MolNFT v1 · #24838 · protein
Crystal structure of vibrio proteolyticus chitobiose phosphorylase in complex with glcnac
1V7W: “Crystal structure of vibrio proteolyticus chitobiose phosphorylase in complex with glcnac”. X-ray diffraction, 4 ligands (NDG, NAG, CA), 3 pockets (best druggability 0.73). MolNFT v1 #24838 on GenesisL1: 3D structure, binding sites…
- PDB
- 1V7W
- 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, CL
- Pockets
- 3 · best druggability 0.73
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 · 3 copies · chains A
- CL · Chloride ion · ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.73 | 0.83 | 55 | NDG, NAG, CL |
| 2 | 99 | 0.62 | 0.88 | 22 | empty |
| 3 | 196 | 0.51 | 0.77 | 29 | empty |
Compared structures
- 1V7W · 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 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 Q76IQ9
- Elsewhere: RCSB PDB 1V7W · PDBe 1V7W · UniProt Q76IQ9
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