MolNFT v1 · #176422 · protein
The structure of the arabidopsis thaliana guanosine deaminase complexed with crotonoside
7DM6: “The structure of the arabidopsis thaliana guanosine deaminase complexed with crotonoside”. X-ray diffraction, 2 ligands (H5F, ZN), 3 pockets (best druggability 0.79). MolNFT v1 #176422 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7DM6
- Type
- protein
- Length
- 314 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanosine deaminase
- EC
- 3.5.4.15
- UniProt
- Q94BU8
- Ligands
- H5F, ZN
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Guanosine deaminase (EC 3.5.4.15) | protein | 157 | 43% helix, 18% strand | Q94BU8 |
Ligands and binding sites
- H5F · 6-azanyl-9-[(2R,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1H-purin-2-one · ligand · 2 copies · chains A, D
- ZN · Zinc ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.79 | 0.97 | 24 | ZN, H5F |
| 2 | 109 | 0.77 | 0.97 | 24 | H5F |
| 3 | 103 | 0.35 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–D · 1639 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7DM6 · The structure of the Arabidopsis thaliana guanosine deaminase complexed with crotonoside · the same entry in another collection · chain A against A, TM-score 1.00
- Q94BU8 · AlphaFold monomer V2.0 prediction for guanosine deaminase (Q94BU8) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q94BU8
- Elsewhere: RCSB PDB 7DM6 · PDBe 7DM6 · UniProt Q94BU8
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