5GW0

Crystal structure of SNX16 PX-Coiled coil

> Summary

Summary for 5GW0

Related5GW1 5GW8
DescriptorSorting nexin-16 (1 entity in total)
Functional Keywordssorting nexin, px domain, endosome sorting, protein transport
Biological sourceHomo sapiens (Human)
Cellular locationEarly endosome membrane; Peripheral membrane protein; Cytoplasmic side P57768
Total number of polymer chains6
Total molecular weight128706.4
Authors
Xu, J.,Liu, J. (deposition date: 2016-09-08, release date: 2017-09-13)
Primary citation
Xu, J.,Zhang, L.,Ye, Y.,Shan, Y.,Wan, C.,Wang, J.,Pei, D.,Shu, X.,Liu, J.
SNX16 Regulates the Recycling of E-Cadherin through a Unique Mechanism of Coordinated Membrane and Cargo Binding.
Structure, 25:1251-1263.e5, 2017
PubMed: 28712807 (PDB entries with the same primary citation)
DOI: 10.1016/j.str.2017.06.015
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (3.3 Å)
?

Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.288110.6%10.0%2.2%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5gw0
no rotation
Molmil generated image of 5gw0
rotated about x axis by 90°
Molmil generated image of 5gw0
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, C, D, E...Sorting nexin-16polymer17921451.16
UniProt (P57768)
Pfam (PF00787)
Homo sapiens (Human)

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains6
Total molecular weight128706.4
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight128706.4
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (3.3 Å)

Cell axes70.380196.78072.960
Cell angles90.00111.7590.00
SpacegroupP 1 21 1
Resolution limits19.99 - 3.30
the highest resolution shell value3.360 - 3.300
R-factor0.239
R-work0.23630
the highest resolution shell value0.371
R-free0.28800
the highest resolution shell value0.384
RMSD bond length0.009
RMSD bond angle1.381

Data Collection Statistics

Resolution limits56.77 - 3.30
the highest resolution shell value -
Number of reflections27200
Rmerge_l_obs0.087
the highest resolution shell value0.633
Completeness98.3
Redundancy3.6
the highest resolution shell value3.6

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION7.5277

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

?

Functional Information from GO Data

ChainGOidnamespacecontents
?

Functional Information from PDB Data

site_idNumber of ResiduesDetails
?

Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
?

Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
?

Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Phosphatidylinositol 3-phosphate; via amide nitrogen and carbonyl oxygen. {ECO:0000250}.
ChainResidueDetails
ATHR47

SWS_FT_FI21Phosphatidylinositol 3-phosphate. {ECO:0000250}.
ChainResidueDetails
AARG85

SWS_FT_FI31Phosphatidylinositol 3-phosphate. {ECO:0000305}.
ChainResidueDetails
AARG45

SWS_FT_FI41Phosphatidylinositol 3-phosphate; via amide nitrogen and carbonyl oxygen. {ECO:0000250}.
ChainResidueDetails
BTHR47

SWS_FT_FI51Phosphatidylinositol 3-phosphate. {ECO:0000250}.
ChainResidueDetails
BARG85

SWS_FT_FI61Phosphatidylinositol 3-phosphate. {ECO:0000305}.
ChainResidueDetails
BARG45

SWS_FT_FI71Phosphatidylinositol 3-phosphate; via amide nitrogen and carbonyl oxygen. {ECO:0000250}.
ChainResidueDetails
CTHR47

SWS_FT_FI81Phosphatidylinositol 3-phosphate. {ECO:0000250}.
ChainResidueDetails
CARG85

SWS_FT_FI91Phosphatidylinositol 3-phosphate. {ECO:0000305}.
ChainResidueDetails
CARG45

SWS_FT_FI101Phosphatidylinositol 3-phosphate; via amide nitrogen and carbonyl oxygen. {ECO:0000250}.
ChainResidueDetails
DTHR47

SWS_FT_FI111Phosphatidylinositol 3-phosphate. {ECO:0000250}.
ChainResidueDetails
DARG85

SWS_FT_FI121Phosphatidylinositol 3-phosphate. {ECO:0000305}.
ChainResidueDetails
DARG45

SWS_FT_FI131Phosphatidylinositol 3-phosphate; via amide nitrogen and carbonyl oxygen. {ECO:0000250}.
ChainResidueDetails
ETHR47

SWS_FT_FI141Phosphatidylinositol 3-phosphate. {ECO:0000250}.
ChainResidueDetails
EARG85

SWS_FT_FI151Phosphatidylinositol 3-phosphate. {ECO:0000305}.
ChainResidueDetails
EARG45

SWS_FT_FI161Phosphatidylinositol 3-phosphate; via amide nitrogen and carbonyl oxygen. {ECO:0000250}.
ChainResidueDetails
FTHR47

SWS_FT_FI171Phosphatidylinositol 3-phosphate. {ECO:0000250}.
ChainResidueDetails
FARG85

SWS_FT_FI181Phosphatidylinositol 3-phosphate. {ECO:0000305}.
ChainResidueDetails
FARG45

?

Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb5gw0.ent.gz (379.3 KB)
Display
all (no-compress)pdb5gw0.ent (1.42 MB)
header onlypdb5gw0.ent.gz (11.79 KB)
Display
PDBx/mmCIF5gw0.cif.gz (436.98 KB)
PDBMLall5gw0.xml.gz (597.28 KB)
Display
no-atom5gw0-noatom.xml.gz (35.13 KB)
Display
ext-atom5gw0-extatom.xml.gz (193.96 KB)
Display
PDBMLplusall5gw0-plus.xml.gz (598.83 KB)
Display
no-atom5gw0-plus-noatom.xml.gz (36.67 KB)
Display
add only5gw0-add.xml.gz (1.54 KB)
Display
RDF5gw0.rdf.gz (73.53 KB)
Display
Structure factorsr5gw0sf.ent.gz (1.77 MB)
Biological unit (PDB format)5gw0.pdb1.gz (124.42 KB) (A,F)
*author and software defined assembly, 2 molecule(s) (dimeric)
Display
5gw0.pdb2.gz (124 KB) (B,D)
*author and software defined assembly, 2 molecule(s) (dimeric)
Display
5gw0.pdb3.gz (126.39 KB) (C,E)
*author and software defined assembly, 2 molecule(s) (dimeric)
Display
Validation reportsPDF5gw0​_validation.pdf.gz (293.06 KB)
Display
PDF-full5gw0​_full​_validation.pdf.gz (315.29 KB)
Display
XML5gw0​_validation.xml.gz (35.94 KB)
Display
PNG5gw0​_multipercentile​_validation.png.gz (162.88 KB)
Display
SVG5gw0​_multipercentile​_validation.svg.gz (940 B)
Display
Sequence (fasta)5gw0​_seq.txt
Display

PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2017 Protein Data Bank Japan