Research workbench
X-ray crystallographic structure of E. COLI apo-efeb
Analyse X-ray crystallographic structure of E. COLI apo-efeb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y4D
- Type
- protein
- Length
- 744 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxidase ycdb
- EC
- 1.11.1.-
- UniProt
- P31545
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxidase ycdb (EC 1.11.1.-) | protein | 372 | 28% helix, 23% strand | P31545 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 13 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.82 | 0.91 | 52 | SO4, PG4 |
| 2 | 590 | 0.81 | 0.87 | 69 | SO4, PG4 |
| 3 | 824 | 0.81 | 0.84 | 98 | GOL |
| 4 | 185 | 0.62 | 0.84 | 26 | empty |
| 5 | 309 | 0.54 | 0.75 | 33 | SO4 |
Interfaces
1 interface between chains.
- A–B · 2230 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
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 P31545
- Elsewhere: RCSB PDB 2Y4D · PDBe 2Y4D · UniProt P31545
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.