helix, 28% strand | P26281 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- PH2 · 2-amino-6-hydroxymethyl-7,8-dihydro-3H-pteridin-4-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.45 | 0.78 | 29 | MG, PH2 |
| 2 | 104 | 0.33 | 0.72 | 18 | empty |
| 3 | 67 | 0.31 | 0.75 | 14 | MG |
Compared structures
- 1RU1 · Crystal structure of a ternary complex of E. COLI HPPK(V83G/DEL84-89) with mgampcpp and… · the same entry in another collection · chain A against A, TM-score 1.00
- P26281 · AlphaFold monomer V2.0 prediction for 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 1RU1 · PDBe 1RU1 · UniProt P26281
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