Research workbench

Structure of a PEPTIDE:N-glycanase-RAD23 complex

Analyse Structure of a PEPTIDE:N-glycanase-RAD23 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1X3Z
Type: protein
Length: 380 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide: N-glycanase; UV excision repair protein RAD23; Peptide phq-val-ala-asp-CF0
EC: 3.5.1.52
UniProt: P32628
Ligands: GLC, FRU, ZN, CF0
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide: N-glycanase (EC 3.5.1.52)	protein	320	49% helix, 19% strand	—
B	UV excision repair protein RAD23	protein	57	72% helix, 0% strand	P32628
I	Peptide phq-val-ala-asp-CF0	protein	3	0% helix, 0% strand	—

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, I
ZN · Zinc ion · metal · chains A
CF0 · Fluoromethane · ion · chains A, I

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

Pockets

5 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	356	0.71	0.83	47	empty
2	94	0.35	0.74	23	empty
3	74	0.33	0.75	17	empty
4	60	0.33	0.77	14	empty
5	50	0.28	0.75	19	empty

Interfaces

2 interfaces between chains.

A–B · 1153 Å² buried · 10 hydrogen bonds · protein-protein
A–I · 294 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1X3Z · Structure of a peptide:N-glycanase-Rad23 complex · the same entry in another collection · chain A against A, TM-score 1.00
P32628 · AlphaFold monomer V2.0 prediction for UV excision repair protein RAD23 (P32628) · a predicted model of the same protein · chain B against A, TM-score 0.71

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 P32628
Elsewhere: RCSB PDB 1X3Z · PDBe 1X3Z · UniProt P32628

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