6N5X: SNX5 PX domain

Crystal structure of the SNX5 PX domain in complex with the CI-MPR (space group P212121 - Form 1). Determined by X-ray diffraction at 2.05 Å resolution. Released 18 Sept 2019.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,482
Mol. weight: 21.71 kDa
Ligands: JEF
Released: 18 Sept 2019

Explore 6N5X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N5X contains 9 α-helices and 5 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	31-40	10	1
β-strand	45-53	9	1
β-strand	62-68	7	1
α-helix	69-80	12
α-helix	83-85	3
α-helix	90-97	8
α-helix	100-111	12
α-helix	113-115	3
α-helix	118-151	34
α-helix	156-158	3
α-helix	160-167	8
α-helix	170-172	3
β-strand	174-179	6	2
β-strand	192-197	6	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sorting nexin-5,Cation-independent mannose-6-phosphate receptor	A	protein	182	Homo sapiens	P11717 (AlphaFold model), Q9Y5X3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6N5X_1 Sorting nexin-5,Cation-independent mannose-6-phosphate receptor (chains A)
GSSVDLNVDPSLQIDIPDALSERDKVKFTVHTKTTLPTFQSPEFSVTRQHEDFVWLHDTL
IETTDYAGLIIPPAPTKPDFDGPREKMQKLGEGEGSMTKEEFAKMKQELEAEYLAVFKKT
VSSHEVFLQRLSSHPVLSKDRNFHVFLEYDQSNVSYKYSKVNKEEETDENETEWLMEEIQ
LP

Ligands and cofactors

ID	Name	Formula	Copies
JEF	O-(O-(2-aminopropyl)-O'-(2-methoxyethyl)polypropylene glycol 500)	C30 H63 N O10	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Molecular identification of a BAR domain-containing coat complex for endosomal recycling of transmembrane proteins. Simonetti, B., Paul, B., Chaudhari, K. et al. Nat Cell Biol (2019) 21:1219-1233. DOI 10.1038/s41556-019-0393-3 · PubMed

Other PDB entries of the same protein (UniProt P11717 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1GP0 1.4 Å, Human IGF2R domain 11
6Z30 1.5 Å, Human cation-independent mannose 6-phosphate/ IGF2 receptor domains 9-10
1E6F 1.75 Å, Human MIR-receptor, repeat 11
1GQB 1.8 Å, Human mir-receptor, repeat 11
1GP3 1.95 Å, Human IGF2R domain 11
1JWG 2.0 Å, VHS Domain of human GGA1 complexed with cation-independent M6PR C-terminal Peptide
6N5Y 2.26 Å, Crystal structure of the SNX5 PX domain in complex with the CI-MPR (space group P212121…
1LF8 2.3 Å, Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide
1JPL 2.4 Å, GGA3 VHS domain complexed with C-terminal peptide from cation-independent mannose…
6V02 2.46 Å, N-terminal 5 domains of CI-MPR
6P8I 2.54 Å, N-terminal 5 domains of IGFIIR
6Z31 2.56 Å, Human cation-independent mannose 6-phosphate/ IGF2 receptor domain 8

Browse structure collections

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