MolNFT v1 · #128840 · protein
Lytic transglycosylase in action
5O2N: “Lytic transglycosylase in action”. X-ray diffraction, 2 ligands (NAG, NDG), 6 pockets (best druggability 0.47). MolNFT v1 #128840 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5O2N
- Type
- protein
- Length
- 577 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transglycosylase
- EC
- 4.2.2.-
- UniProt
- A0A0Y5YPU4
- Ligands
- NAG, NDG
- Pockets
- 6 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transglycosylase (EC 4.2.2.-) | protein | 577 | 67% helix, 1% strand | A0A0Y5YPU4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
- FLC · Citrate anion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.47 | 0.76 | 28 | empty |
| 2 | 132 | 0.46 | 0.78 | 19 | empty |
| 3 | 196 | 0.43 | 0.73 | 32 | NAG |
| 4 | 87 | 0.38 | 0.76 | 19 | NDG, NAG |
| 5 | 84 | 0.36 | 0.76 | 19 | empty |
Modifications
Observed in the structure: 13 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 5O2N · Lytic transglycosylase in action · 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 A0A0Y5YPU4
- Elsewhere: RCSB PDB 5O2N · PDBe 5O2N · UniProt A0A0Y5YPU4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.