MolNFT v1 · #11574 · protein

Crystal structure of PEX13P(301-386) SH3 domain

1JQQ · Peroxisomal membrane protein PAS20: “Crystal structure of PEX13P(301-386) SH3 domain”. X-ray diffraction, 3 pockets (best druggability 0.71). MolNFT v1 #11574 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1JQQ
Type: protein
Length: 304 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxisomal membrane protein PAS20
UniProt: P80667
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxisomal membrane protein PAS20	protein	79	4% helix, 43% strand	P80667
B	Peroxisomal membrane protein PAS20	protein	82	7% helix, 44% strand	P80667
C	Peroxisomal membrane protein PAS20	protein	70	4% helix, 46% strand	P80667
D	Peroxisomal membrane protein PAS20	protein	73	4% helix, 44% strand	P80667

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	863	0.71	0.76	78	empty
2	68	0.32	0.75	16	empty
3	52	0.25	0.73	10	empty

Interfaces

6 interfaces between chains.

A–B · 318 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 273 Å² buried · 1 hydrogen bond · protein-protein
B–C · 270 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 167 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 45 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1JQQ · Crystal structure of Pex13p(301-386) SH3 domain · the same entry in another collection · chain D against D, TM-score 1.00
P80667 · AlphaFold monomer V2.0 prediction for peroxisomal membrane protein PAS20 (P80667) · a predicted model of the same protein · chain D against A, TM-score 0.91

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 P80667
Elsewhere: RCSB PDB 1JQQ · PDBe 1JQQ · UniProt P80667

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