Research workbench
Crystal structure of the NF90-NF45 dimerisation domain complex with CTP
Analyse Crystal structure of the NF90-NF45 dimerisation domain complex with CTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ATB
- Type
- protein
- Length
- 1,291 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin enhancer-binding factor 2; Interleukin enhancer-binding factor 3
- UniProt
- Q9CXY6, Q9Z1X4
- Ligands
- CTP, MG
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin enhancer-binding factor 2 | protein | 334 | 50% helix, 14% strand | Q9CXY6 |
| B | Interleukin enhancer-binding factor 3 | protein | 319 | 52% helix, 11% strand | Q9Z1X4 |
| C | Interleukin enhancer-binding factor 2 | protein | 332 | 49% helix, 12% strand | Q9CXY6 |
| D | Interleukin enhancer-binding factor 3 | protein | 306 | 52% helix, 11% strand | Q9Z1X4 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.76 | 0.81 | 83 | empty |
| 2 | 117 | 0.60 | 0.86 | 25 | empty |
| 3 | 236 | 0.57 | 0.79 | 27 | empty |
| 4 | 283 | 0.54 | 0.76 | 32 | CTP, MG |
| 5 | 260 | 0.53 | 0.76 | 30 | MG, CTP |
Interfaces
5 interfaces between chains.
- A–B · 1751 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1708 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 266 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 144 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 93 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4ATB · Crystal structure of the NF90-NF45 dimerisation domain complex with CTP · the same entry in another collection · chain D against D, TM-score 1.00
- Q9Z1X4 · AlphaFold monomer V2.0 prediction for interleukin enhancer-binding factor 3 (Q9Z1X4) · a predicted model of the same protein · chain D against A, TM-score 1.00
- Q9CXY6 · AlphaFold monomer V2.0 prediction for interleukin enhancer-binding factor 2 (Q9CXY6) · 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 Q9CXY6
- Every structure of UniProt Q9Z1X4
- Elsewhere: RCSB PDB 4ATB · PDBe 4ATB · UniProt Q9CXY6 · UniProt Q9Z1X4
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