Research workbench
Crystal structure of galacto-N-BIOSE/LACTO-N-biose I phosphorylase in complex with glcnac, ethylene glycol, and nitrate
Analyse Crystal structure of galacto-N-BIOSE/LACTO-N-biose I phosphorylase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZUV
- Type
- protein
- Length
- 1,481 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lacto-N-biose phosphorylase
- EC
- 2.4.1.211
- UniProt
- Q5NU17
- Ligands
- NDG, MG, NO3
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lacto-N-biose phosphorylase (EC 2.4.1.211) | protein | 741 | 31% helix, 24% strand | Q5NU17 |
| B | Lacto-N-biose phosphorylase (EC 2.4.1.211) | protein | 740 | 30% helix, 24% strand | Q5NU17 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, B
- NO3 · Nitrate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.80 | 0.87 | 86 | MG, EDO |
| 2 | 874 | 0.79 | 0.82 | 88 | NDG, NO3, EDO |
| 3 | 437 | 0.77 | 0.86 | 46 | MG |
| 4 | 452 | 0.76 | 0.85 | 42 | MG |
| 5 | 832 | 0.73 | 0.78 | 60 | NDG |
Interfaces
1 interface between chains.
- A–B · 3440 Ų buried · 73 hydrogen bonds · protein-protein
Compared structures
- 2ZUV · Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with… · 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 Q5NU17
- Elsewhere: RCSB PDB 2ZUV · PDBe 2ZUV · UniProt Q5NU17
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.