Research workbench
The crystal structure of a periplasmic binding protein from veillonella parvula dsm 2008
Analyse The crystal structure of a periplasmic binding protein from veillonella parvula… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LJS
- Type
- protein
- Length
- 316 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic binding protein
- UniProt
- D1BQD8
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic binding protein | protein | 316 | 43% helix, 21% strand | D1BQD8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.45 | 0.79 | 14 | empty |
| 2 | 94 | 0.40 | 0.77 | 17 | empty |
| 3 | 80 | 0.34 | 0.75 | 24 | empty |
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 4LJS · The crystal structure of a periplasmic binding protein from Veillonella parvula DSM 2008 · 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 D1BQD8
- Elsewhere: RCSB PDB 4LJS · PDBe 4LJS · UniProt D1BQD8
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