MolNFT v1 · #142123 · protein + DNA
Crystal structure of bz junction in diverse sequence
5ZU1 · Double-stranded RNA-specific adenosine deaminase: “Crystal structure of bz junction in diverse sequence”. X-ray diffraction, 4 pockets (best druggability 0.69). MolNFT v1 #142123 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5ZU1
- Type
- protein + DNA
- Length
- 262 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Double-stranded RNA-specific adenosine deaminase; DNA (5'…
- EC
- 3.5.4.37
- UniProt
- P55265
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.37) | protein | 63 | 54% helix, 11% strand | P55265 |
| B | Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.37) | protein | 60 | 55% helix, 10% strand | P55265 |
| C | Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.37) | protein | 61 | 54% helix, 13% strand | P55265 |
| D | Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.37) | protein | 47 | 49% helix, 13% strand | P55265 |
| E | DNA (5'- D(*GP*TP*CP*GP*CP*GP*CP*GP*CP*CP*TP*TP*AP*AP*AP*CP*C)-3') | dna | 17 | — | — |
| F | DNA (5'- D(*AP*CP*GP*GP*TP*TP*TP*AP*AP*GP*GP*CP*GP*CP*GP*CP*G)-3') | dna | 14 | — | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.69 | 0.79 | 47 | empty |
| 2 | 417 | 0.58 | 0.75 | 28 | empty |
| 3 | 251 | 0.50 | 0.75 | 21 | empty |
| 4 | 51 | 0.24 | 0.72 | 10 | empty |
Interfaces
11 interfaces between chains.
- E–F · 712 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- A–F · 460 Ų buried · 4 hydrogen bonds · protein-nucleic
- C–E · 397 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–F · 370 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–E · 286 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 5ZU1 · Crystal Structure of BZ junction in diverse sequence · 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 0.95
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 5ZU1 · PDBe 5ZU1 · UniProt P55265
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