Research workbench
Crystal structure of zalpha in complex with D(CACGTG)
Analyse Crystal structure of zalpha in complex with D(CACGTG) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F21
- Type
- protein + DNA
- Length
- 212 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 0.54
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-) | protein | 67 | 52% helix, 13% strand | P55265 |
| B | Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-) | protein | 63 | 51% helix, 17% strand | P55265 |
| C | Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-) | protein | 64 | 58% helix, 11% strand | P55265 |
| D, E, F | DNA (5'-D(*DTP*DCP*DAP*DCP*DGP*DTP*DG)-3') | dna | 6 | — | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.54 | 0.78 | 30 | empty |
| 2 | 234 | 0.49 | 0.75 | 21 | empty |
Interfaces
7 interfaces between chains.
- B–E · 428 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–F · 407 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–D · 376 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–E · 324 Ų buried · 26 hydrogen bonds · nucleic-nucleic
- B–C · 154 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3F21 · Crystal structure of Zalpha in complex with d(CACGTG) · 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 C against A, TM-score 0.96
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 3F21 · PDBe 3F21 · UniProt P55265
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