Research workbench
Crystal structure of the KAP1 RBCC domain in complex with the SMARCAD1 CUE1 domain.
Analyse Crystal structure of the KAP1 RBCC domain in complex with the SMARCAD1 CUE1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H3A
- Type
- protein
- Length
- 644 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 5.505
- Source
- Homo sapiens
- Molecule
- SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A…
- EC
- 3.6.4.12, 2.3.2.27
- UniProt
- Q9H4L7, Q13263
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · resolution 5.505 · 4 distinct chains · 57% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (EC 3.6.4.12) | protein | 53 | 70% helix, 0% strand | Q9H4L7 |
| A | Transcription intermediary factor 1-beta (EC 2.3.2.27) | protein | 266 | 56% helix, 7% strand | Q13263 |
| B | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (EC 3.6.4.12) | protein | 57 | 68% helix, 0% strand | Q9H4L7 |
| F | Transcription intermediary factor 1-beta (EC 2.3.2.27) | protein | 268 | 53% helix, 8% strand | Q13263 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.80 | 0.85 | 85 | empty |
| 2 | 516 | 0.75 | 0.83 | 59 | empty |
| 3 | 84 | 0.70 | 0.94 | 23 | empty |
| 4 | 208 | 0.69 | 0.86 | 37 | empty |
| 5 | 153 | 0.66 | 0.87 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–F · 4995 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 642 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 619 Ų buried · 3 hydrogen bonds · protein-protein
- D–A · 158 Ų buried · 0 hydrogen bonds · protein-protein
- B–F · 152 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6H3A · Crystal structure of the KAP1 rbcc domain in complex with the SMARCAD1 CUE1 domain. · the same entry in another collection · chain F against F, TM-score 1.00
- Q9H4L7 · AlphaFold monomer V2.0 prediction for SWI/SNF-related matrix- associated actin-dependent… · a predicted model of the same protein · chain D against A, TM-score 0.84
- Q13263 · AlphaFold monomer V2.0 prediction for transcription intermediary factor 1-beta (Q13263) · a predicted model of the same protein · chain F against A, TM-score 0.81
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 Q9H4L7
- Every structure of UniProt Q13263
- Elsewhere: RCSB PDB 6H3A · PDBe 6H3A · UniProt Q9H4L7 · UniProt Q13263
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