MolNFT v1 · #117502 · protein
Crystal structure of SMARCA4 bromodomain in complex with mpd
5EA1 · Transcription activator BRG1: “Crystal structure of SMARCA4 bromodomain in complex with mpd”. X-ray diffraction, 6 pockets (best druggability 0.78). MolNFT v1 #117502 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5EA1
- Type
- protein
- Length
- 361 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription activator BRG1
- EC
- 3.6.4.-
- UniProt
- P51532
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription activator BRG1 (EC 3.6.4.-) | protein | 114 | 63% helix, 2% strand | P51532 |
| B | Transcription activator BRG1 (EC 3.6.4.-) | protein | 128 | 64% helix, 2% strand | P51532 |
| C | Transcription activator BRG1 (EC 3.6.4.-) | protein | 119 | 61% helix, 2% strand | P51532 |
Ligands and binding sites
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 3 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.78 | 0.96 | 26 | MRD, MPD |
| 2 | 545 | 0.62 | 0.74 | 46 | empty |
| 3 | 61 | 0.45 | 0.82 | 14 | MRD, MPD |
| 4 | 63 | 0.44 | 0.82 | 15 | MRD, MPD |
| 5 | 202 | 0.44 | 0.73 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 808 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 325 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 70 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5EA1 · Crystal Structure of SMARCA4 bromodomain in complex with MPD · the same entry in another collection · chain A against A, TM-score 1.00
- P51532 · AlphaFold monomer V2.0 prediction for transcription activator BRG1 (P51532) · a predicted model of the same protein · chain A 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 P51532
- Elsewhere: RCSB PDB 5EA1 · PDBe 5EA1 · UniProt P51532
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