Research workbench
Crystal structure of a diaminohydroxyphosphoribosylaminopyrimidine deaminase/ 5-amino-6-(5-PHOSPHORIBOSYLAMINO)URACIL reductase (TM1828) from thermotoga maritima at 1.80 a resolution
Analyse Crystal structure of a diaminohydroxyphosphoribosylaminopyrimidine deaminase/… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HXV
- Type
- protein
- Length
- 349 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminohydroxyphosphoribosylaminopyrimidine deaminase/ 5…
- EC
- 3.5.4.26, 1.1.1.193
- UniProt
- Q9X2E8
- Ligands
- NDP, ZN, CL
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminohydroxyphosphoribosylaminopyrimidine deaminase/ 5- amino-6-(5-PHOSPHORIBOSYLAMINO)URACIL reductase (EC 3.5.4.26, 1.1.1.193) | protein | 349 | 29% helix, 26% strand | Q9X2E8 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.70 | 0.80 | 48 | CL, NDP, GOL |
| 2 | 166 | 0.58 | 0.82 | 32 | empty |
| 3 | 247 | 0.58 | 0.78 | 21 | GOL |
| 4 | 103 | 0.34 | 0.72 | 18 | empty |
| 5 | 54 | 0.26 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 2HXV · Crystal structure of a diaminohydroxyphosphoribosylaminopyrimidine deaminase/… · 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 Q9X2E8
- Elsewhere: RCSB PDB 2HXV · PDBe 2HXV · UniProt Q9X2E8
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