MolNFT v1 · #85766 · protein

Crystal structure of the glycosyltransferase snogd from streptomyces nogalater

4AMB: “Crystal structure of the glycosyltransferase snogd from streptomyces nogalater”. X-ray diffraction, 1 ligand (DUD), 9 pockets (best druggability 0.77). MolNFT v1 #85766 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4AMB
Type: protein
Length: 743 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Snogd
UniProt: Q9RN61
Ligands: DUD
Pockets: 9 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Snogd	protein	370	43% helix, 15% strand	Q9RN61
B	Snogd	protein	373	43% helix, 15% strand	Q9RN61

Ligands and binding sites

DUD · Deoxyuridine-5'-diphosphate · ligand · chains B

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	341	0.77	0.88	50	empty
2	704	0.72	0.79	65	DUD
3	301	0.72	0.85	43	empty
4	599	0.71	0.79	62	empty
5	66	0.54	0.88	25	empty

Interfaces

1 interface between chains.

A–B · 1492 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

4AMB · Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater · 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 Q9RN61
Elsewhere: RCSB PDB 4AMB · PDBe 4AMB · UniProt Q9RN61

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