MolNFT v2 · #227081 · protein
Structure of penguinpox cGAMP PDE in apo and post reaction states
9BKQ: “Structure of penguinpox cGAMP PDE in apo and post reaction states”. X-ray diffraction at 2.1, 2 ligands (A1AQN, GUN), 9 pockets (best druggability 0.84). MolNFT v2 #227081 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 9BKQ
- Type
- protein
- Length
- 808 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Penguinpox virus
- Molecule
- Penguinpox cGAMP PDE
- UniProt
- A0A068EGP0
- Ligands
- A1AQN, GUN
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Penguinpox cGAMP PDE | protein | 203 | 34% helix, 26% strand | A0A068EGP0 |
| B, C | Penguinpox cGAMP PDE | protein | 201 | 33% helix, 26% strand | A0A068EGP0 |
Ligands and binding sites
- A1AQN · 9-{3-O-[(S)-thiophosphono]-alpha-L-lyxofuranosyl}-9H-purin-6-amine · ligand · 2 copies · chains A, D
- GUN · Guanine · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.84 | 0.85 | 87 | A1AQN, GUN |
| 2 | 1197 | 0.82 | 0.83 | 91 | A1AQN, GUN |
| 3 | 633 | 0.69 | 0.77 | 75 | empty |
| 4 | 649 | 0.65 | 0.75 | 68 | empty |
| 5 | 91 | 0.51 | 0.83 | 22 | empty |
Interfaces
2 interfaces between chains.
- C–D · 787 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 745 Ų buried · 11 hydrogen bonds · protein-protein
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 A0A068EGP0
- Elsewhere: RCSB PDB 9BKQ · PDBe 9BKQ · UniProt A0A068EGP0
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