Research workbench

X-ray crystal structure of PEX19P

Analyse X-ray crystal structure of PEX19P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2WL8
Type: protein
Length: 432 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxisomal biogenesis factor 19
UniProt: P40855
Pockets: 9 · best druggability 0.50

Structure

x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxisomal biogenesis factor 19	protein	110	73% helix, 0% strand	P40855
B	Peroxisomal biogenesis factor 19	protein	104	74% helix, 0% strand	P40855
C, D	Peroxisomal biogenesis factor 19	protein	109	73% helix, 0% strand	P40855

Pockets

9 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	113	0.50	0.80	18	empty
2	198	0.48	0.75	25	empty
3	111	0.46	0.79	17	empty
4	128	0.42	0.76	27	empty
5	129	0.42	0.75	22	empty

Interfaces

5 interfaces between chains.

A–D · 904 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 868 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 559 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 328 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 298 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2WL8 · X-ray crystal structure of Pex19p · the same entry in another collection · chain A against A, TM-score 1.00
P40855 · AlphaFold monomer V2.0 prediction for peroxisomal biogenesis factor 19 (P40855) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P40855
Elsewhere: RCSB PDB 2WL8 · PDBe 2WL8 · UniProt P40855

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