Research workbench
Crystal structure of the human CNOT6L nuclease domain in complex with POLY(A) DNA
Analyse Crystal structure of the human CNOT6L nuclease domain in complex with POLY(A)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NGO
- Type
- protein + DNA
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CCR4-not transcription complex subunit 6-like; 5'-D(*AP*AP*AP*A)-3'
- EC
- 3.1.-.-
- UniProt
- Q96LI5
- Ligands
- MG
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CCR4-not transcription complex subunit 6-like (EC 3.1.-.-) | protein | 337 | 30% helix, 31% strand | Q96LI5 |
| B | 5'-D(*AP*AP*AP*A)-3' | dna | 3 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
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 | 151 | 0.52 | 0.79 | 26 | empty |
| 2 | 70 | 0.41 | 0.79 | 19 | empty |
| 3 | 106 | 0.40 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 513 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 3NGO · Crystal structure of the human CNOT6L nuclease domain in complex with poly(A) DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q96LI5 · AlphaFold monomer V2.0 prediction for CCR4-not transcription complex subunit 6-like… · a predicted model of the same protein · chain A 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 Q96LI5
- Elsewhere: RCSB PDB 3NGO · PDBe 3NGO · UniProt Q96LI5
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