MolNFT v1 · #156309 · protein
N409A mutant of chitin-specific solute binding protein from vibrio harveyi co-crystalized with chitobiose
6LZT · Peptide ABC transporter, periplasmic peptide-binding protein: “N409A mutant of chitin-specific solute binding protein from vibrio harveyi co-crystalized with chitobiose”. X-ray diffraction, 3 ligands (NAG, MG, CA), 3 pockets (best…
- PDB
- 6LZT
- Type
- protein
- Length
- 530 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
- NAG, MG, CA
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide ABC transporter, periplasmic peptide-binding protein | protein | 530 | 32% helix, 19% strand | D0XC84 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.86 | 0.88 | 95 | NAG |
| 2 | 60 | 0.44 | 0.82 | 18 | empty |
| 3 | 76 | 0.37 | 0.77 | 19 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6LZT · N409A mutant of chitin-specific solute binding protein from Vibrio harveyi co-crystalized… · 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 6LZT · PDBe 6LZT · UniProt D0XC84
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