MolNFT v1 · #82424 · protein

Crystal structure of dextranase from streptococcus mutans in complex with 4,5-epoxypentyl alpha-D-glucopyranoside

3VMP: “Crystal structure of dextranase from streptococcus mutans in complex with 4,5-epoxypentyl…”. X-ray diffraction, 2 ligands (E5G, PO4), 4 pockets (best druggability 0.62). MolNFT v1 #82424 on GenesisL1: 3D structure, binding sites and…

PDB: 3VMP
Type: protein
Length: 632 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: E5G, PO4
Pockets: 4 · best druggability 0.62

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	632	24% helix, 32% strand	F5BA50

Ligands and binding sites

E5G · 5-hydroxypentyl alpha-D-glucopyranoside · ligand · 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	336	0.62	0.78	39	E5G
2	171	0.50	0.78	18	empty
3	64	0.37	0.78	23	empty
4	80	0.36	0.76	23	empty

Compared structures

3VMP · Crystal structure of dextranase from Streptococcus mutans in complex with 4,5-epoxypentyl… · 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 3VMP · PDBe 3VMP · UniProt F5BA50

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