Research workbench
Crystal structure of glycosylated K135E PEB3
Analyse Crystal structure of glycosylated K135E PEB3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FIR
- Type
- protein
- Length
- 462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major antigenic peptide PEB3
- UniProt
- Q0PBL7
- Ligands
- B6D, NGZ
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Major antigenic peptide PEB3 | protein | 231 | 39% helix, 22% strand | Q0PBL7 |
Ligands and binding sites
- B6D · 2,4-bisacetamido-2,4,6-trideoxy-beta-D-glucopyranose · ligand · 2 copies · chains A, B
- NGZ · 2-acetamido-2-deoxy-alpha-L-glucopyranose · sugar · 2 copies
- FLC · Citrate anion · additive · 2 copies · chains A, B
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 | 99 | 0.59 | 0.88 | 25 | empty |
| 2 | 105 | 0.56 | 0.85 | 28 | FLC |
| 3 | 112 | 0.55 | 0.83 | 29 | FLC |
Interfaces
1 interface between chains.
- A–B · 1869 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3FIR · Crystal structure of Glycosylated K135E PEB3 · 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 Q0PBL7
- Elsewhere: RCSB PDB 3FIR · PDBe 3FIR · UniProt Q0PBL7
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