Research workbench
Csl (rbp-jk) with corepressor KYOT2 bound to DNA
Analyse Csl (rbp-jk) with corepressor KYOT2 bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J2X
- Type
- protein + DNA
- Length
- 931 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Recombining binding protein suppressor of hairless; Four and a half lim domains protein…
- UniProt
- P31266, P97447
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Recombining binding protein suppressor of hairless | protein | 420 | 10% helix, 45% strand | P31266 |
| B, D | Four and a half lim domains protein 1 | protein | 15 | 0% helix, 33% strand | P97447 |
| C | Recombining binding protein suppressor of hairless | protein | 421 | 9% helix, 46% strand | P31266 |
| E, G | 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3' | dna | 15 | — | — |
| F, H | 5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3' | dna | 15 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.78 | 0.85 | 58 | empty |
| 2 | 601 | 0.77 | 0.83 | 63 | empty |
| 3 | 1086 | 0.77 | 0.79 | 100 | empty |
| 4 | 510 | 0.67 | 0.78 | 41 | empty |
| 5 | 158 | 0.57 | 0.82 | 26 | empty |
Interfaces
11 interfaces between chains.
- A–B · 970 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 897 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 619 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–G · 618 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–E · 617 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 4J2X · CSL (RBP-Jk) with corepressor KyoT2 bound to DNA · the same entry in another collection · chain H against H, TM-score 1.00
- P31266 · AlphaFold monomer V2.0 prediction for recombining binding protein suppressor of hairless… · a predicted model of the same protein · chain C against A, TM-score 0.98
- P97447 · AlphaFold monomer V2.0 prediction for four and a half lim domains protein 1 (P97447) · a predicted model of the same protein · chain B against A, TM-score 0.29
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 P31266
- Every structure of UniProt P97447
- Elsewhere: RCSB PDB 4J2X · PDBe 4J2X · UniProt P31266 · UniProt P97447
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