MolNFT v1 · #7562 · protein
Crystal structure of the ADP-ribose pyrophosphatase in complex with GD+3
1GA7 · Hypothetical 23.7 kda protein in icc-tolc intergenic region: “Crystal structure of the ADP-ribose pyrophosphatase in complex with GD+3”. X-ray diffraction, 1 ligand (GD3), 4 pockets (best druggability 0.72). MolNFT v1 #7562 on…
- PDB
- 1GA7
- Type
- protein
- Length
- 406 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical 23.7 kda protein in icc-tolc intergenic region
- EC
- 3.6.1.13
- UniProt
- Q93K97
- Ligands
- GD3
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical 23.7 kda protein in icc-tolc intergenic region (EC 3.6.1.13) | protein | 204 | 26% helix, 39% strand | Q93K97 |
| B | Hypothetical 23.7 kda protein in icc-tolc intergenic region (EC 3.6.1.13) | protein | 202 | 26% helix, 36% strand | Q93K97 |
Ligands and binding sites
- GD3 · Gadolinium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.72 | 0.86 | 39 | GD3 |
| 2 | 347 | 0.69 | 0.82 | 51 | empty |
| 3 | 58 | 0.46 | 0.84 | 15 | empty |
| 4 | 60 | 0.32 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 4003 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 1GA7 · Crystal structure of the ADP-ribose pyrophosphatase in complex with GD+3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q93K97 · AlphaFold monomer V2.0 prediction for ADP-ribose pyrophosphatase (Q93K97) · a predicted model of the same protein · chain B 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 Q93K97
- Elsewhere: RCSB PDB 1GA7 · PDBe 1GA7 · UniProt Q93K97
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