MolNFT v1 · #87409 · protein

Structure of the not-box domain of human CNOT2

4C0F · CCR4-not transcription complex subunit 2: “Structure of the not-box domain of human CNOT2”. X-ray diffraction, 2 pockets (best druggability 0.72). MolNFT v1 #87409 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4C0F
Type: protein
Length: 411 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CCR4-not transcription complex subunit 2
UniProt: Q9NZN8
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CCR4-not transcription complex subunit 2	protein	96	30% helix, 32% strand	Q9NZN8
B	CCR4-not transcription complex subunit 2	protein	103	37% helix, 30% strand	Q9NZN8
C	CCR4-not transcription complex subunit 2	protein	112	32% helix, 28% strand	Q9NZN8
D	CCR4-not transcription complex subunit 2	protein	100	30% helix, 31% strand	Q9NZN8

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	537	0.72	0.80	50	empty
2	50	0.30	0.77	13	empty

Interfaces

6 interfaces between chains.

C–D · 2053 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1860 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 726 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 703 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 605 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4C0F · Structure of the NOT-box domain of human CNOT2 · the same entry in another collection · chain D against D, TM-score 1.00
Q9NZN8 · AlphaFold monomer V2.0 prediction for CCR4-not transcription complex subunit 2 (Q9NZN8) · a predicted model of the same protein · chain A against A, TM-score 0.77

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 Q9NZN8
Elsewhere: RCSB PDB 4C0F · PDBe 4C0F · UniProt Q9NZN8

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