Research workbench
Crystal structure of an NCOR1BBD2-BCL6BTB chimera in complex with NEBULINSH3-NCOR1BBD1
Analyse Crystal structure of an NCOR1BBD2-BCL6BTB chimera in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y17
- Type
- protein
- Length
- 417 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor corepressor 1,B-cell lymphoma 6 protein; NEBULIN,NUCLEAR receptor…
- UniProt
- O75376, P41182, H0Y786
- Ligands
- NA
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor corepressor 1,B-cell lymphoma 6 protein | protein | 129 | 48% helix, 18% strand | O75376, P41182 |
| B | Nuclear receptor corepressor 1,B-cell lymphoma 6 protein | protein | 130 | 50% helix, 18% strand | O75376, P41182 |
| C | NEBULIN,NUCLEAR receptor corepressor 1 | protein | 76 | 4% helix, 42% strand | O75376, H0Y786 |
| D | NEBULIN,NUCLEAR receptor corepressor 1 | protein | 82 | 4% helix, 46% strand | O75376, H0Y786 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.33 | 0.78 | 13 | empty |
| 2 | 100 | 0.33 | 0.73 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2287 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 914 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 870 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 446 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 398 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6Y17 · Crystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with nebulinSH3-NCoR1BBD1 · the same entry in another collection · chain A against A, TM-score 1.00
- O75376 · AlphaFold monomer V2.0 prediction for nuclear receptor corepressor 1 (O75376) · a predicted model of the same protein · chain D against A, TM-score 0.33
- P41182 · AlphaFold monomer V2.0 prediction for B-cell lymphoma 6 protein (P41182) · a predicted model of the same protein · chain B against A, TM-score 0.32
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 O75376
- Every structure of UniProt P41182
- Every structure of UniProt H0Y786
- Elsewhere: RCSB PDB 6Y17 · PDBe 6Y17 · UniProt O75376 · UniProt P41182 · UniProt H0Y786
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.