MolNFT v1 · #117002 · protein
Crystal structure of human CNOT6L in complex with neomycin
5DV4 · CCR4-not transcription complex subunit 6-like: “Crystal structure of human CNOT6L in complex with neomycin”. X-ray diffraction, 2 ligands (NMY, SO4), 4 pockets (best druggability 0.57). MolNFT v1 #117002 on GenesisL1: 3D structure…
- PDB
- 5DV4
- Type
- protein
- Length
- 344 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CCR4-not transcription complex subunit 6-like
- EC
- 3.1.13.4
- UniProt
- Q96LI5
- Ligands
- NMY, SO4
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CCR4-not transcription complex subunit 6-like (EC 3.1.13.4) | protein | 344 | 32% helix, 31% strand | Q96LI5 |
Ligands and binding sites
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 | 309 | 0.57 | 0.77 | 40 | NMY, SO4 |
| 2 | 140 | 0.55 | 0.82 | 26 | empty |
| 3 | 69 | 0.43 | 0.81 | 20 | empty |
| 4 | 61 | 0.37 | 0.79 | 19 | empty |
Compared structures
- 5DV4 · Crystal structure of human CNOT6L in complex with neomycin · 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 5DV4 · PDBe 5DV4 · UniProt Q96LI5
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