MolNFT v1 · #63189 · protein + DNA
Crystal structure of zalpha in complex with D(CGGCCG)
3F23 · Double-stranded RNA-specific adenosine deaminase: “Crystal structure of zalpha in complex with D(CGGCCG)”. X-ray diffraction, 2 pockets (best druggability 0.51). MolNFT v1 #63189 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3F23
- Type
- protein + DNA
- Length
- 211 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Double-stranded RNA-specific adenosine deaminase; DNA…
- EC
- 3.5.4.-
- UniProt
- P55265
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-) | protein | 65 | 58% helix, 14% strand | P55265 |
| B | Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-) | protein | 62 | 44% helix, 13% strand | P55265 |
| C | Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-) | protein | 66 | 56% helix, 11% strand | P55265 |
| D, E, F | DNA (5'-D(*DTP*DCP*DGP*DGP*DCP*DCP*DG)-3') | dna | 6 | — | — |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.51 | 0.74 | 22 | empty |
| 2 | 190 | 0.50 | 0.77 | 24 | empty |
Interfaces
7 interfaces between chains.
- C–F · 426 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–E · 406 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 391 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–E · 379 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- B–C · 183 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3F23 · Crystal structure of Zalpha in complex with d(CGGCCG) · the same entry in another collection · chain F against F, TM-score 1.00
- P55265 · AlphaFold monomer V2.0 prediction for double-stranded RNA-specific adenosine deaminase… · a predicted model of the same protein · chain A 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 P55265
- Elsewhere: RCSB PDB 3F23 · PDBe 3F23 · UniProt P55265
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