Research workbench
Structure of mRNA stem-loop, human stem-loop binding protein and 3'HEXO ternary complex
Analyse Structure of mRNA stem-loop, human stem-loop binding protein and 3'HEXO ternary… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L8R
- Type
- protein + RNA
- Length
- 661 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone mRNA stem-loop; 3'-5' exoribonuclease 1; Histone RNA hairpin-binding protein
- EC
- 3.1.-.-
- UniProt
- Q8IV48, Q14493
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone mRNA stem-loop | rna | 26 | — | — |
| B | 3'-5' exoribonuclease 1 (EC 3.1.-.-) | protein | 276 | 42% helix, 17% strand | Q8IV48 |
| C | Histone RNA hairpin-binding protein | protein | 67 | 63% helix, 0% strand | Q14493 |
| D | Histone mRNA stem-loop | rna | 18 | — | — |
| E | 3'-5' exoribonuclease 1 (EC 3.1.-.-) | protein | 274 | 41% helix, 18% strand | Q8IV48 |
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.76 | 0.82 | 57 | empty |
| 2 | 246 | 0.63 | 0.82 | 39 | empty |
| 3 | 252 | 0.62 | 0.81 | 33 | empty |
| 4 | 292 | 0.59 | 0.78 | 39 | empty |
| 5 | 181 | 0.54 | 0.79 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1268 Ų buried · 29 hydrogen bonds · protein-nucleic
- D–E · 1172 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–C · 961 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–E · 904 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 78 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4L8R · Structure of mrna stem-loop, human stem-loop binding protein and 3'hexo ternary complex · the same entry in another collection · chain E against E, TM-score 1.00
- Q8IV48 · AlphaFold monomer V2.0 prediction for 3'-5' exoribonuclease 1 (Q8IV48) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q14493 · AlphaFold monomer V2.0 prediction for histone RNA hairpin-binding protein (Q14493) · 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 Q8IV48
- Every structure of UniProt Q14493
- Elsewhere: RCSB PDB 4L8R · PDBe 4L8R · UniProt Q8IV48 · UniProt Q14493
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