Research workbench

apo form of the TPR domain of the pex5p receptor

Analyse apo form of the TPR domain of the pex5p receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2C0M
Type: protein
Length: 1,198 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.5
Source: HOMO SAPIENS
Molecule: Peroxisomal targeting signal 1 receptor
UniProt: P50542
Pockets: 12 · best druggability 0.81

Structure

x-ray diffraction · resolution 2.5 · 2 distinct chains · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Peroxisomal targeting signal 1 receptor	protein	297	70% helix, 0% strand	P50542
C, F	Peroxisomal targeting signal 1 receptor	protein	302	69% helix, 0% strand	P50542

Pockets

12 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	890	0.81	0.83	83	empty
2	1053	0.78	0.80	83	empty
3	954	0.72	0.76	85	empty
4	261	0.63	0.81	45	empty
5	290	0.62	0.80	28	empty

Interfaces

5 interfaces between chains.

B–C · 923 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 537 Å² buried · 8 hydrogen bonds · protein-protein
C–F · 413 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 335 Å² buried · 8 hydrogen bonds · protein-protein
B–F · 31 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2C0M · Apo form of the tpr domain of the PEX5P receptor · the same entry in another collection · chain A against A, TM-score 1.00
P50542 · AlphaFold monomer V2.0 prediction for peroxisomal targeting signal 1 receptor (P50542) · a predicted model of the same protein · chain A against A, TM-score 0.88

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 P50542
Elsewhere: RCSB PDB 2C0M · PDBe 2C0M · UniProt P50542

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