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Crystal structure of the intramolecular trans-sialidase from ruminococcus gnavus in complex with siastatin B

Analyse Crystal structure of the intramolecular trans-sialidase from ruminococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4X6K
Type: protein
Length: 485 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anhydrosialidase
UniProt: V8BWT1
Ligands: ACE, 3XR
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Anhydrosialidase	protein	485	4% helix, 44% strand	V8BWT1

Ligands and binding sites

ACE · Acetyl group · ligand · chains A
3XR · (2S,3R,4S,5S)-2-(acetylamino)-5-carboxy-3,4-dihydroxypiperidinium · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	270	0.64	0.81	37	empty
2	240	0.60	0.80	31	3XR
3	162	0.43	0.74	29	ACE
4	50	0.24	0.73	17	empty

Compared structures

4X6K · Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt V8BWT1
Elsewhere: RCSB PDB 4X6K · PDBe 4X6K · UniProt V8BWT1

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