Research workbench
Structure of the E. COLI inosine triphosphate pyrophosphatase rgdb in complex with itp
Analyse Structure of the E. COLI inosine triphosphate pyrophosphatase rgdb in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q16
- Type
- protein
- Length
- 390 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HAM1 protein homolog
- EC
- 3.6.1.19
- UniProt
- P52061
- Ligands
- ITT, NA, CA, SO4
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HAM1 protein homolog (EC 3.6.1.19) | protein | 197 | 41% helix, 23% strand | P52061 |
| B | HAM1 protein homolog (EC 3.6.1.19) | protein | 193 | 41% helix, 23% strand | P52061 |
Ligands and binding sites
- ITT · Inosine 5'-triphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 5 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.66 | 0.82 | 43 | CA, NA, ITT |
| 2 | 324 | 0.63 | 0.79 | 39 | empty |
| 3 | 243 | 0.63 | 0.82 | 42 | CA, NA, ITT |
Interfaces
1 interface between chains.
- A–B · 664 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 2Q16 · Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP · the same entry in another collection · chain A against A, TM-score 1.00
- P52061 · AlphaFold monomer V2.0 prediction for DITP/XTP pyrophosphatase (P52061) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P52061
- Elsewhere: RCSB PDB 2Q16 · PDBe 2Q16 · UniProt P52061
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