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Human POGLUT1 in complex with EGF(+) and udp

Analyse Human POGLUT1 in complex with EGF(+) and udp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5L0T
Type: protein
Length: 396 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein O-glucosyltransferase 1; EGF(+)
EC: 2.4.1.-, 2.4.2.26
UniProt: Q8NBL1
Ligands: UDP, NAG, CA, CL
Pockets: 4 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein O-glucosyltransferase 1 (EC 2.4.1.-, 2.4.2.26)	protein	356	42% helix, 16% strand	Q8NBL1
B	EGF(+)	protein	40	10% helix, 30% strand	—

Ligands and binding sites

UDP · Uridine-5'-diphosphate · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
CA · Calcium ion · metal · 3 copies · chains A, B
CL · Chloride ion · ion · chains A, B
GOL · Glycerol · additive · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	249	0.83	0.95	35	UDP, GOL
2	85	0.40	0.78	21	empty
3	81	0.38	0.77	14	empty
4	65	0.32	0.75	18	empty

Interfaces

1 interface between chains.

A–B · 809 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

5L0T · human POGLUT1 in complex with EGF(+) and UDP · the same entry in another collection · chain A against A, TM-score 1.00
Q8NBL1 · AlphaFold monomer V2.0 prediction for protein O-glucosyltransferase 1 (Q8NBL1) · a predicted model of the same protein · 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 Q8NBL1
Elsewhere: RCSB PDB 5L0T · PDBe 5L0T · UniProt Q8NBL1

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