MolNFT v1 · #80621 · protein + RNA
Eal domain of phosphodiesterase pdea in complex with 5'-pgpg and mg++
3U2E · Ggdef family protein: “Eal domain of phosphodiesterase pdea in complex with 5'-pgpg and mg++”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.41). MolNFT v1 #80621 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3U2E
- Type
- protein + RNA
- Length
- 519 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ggdef family protein; RNA (5'-R(P*GP*G)-3')
- UniProt
- Q9A310
- Ligands
- MG
- Pockets
- 2 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ggdef family protein | protein | 260 | 45% helix, 22% strand | Q9A310 |
| B | Ggdef family protein | protein | 255 | 45% helix, 22% strand | Q9A310 |
| C, D | RNA (5'-R(P*GP*G)-3') | rna | 2 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.41 | 0.80 | 22 | empty |
| 2 | 74 | 0.39 | 0.79 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 902 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 565 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–C · 564 Ų buried · 22 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3U2E · EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++ · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9A310
- Elsewhere: RCSB PDB 3U2E · PDBe 3U2E · UniProt Q9A310
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