MolNFT v1 · #24839 · protein
Crystal structure of vibrio proteolyticus chitobiose phosphorylase in complex with glcnac and sulfate
1V7X: “Crystal structure of vibrio proteolyticus chitobiose phosphorylase in complex with glcnac and sulfate”. X-ray diffraction, 4 ligands (NDG, NAG, CA), 5 pockets (best druggability 0.66). MolNFT v1 #24839 on GenesisL1: 3D structure…
- PDB
- 1V7X
- Type
- protein
- Length
- 779 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitobiose phosphorylase
- EC
- 2.4.1.-
- UniProt
- Q76IQ9
- Ligands
- NDG, NAG, CA, SO4
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitobiose phosphorylase (EC 2.4.1.-) | protein | 779 | 31% helix, 29% strand | Q76IQ9 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.66 | 0.84 | 32 | NDG, NAG, SO4 |
| 2 | 95 | 0.63 | 0.89 | 21 | empty |
| 3 | 198 | 0.56 | 0.79 | 32 | empty |
| 4 | 189 | 0.50 | 0.77 | 29 | empty |
| 5 | 57 | 0.33 | 0.77 | 15 | empty |
Compared structures
- 1V7X · Crystal structure of Vibrio proteolyticus chitobiose phosphorylase in complex with GlcNAc… · the same entry in another collection · chain A against A, TM-score 1.00
- Q76IQ9 · AlphaFold monomer V2.0 prediction for N,N'-diacetylchitobiose phosphorylase (Q76IQ9) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q76IQ9
- Elsewhere: RCSB PDB 1V7X · PDBe 1V7X · UniProt Q76IQ9
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