MolNFT v1 · #33956 · protein

Crystal structure of human glcat-S apo form

2D0J · Galactosylgalactosylxylosylprotein 3-beta…: “Crystal structure of human glcat-S apo form”. X-ray diffraction, 11 pockets (best druggability 0.69). MolNFT v1 #33956 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2D0J
Type: protein
Length: 967 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase 2
EC: 2.4.1.135
UniProt: Q9NPZ5
Pockets: 11 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase 2 (EC 2.4.1.135)	protein	242	28% helix, 23% strand	Q9NPZ5
D	Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase 2 (EC 2.4.1.135)	protein	241	28% helix, 22% strand	Q9NPZ5

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	609	0.69	0.78	46	empty
2	596	0.69	0.78	55	empty
3	472	0.67	0.79	49	empty
4	489	0.66	0.78	48	empty
5	492	0.65	0.77	49	empty

Interfaces

3 interfaces between chains.

A–B · 2324 Å² buried · 52 hydrogen bonds · protein-protein
C–D · 2269 Å² buried · 44 hydrogen bonds · protein-protein
A–D · 447 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2D0J · Crystal Structure of Human GlcAT-S Apo Form · the same entry in another collection · chain D against D, TM-score 1.00
Q9NPZ5 · AlphaFold monomer V2.0 prediction for galactosylgalactosylxylosylprotein… · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q9NPZ5
Elsewhere: RCSB PDB 2D0J · PDBe 2D0J · UniProt Q9NPZ5

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