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Crystal structure of human NOT1 MIF4G domain

Analyse Crystal structure of human NOT1 MIF4G domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GML
Type: protein
Length: 1,385 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CCR4-not transcription complex subunit 1
UniProt: A5YKK6
Pockets: 14 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 66% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	CCR4-not transcription complex subunit 1	protein	235	66% helix, 0% strand	A5YKK6
C	CCR4-not transcription complex subunit 1	protein	223	67% helix, 0% strand	A5YKK6
D, F	CCR4-not transcription complex subunit 1	protein	233	65% helix, 0% strand	A5YKK6
E	CCR4-not transcription complex subunit 1	protein	226	66% helix, 0% strand	A5YKK6

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1056	0.81	0.82	96	empty
2	1110	0.80	0.81	83	empty
3	444	0.66	0.78	64	empty
4	548	0.64	0.75	50	empty
5	239	0.61	0.80	32	empty

Interfaces

8 interfaces between chains.

B–F · 1460 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1005 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 958 Å² buried · 9 hydrogen bonds · protein-protein
C–E · 813 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 404 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4GML · Crystal structure of human NOT1 MIF4G domain · the same entry in another collection · chain F against F, TM-score 1.00
A5YKK6 · AlphaFold monomer V2.0 prediction for CCR4-not transcription complex subunit 1 (A5YKK6) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 A5YKK6
Elsewhere: RCSB PDB 4GML · PDBe 4GML · UniProt A5YKK6

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