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Structure and function of a novel periplasmic chitooligosaccharide- binding protein from marine vibrio bacteria
Analyse Structure and function of a novel periplasmic chitooligosaccharide- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YQW
- Type
- protein
- Length
- 532 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide ABC transporter, periplasmic peptide-binding protein
- UniProt
- D0XC84
- Ligands
- P4G, NAG, NI
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide ABC transporter, periplasmic peptide-binding protein | protein | 532 | 32% helix, 20% strand | D0XC84 |
Ligands and binding sites
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- NI · Nickel (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.87 | 0.88 | 109 | NAG, P4G |
| 2 | 78 | 0.38 | 0.77 | 19 | empty |
| 3 | 111 | 0.37 | 0.74 | 17 | empty |
| 4 | 52 | 0.30 | 0.76 | 11 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5YQW · Structure and function of a novel periplasmic chitooligosaccharide-binding protein from… · 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 D0XC84
- Elsewhere: RCSB PDB 5YQW · PDBe 5YQW · UniProt D0XC84
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