MolNFT v1 · #189433 · protein

Crystal structure of sdgb (sd peptide-binding form)

7VFN · Glycosyl transferase, group 1 family protein: “Crystal structure of sdgb (sd peptide-binding form)”. X-ray diffraction, 8 pockets (best druggability 0.75). MolNFT v1 #189433 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7VFN
Type: protein
Length: 984 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycosyl transferase, group 1 family protein; Asp-ser-asp
UniProt: A0A0H2XGN0
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycosyl transferase, group 1 family protein	protein	491	34% helix, 26% strand	A0A0H2XGN0
C	Glycosyl transferase, group 1 family protein	protein	490	34% helix, 26% strand	A0A0H2XGN0
B	Asp-ser-asp	protein	3	0% helix, 0% strand	—

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	795	0.75	0.79	89	empty
2	719	0.72	0.79	72	empty
3	478	0.66	0.78	74	empty
4	109	0.42	0.76	17	empty
5	109	0.40	0.75	17	empty

Interfaces

2 interfaces between chains.

A–C · 1498 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 249 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7VFN · Crystal structure of SdgB (SD peptide-binding form) · 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 A0A0H2XGN0
Elsewhere: RCSB PDB 7VFN · PDBe 7VFN · UniProt A0A0H2XGN0

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