MolNFT v1 · #82423 · protein

Crystal structure of dextranase from streptococcus mutans in complex with isomaltotriose

3VMO: “Crystal structure of dextranase from streptococcus mutans in complex with isomaltotriose”. X-ray diffraction, 3 ligands (GLC, BGC, PO4), 4 pockets (best druggability 0.60). MolNFT v1 #82423 on GenesisL1: 3D structure, binding sites…

PDB: 3VMO
Type: protein
Length: 628 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dextranase
EC: 3.2.1.11
UniProt: F5BA50
Ligands: GLC, BGC, PO4
Pockets: 4 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dextranase (EC 3.2.1.11)	protein	628	24% helix, 32% strand	F5BA50

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 5 copies · chains A
BGC · beta-D-glucopyranose · sugar · chains A
PO4 · Phosphate ion · ion · 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	324	0.60	0.78	30	BGC, GLC
2	191	0.54	0.79	23	empty
3	76	0.35	0.76	22	empty
4	64	0.32	0.76	16	empty

Compared structures

3VMO · Crystal structure of dextranase from Streptococcus mutans in complex with isomaltotriose · 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 F5BA50
Elsewhere: RCSB PDB 3VMO · PDBe 3VMO · UniProt F5BA50

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