MolNFT v1 · #66647 · protein
Crystal structure of the second phr domain of mouse myc-binding protein 2 (mycbp-2)
3HWJ · E3 ubiquitin-protein ligase MYCBP2: “Crystal structure of the second phr domain of mouse myc-binding protein 2 (mycbp-2)”. X-ray diffraction, 2 pockets (best druggability 0.60). MolNFT v1 #66647 on GenesisL1: 3D structure, binding…
- PDB
- 3HWJ
- Type
- protein
- Length
- 299 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MYCBP2
- EC
- 6.3.2.-
- UniProt
- Q7TPH6
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MYCBP2 (EC 6.3.2.-) | protein | 149 | 2% helix, 53% strand | Q7TPH6 |
| B | E3 ubiquitin-protein ligase MYCBP2 (EC 6.3.2.-) | protein | 150 | 2% helix, 52% strand | Q7TPH6 |
Ligands and binding sites
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.60 | 0.78 | 35 | empty |
| 2 | 271 | 0.56 | 0.77 | 33 | DMS |
Interfaces
1 interface between chains.
- A–B · 450 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, engineered).
Compared structures
- 3HWJ · Crystal structure of the second PHR domain of Mouse Myc-binding protein 2 (MYCBP-2) · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7TPH6
- Elsewhere: RCSB PDB 3HWJ · PDBe 3HWJ · UniProt Q7TPH6
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