MolNFT v1 · #177228 · protein
W363A mutant of chitin-specific solute binding protein from vibrio harveyi in complex with chitobiose.
7EBM · Peptide ABC transporter, periplasmic peptide-binding protein: “W363A mutant of chitin-specific solute binding protein from vibrio harveyi in complex with chitobiose.”. X-ray diffraction, 4 ligands (NAG, CA, MG), 2 pockets (best…
- PDB
- 7EBM
- 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, CA, MG, CL
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide ABC transporter, periplasmic peptide-binding protein | protein | 530 | 33% helix, 19% strand | D0XC84 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.86 | 0.87 | 113 | NAG |
| 2 | 80 | 0.32 | 0.74 | 18 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7EBM · W363A mutant of Chitin-specific solute binding protein from Vibrio harveyi in complex… · 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 7EBM · PDBe 7EBM · UniProt D0XC84
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