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A novel conformation for the tpr domain of PEX5P

Analyse A novel conformation for the tpr domain of PEX5P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2J9Q
Type: protein
Length: 569 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxisomal targeting signal 1 receptor
UniProt: P50542
Ligands: SR
Pockets: 6 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxisomal targeting signal 1 receptor	protein	300	71% helix, 0% strand	P50542
B	Peroxisomal targeting signal 1 receptor	protein	269	74% helix, 0% strand	P50542

Ligands and binding sites

SR · Strontium ion · metal · 2 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1002	0.85	0.86	98	empty
2	410	0.79	0.88	45	empty
3	191	0.50	0.77	25	empty
4	119	0.47	0.79	23	empty
5	55	0.33	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 1188 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

2J9Q · A novel conformation for the TPR domain of pex5p · 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 B against A, TM-score 0.86

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 2J9Q · PDBe 2J9Q · UniProt P50542

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