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Crystal structure of yeast protein disulfide isomerase

Analyse Crystal structure of yeast protein disulfide isomerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2B5E
Type: protein
Length: 483 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein disulfide-isomerase
EC: 5.3.4.1
UniProt: P17967
Ligands: BA
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein disulfide-isomerase (EC 5.3.4.1)	protein	483	37% helix, 20% strand	P17967

Ligands and binding sites

BA · Barium ion · metal · chains A
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

3 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	416	0.59	0.75	48	empty
2	66	0.34	0.76	15	empty
3	51	0.32	0.77	14	empty

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2B5E · Crystal Structure of Yeast Protein Disulfide Isomerase · the same entry in another collection · chain A against A, TM-score 1.00
P17967 · AlphaFold monomer V2.0 prediction for protein disulfide-isomerase (P17967) · a predicted model of the same protein · chain A against A, TM-score 0.82

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 P17967
Elsewhere: RCSB PDB 2B5E · PDBe 2B5E · UniProt P17967

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