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Crystal structure of the px domain of human sorting nexin 3

Analyse Crystal structure of the px domain of human sorting nexin 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YPS
Type: protein
Length: 408 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sorting nexin-3
UniProt: O60493
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 46% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sorting nexin-3	protein	107	44% helix, 18% strand	O60493
B	Sorting nexin-3	protein	102	47% helix, 21% strand	O60493
C	Sorting nexin-3	protein	98	47% helix, 21% strand	O60493
D	Sorting nexin-3	protein	101	46% helix, 21% strand	O60493

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	846	0.65	0.73	71	empty
2	104	0.39	0.76	20	empty
3	51	0.36	0.80	14	empty

Interfaces

4 interfaces between chains.

A–B · 637 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 527 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 479 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 477 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

2YPS · Crystal structure of the PX domain of human sorting nexin 3 · the same entry in another collection · chain D against D, TM-score 1.00
O60493 · AlphaFold monomer V2.0 prediction for sorting nexin-3 (O60493) · a predicted model of the same protein · chain C against A, TM-score 0.94

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 O60493
Elsewhere: RCSB PDB 2YPS · PDBe 2YPS · UniProt O60493

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