Research workbench
Structure of human NOT1 MIF4G domain co-crystallized with CAF1
Analyse Structure of human NOT1 MIF4G domain co-crystallized with CAF1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GMJ
- Type
- protein
- Length
- 1,466 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CCR4-not transcription complex subunit 1; CCR4-not transcription complex subunit 7
- UniProt
- A5YKK6, Q9UIV1
- Ligands
- MG, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | CCR4-not transcription complex subunit 1 | protein | 229 | 68% helix, 0% strand | A5YKK6 |
| B | CCR4-not transcription complex subunit 7 | protein | 264 | 43% helix, 12% strand | Q9UIV1 |
| C | CCR4-not transcription complex subunit 1 | protein | 225 | 68% helix, 0% strand | A5YKK6 |
| D | CCR4-not transcription complex subunit 7 | protein | 259 | 41% helix, 13% strand | Q9UIV1 |
| F | CCR4-not transcription complex subunit 7 | protein | 260 | 43% helix, 12% strand | Q9UIV1 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains B, D, F
- CL · Chloride ion · ion · 3 copies · chains B, D, F
- GOL · Glycerol · additive · 3 copies · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.76 | 0.79 | 97 | GOL |
| 2 | 214 | 0.64 | 0.83 | 30 | MG, GOL |
| 3 | 170 | 0.64 | 0.85 | 28 | GOL |
| 4 | 420 | 0.63 | 0.77 | 48 | empty |
| 5 | 204 | 0.58 | 0.80 | 25 | empty |
Interfaces
5 interfaces between chains.
- C–D · 767 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 759 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 758 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 512 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 468 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4GMJ · Structure of human NOT1 MIF4G domain co-crystallized with CAF1 · 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 0.99
- Q9UIV1 · AlphaFold monomer V2.0 prediction for CCR4-not transcription complex subunit 7 (Q9UIV1) · a predicted model of the same protein · chain F 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
- Every structure of UniProt Q9UIV1
- Elsewhere: RCSB PDB 4GMJ · PDBe 4GMJ · UniProt A5YKK6 · UniProt Q9UIV1
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