Research workbench
Structure of the rbp from lactococcal phage 1358 in complex with glycerol
Analyse Structure of the rbp from lactococcal phage 1358 in complex with glycerol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L99
- Type
- protein
- Length
- 781 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor binding protein
- UniProt
- D3W0F1
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor binding protein | protein | 390 | 8% helix, 42% strand | D3W0F1 |
| B | Receptor binding protein | protein | 391 | 8% helix, 41% strand | D3W0F1 |
Ligands and binding sites
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 | 538 | 0.59 | 0.73 | 42 | empty |
| 2 | 244 | 0.54 | 0.77 | 26 | empty |
| 3 | 225 | 0.52 | 0.77 | 26 | empty |
| 4 | 172 | 0.43 | 0.74 | 20 | empty |
| 5 | 82 | 0.31 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 229 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4L99 · Structure of the RBP from lactococcal phage 1358 in complex with glycerol · 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 4L99 · PDBe 4L99 · UniProt D3W0F1
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