MolNFT v1 · #128822 · protein
Lytic transglycosylase in action
5O24: “Lytic transglycosylase in action”. X-ray diffraction, 5 pockets (best druggability 0.51). MolNFT v1 #128822 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5O24
- Type
- protein
- Length
- 576 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transglycosylase
- EC
- 4.2.2.-
- UniProt
- A0A0Y5YPU4
- Pockets
- 5 · best druggability 0.51
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 | 576 | 67% helix, 1% strand | A0A0Y5YPU4 |
Ligands and binding sites
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 3 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.51 | 0.74 | 45 | empty |
| 2 | 105 | 0.45 | 0.79 | 14 | empty |
| 3 | 155 | 0.43 | 0.75 | 26 | empty |
| 4 | 128 | 0.38 | 0.74 | 21 | empty |
| 5 | 53 | 0.30 | 0.76 | 15 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5O24 · 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 5O24 · PDBe 5O24 · UniProt A0A0Y5YPU4
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