MolNFT v1 · #186611 · protein
Crystal structure of human bromodomain containing protein 3 (BRD3) in complex with shmt
7RJL · Bromodomain-containing protein 3: “Crystal structure of human bromodomain containing protein 3 (BRD3) in complex with shmt”. X-ray diffraction, 1 ligand (ALY), 3 pockets (best druggability 0.66). MolNFT v1 #186611 on GenesisL1: 3D…
- PDB
- 7RJL
- Type
- protein
- Length
- 241 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 3; Serine hydroxymethyltransferase, cytosolic
- EC
- 2.1.2.1
- UniProt
- Q15059, P34896
- Ligands
- ALY
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 3 | protein | 122 | 55% helix, 0% strand | Q15059 |
| B | Bromodomain-containing protein 3 | protein | 113 | 59% helix, 0% strand | Q15059 |
| C | Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) | protein | 6 | 0% helix, 0% strand | P34896 |
Ligands and binding sites
- ALY · N(6)-acetyllysine · ligand · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.66 | 0.81 | 37 | EDO |
| 2 | 107 | 0.51 | 0.81 | 18 | ALY |
| 3 | 72 | 0.37 | 0.77 | 20 | EDO |
Interfaces
2 interfaces between chains.
- A–B · 936 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 582 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (acetylation).
Compared structures
- 7RJL · Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with SHMT · the same entry in another collection · chain A against A, TM-score 1.00
- Q15059 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 3 (Q15059) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P34896 · AlphaFold monomer V2.0 prediction for serine hydroxymethyltransferase, cytosolic (P34896) · a predicted model of the same protein · chain C against A, TM-score 0.62
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 Q15059
- Every structure of UniProt P34896
- Elsewhere: RCSB PDB 7RJL · PDBe 7RJL · UniProt Q15059 · UniProt P34896
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