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Lytic transglycosylase in action

Analyse Lytic transglycosylase in action in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5O2O
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
Ligands: NAG
Pockets: 5 · best druggability 0.53

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

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	302	0.53	0.75	46	NAG
2	108	0.44	0.78	14	empty
3	150	0.43	0.75	24	empty
4	136	0.40	0.74	22	empty
5	57	0.30	0.76	15	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5O2O · 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 5O2O · PDBe 5O2O · UniProt A0A0Y5YPU4

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