Research workbench
Crystal structure of the bromodomain of human crebbp in complex with dimethyl sulfoxide (dmso)
Analyse Crystal structure of the bromodomain of human crebbp in complex with dimethyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P1E
- Type
- protein
- Length
- 226 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Creb-binding protein
- EC
- 2.3.1.48
- UniProt
- Q92793
- Ligands
- K, SCN
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Creb-binding protein (EC 2.3.1.48) | protein | 114 | 68% helix, 0% strand | Q92793 |
| B | Creb-binding protein (EC 2.3.1.48) | protein | 112 | 65% helix, 0% strand | Q92793 |
Ligands and binding sites
- K · Potassium ion · metal · chains B
- SCN · Thiocyanate ion · ion · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.46 | 0.81 | 15 | DMS |
| 2 | 74 | 0.42 | 0.80 | 18 | DMS |
| 3 | 82 | 0.40 | 0.78 | 17 | empty |
| 4 | 66 | 0.29 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 451 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3P1E · Crystal structure of the bromodomain of human CREBBP in complex with dimethyl sulfoxide… · the same entry in another collection · chain A against A, TM-score 1.00
- Q92793 · AlphaFold monomer V2.0 prediction for creb-binding protein (Q92793) · a predicted model of the same protein · chain B 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 Q92793
- Elsewhere: RCSB PDB 3P1E · PDBe 3P1E · UniProt Q92793
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