MolNFT v2 · #197954 · protein

The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with methyl alpha-D-glucoside

7VL1: “The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with methyl alpha-D-glucoside”. X-ray diffraction at 1.6, 2 ligands (GYP, CA), 17 pockets (best druggability 0.82). MolNFT v2 #197954 on GenesisL1: 3D…

PDB: 7VL1
Type: protein
Length: 1,408 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.6
Source: Ignavibacterium album (strain DSM 19864 / JCM 16511 / NBRC 101810 / Mat9-16)
Molecule: beta-1,2-glucosyltransferase
UniProt: I0AIT9
Ligands: GYP, CA
Pockets: 17 · best druggability 0.82

Structure

x-ray diffraction · resolution 1.6 · 2 distinct chains · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	beta-1,2-glucosyltransferase	protein	706	35% helix, 25% strand	I0AIT9
B	beta-1,2-glucosyltransferase	protein	702	36% helix, 24% strand	I0AIT9

Ligands and binding sites

GYP · methyl alpha-D-glucopyranoside · sugar · chains A
CA · Calcium ion · metal · chains B

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

Pockets

17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1092	0.82	0.83	119	GYP
2	324	0.73	0.85	48	empty
3	357	0.66	0.80	55	empty
4	378	0.66	0.80	57	empty
5	299	0.56	0.76	42	empty

Interfaces

1 interface between chains.

A–B · 1909 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

7VL1 · The complex structure of beta-1,2-glucosyltransferase from ignavibacterium album with… · 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 I0AIT9
Elsewhere: RCSB PDB 7VL1 · PDBe 7VL1 · UniProt I0AIT9

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