Research workbench
Crystal structure of a Z-Z junction (with hepes intercalating)
Analyse Crystal structure of a Z-Z junction (with hepes intercalating) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IRR
- Type
- protein + DNA
- Length
- 279 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
- 3 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-) | protein | 63 | 49% helix, 11% strand | P55265 |
| B, C | Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-) | protein | 62 | 53% helix, 15% strand | P55265 |
| F | DNA (5'-D(*G*TP*CP*GP*CP*GP*CP*GP*TP*CP*GP*CP*GP*CP*G)-3') | dna | 14 | — | — |
| G | DNA (5'-D(*A*CP*CP*GP*CP*GP*CP*GP*AP*CP*GP*CP*GP*CP*G)-3') | dna | 14 | — | — |
| D | Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-) | protein | 64 | 50% helix, 14% strand | P55265 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.69 | 0.76 | 61 | empty |
| 2 | 107 | 0.42 | 0.78 | 14 | empty |
| 3 | 101 | 0.32 | 0.73 | 13 | EPE |
Interfaces
8 interfaces between chains.
- F–G · 678 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- F–D · 399 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–F · 372 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–G · 361 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–G · 339 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 3IRR · Crystal Structure of a Z-Z junction (with HEPES intercalating) · the same entry in another collection · chain D against D, 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 0.97
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 3IRR · PDBe 3IRR · UniProt P55265
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