MolNFT v1 · #72709 · protein
Crystal structure of the human CNOT6L nuclease domain in complex with AMP
3NGN · CCR4-not transcription complex subunit 6-like: “Crystal structure of the human CNOT6L nuclease domain in complex with AMP”. X-ray diffraction, 1 ligand (AMP), 4 pockets (best druggability 0.59). MolNFT v1 #72709 on GenesisL1: 3D…
- PDB
- 3NGN
- Type
- protein
- Length
- 324 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CCR4-not transcription complex subunit 6-like
- EC
- 3.1.-.-
- UniProt
- Q96LI5
- Ligands
- AMP
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CCR4-not transcription complex subunit 6-like (EC 3.1.-.-) | protein | 324 | 30% helix, 31% strand | Q96LI5 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 330 | 0.59 | 0.77 | 36 | AMP |
| 2 | 144 | 0.51 | 0.79 | 25 | empty |
| 3 | 73 | 0.43 | 0.80 | 19 | empty |
| 4 | 68 | 0.33 | 0.75 | 16 | empty |
Compared structures
- 3NGN · Crystal structure of the human CNOT6L nuclease domain in complex with AMP · 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 3NGN · PDBe 3NGN · UniProt Q96LI5
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