MolNFT v1 · #153882 · protein

Crystal structure of TCCGT1 in complex with udp

6JTD · C-glycosyltransferase: “Crystal structure of TCCGT1 in complex with udp”. X-ray diffraction, 1 ligand (UDP), 11 pockets (best druggability 0.83). MolNFT v1 #153882 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6JTD
Type: protein
Length: 948 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-glycosyltransferase
Ligands: UDP
Pockets: 11 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	C-glycosyltransferase	protein	477	45% helix, 14% strand	—
B	C-glycosyltransferase	protein	471	46% helix, 13% strand	—

Ligands and binding sites

UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 60 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	407	0.83	0.91	55	UDP, EDO
2	1025	0.82	0.83	111	UDP, EDO
3	576	0.72	0.80	51	EDO
4	337	0.57	0.75	44	EDO
5	92	0.47	0.80	17	EDO

Interfaces

1 interface between chains.

A–B · 892 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6JTD · Crystal structure of TcCGT1 in complex with UDP · 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
Elsewhere: RCSB PDB 6JTD · PDBe 6JTD

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