MolNFT v1 · #103774 · protein

Crystal structure of human SNX14 px domain in space group P43212

4PQP · Sorting nexin-14: “Crystal structure of human SNX14 px domain in space group P43212”. X-ray diffraction, 3 pockets (best druggability 0.78). MolNFT v1 #103774 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PQP
Type: protein
Length: 404 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sorting nexin-14
UniProt: Q9Y5W7
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sorting nexin-14	protein	102	40% helix, 20% strand	Q9Y5W7
B	Sorting nexin-14	protein	103	43% helix, 23% strand	Q9Y5W7
C	Sorting nexin-14	protein	102	39% helix, 21% strand	Q9Y5W7
D	Sorting nexin-14	protein	97	42% helix, 24% strand	Q9Y5W7

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B, C

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	878	0.78	0.81	82	GOL
2	308	0.58	0.77	35	empty
3	103	0.48	0.80	20	empty

Interfaces

6 interfaces between chains.

A–B · 404 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 313 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 304 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 290 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 208 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4PQP · Crystal structure of human SNX14 PX domain in space group P43212 · the same entry in another collection · chain D against D, TM-score 1.00
Q9Y5W7 · AlphaFold monomer V2.0 prediction for sorting nexin-14 (Q9Y5W7) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 Q9Y5W7
Elsewhere: RCSB PDB 4PQP · PDBe 4PQP · UniProt Q9Y5W7

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