MolNFT v1 · #48694 · protein
Structure of the E. COLI inosine triphosphate pyrophosphatase rgdb in complex with itp
2Q16 · HAM1 protein homolog: “Structure of the E. COLI inosine triphosphate pyrophosphatase rgdb in complex with itp”. X-ray diffraction, 4 ligands (ITT, NA, CA), 3 pockets (best druggability 0.66). MolNFT v1 #48694 on GenesisL1: 3D…
- 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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