Research workbench
3'-end specific recognition of histone mRNA stem-loop by 3'- exonuclease
Analyse 3'-end specific recognition of histone mRNA stem-loop by 3'- exonuclease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZBH
- Type
- protein + RNA
- Length
- 1,060 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*CP*GP*GP*CP*UP*CP*UP*UP*UP*UP*CP*AP*GP*AP*GP*CP*CP *GP*G)-3'; 3'-5' exonuclease…
- EC
- 3.1.-.-
- UniProt
- Q8IV48
- Ligands
- AMP, MG
- Pockets
- 18 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, E | 5'-R(*CP*CP*GP*GP*CP*UP*CP*UP*UP*UP*UP*CP*AP*GP*AP*GP*CP*CP *GP*G)-3' | rna | 16 | — | — |
| A, D | 3'-5' exonuclease ERI1 (EC 3.1.-.-) | protein | 289 | 44% helix, 17% strand | Q8IV48 |
| B, C | 3'-5' exonuclease ERI1 (EC 3.1.-.-) | protein | 225 | 35% helix, 20% strand | Q8IV48 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.67 | 0.76 | 63 | empty |
| 2 | 353 | 0.64 | 0.80 | 37 | empty |
| 3 | 439 | 0.62 | 0.76 | 49 | empty |
| 4 | 305 | 0.57 | 0.77 | 34 | empty |
| 5 | 291 | 0.57 | 0.78 | 32 | empty |
Interfaces
8 interfaces between chains.
- A–D · 1091 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 802 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 651 Ų buried · 11 hydrogen bonds · protein-protein
- E–A · 507 Ų buried · 7 hydrogen bonds · protein-nucleic
- F–D · 487 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 1ZBH · 3'-end specific recognition of histone mRNA stem-loop by 3'-exonuclease · the same entry in another collection · chain D against D, TM-score 1.00
- Q8IV48 · AlphaFold monomer V2.0 prediction for 3'-5' exoribonuclease 1 (Q8IV48) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q8IV48
- Elsewhere: RCSB PDB 1ZBH · PDBe 1ZBH · UniProt Q8IV48
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.