Research workbench
Structure of EDEYA2 complexed with BEF3
Analyse Structure of EDEYA2 complexed with BEF3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HB0
- Type
- protein
- Length
- 1,027 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eyes absent homolog 2 (drosophila)
- EC
- 3.1.3.48
- UniProt
- Q86U84
- Ligands
- BEF, MG
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Eyes absent homolog 2 (drosophila) (EC 3.1.3.48) | protein | 259 | 56% helix, 11% strand | Q86U84 |
| B | Eyes absent homolog 2 (drosophila) (EC 3.1.3.48) | protein | 253 | 56% helix, 10% strand | Q86U84 |
| D | Eyes absent homolog 2 (drosophila) (EC 3.1.3.48) | protein | 256 | 57% helix, 10% strand | Q86U84 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.77 | 0.80 | 61 | BEF, MG |
| 2 | 1002 | 0.77 | 0.79 | 58 | MG |
| 3 | 951 | 0.74 | 0.77 | 95 | empty |
Interfaces
4 interfaces between chains.
- B–C · 888 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 840 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 804 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 765 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3HB0 · Structure of edeya2 complexed with bef3 · 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 Q86U84
- Elsewhere: RCSB PDB 3HB0 · PDBe 3HB0 · UniProt Q86U84
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