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Structure of the RBP from lactococcal phage 1358 in complex with 2 GlcNAc molecules
Analyse Structure of the RBP from lactococcal phage 1358 in complex with 2 GlcNAc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L92
- Type
- protein
- Length
- 781 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Lactococcus phage 1358
- Molecule
- Receptor Binding Protein
- UniProt
- D3W0F1
- Ligands
- NAG, NDG, ZN
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 9% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor Binding Protein | protein | 390 | 9% helix, 42% strand | D3W0F1 |
| B | Receptor Binding Protein | protein | 391 | 9% helix, 41% strand | D3W0F1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.59 | 0.74 | 40 | empty |
| 2 | 256 | 0.53 | 0.76 | 28 | empty |
| 3 | 230 | 0.53 | 0.77 | 27 | empty |
| 4 | 186 | 0.43 | 0.73 | 23 | empty |
| 5 | 53 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 232 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4L92 · Structure of the rbp from lactococcal phage 1358 in complex with 2 glcnac molecules · 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 D3W0F1
- Elsewhere: RCSB PDB 4L92 · PDBe 4L92 · UniProt D3W0F1
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