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X-ray crystal structure of C-C bond-forming dtdp-D-olivose-transferase URDGT2

Analyse X-ray crystal structure of C-C bond-forming dtdp-D-olivose-transferase URDGT2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2P6P
Type: protein
Length: 758 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycosyl transferase
UniProt: Q9RPA7
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycosyl transferase	protein	382	47% helix, 14% strand	Q9RPA7
B	Glycosyl transferase	protein	376	49% helix, 16% strand	Q9RPA7

Ligands and binding sites

GOL · Glycerol · additive · 7 copies · chains B, A

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	876	0.78	0.81	82	GOL
2	234	0.68	0.84	40	GOL
3	168	0.66	0.86	31	GOL
4	196	0.65	0.84	38	empty
5	135	0.56	0.83	19	empty

Interfaces

1 interface between chains.

A–B · 1415 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

2P6P · X-ray crystal structure of C-C bond-forming dTDP-D-Olivose-transferase UrdGT2 · 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 Q9RPA7
Elsewhere: RCSB PDB 2P6P · PDBe 2P6P · UniProt Q9RPA7

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