Research workbench
Structure of the rbpj-sharp-DNA repressor complex
Analyse Structure of the rbpj-sharp-DNA repressor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DKS
- Type
- protein + DNA
- Length
- 1,711 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)- 3'); DNA…
- UniProt
- P31266, P0AEY0
- Ligands
- GLC
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | DNA (5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)- 3') | dna | 15 | — | — |
| B, F | DNA (5'-D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)- 3') | dna | 15 | — | — |
| C | Recombining binding protein suppressor of hairless | protein | 417 | 7% helix, 45% strand | P31266 |
| D | MALTOSE/MALTODEXTRIN-binding periplasmic protein | protein | 407 | 41% helix, 24% strand | P0AEY0 |
| G | Recombining binding protein suppressor of hairless | protein | 422 | 8% helix, 45% strand | P31266 |
| H | MALTOSE/MALTODEXTRIN-binding periplasmic protein | protein | 405 | 41% helix, 24% strand | P0AEY0 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.75 | 0.80 | 81 | empty |
| 2 | 863 | 0.75 | 0.79 | 86 | empty |
| 3 | 249 | 0.72 | 0.86 | 30 | GLC |
| 4 | 317 | 0.70 | 0.84 | 32 | GLC |
| 5 | 62 | 0.61 | 0.91 | 22 | empty |
Interfaces
10 interfaces between chains.
- G–H · 1691 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1673 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 603 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- A–B · 602 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- A–C · 448 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 6DKS · Structure of the Rbpj-SHARP-DNA Repressor Complex · 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 0.96
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 P0AEY0
- Elsewhere: RCSB PDB 6DKS · PDBe 6DKS · UniProt P31266 · UniProt P0AEY0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.