5GW1

Crystal structure of SNX16 PX-Coiled coil in space group P212121

> Summary

Summary for 5GW1

Related5GW0 5GW8
DescriptorSorting nexin-16 (1 entity in total)
Functional Keywordssortin 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 chains8
Total molecular weight171608.53
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 (3.35 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.295131.5%9.5%4.5%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5gw1
no rotation
Molmil generated image of 5gw1
rotated about x axis by 90°
Molmil generated image of 5gw1
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-16polymer17921451.18
UniProt (P57768)
Pfam (PF00787)
Homo sapiens (Human)

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains8
Total molecular weight171608.5
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight171608.5
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (3.35 Å)

Cell axes75.670133.060215.370
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits20.00 - 3.35
the highest resolution shell value3.405 - 3.350
R-factor0.2586
R-work0.25720
the highest resolution shell value0.347
R-free0.28630
the highest resolution shell value0.441
RMSD bond length0.008
RMSD bond angle1.468

Data Collection Statistics

Resolution limits61.91 - 3.35
the highest resolution shell value -
Number of reflections32016
Rmerge_l_obs0.098
the highest resolution shell value0.704
Completeness99.7
Redundancy4.3
the highest resolution shell value4.5

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

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

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

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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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

SWS_FT_FI191Phosphatidylinositol 3-phosphate; via amide nitrogen and carbonyl oxygen. {ECO:0000250}.
ChainResidueDetails
GTHR47

SWS_FT_FI201Phosphatidylinositol 3-phosphate. {ECO:0000250}.
ChainResidueDetails
GARG85

SWS_FT_FI211Phosphatidylinositol 3-phosphate. {ECO:0000305}.
ChainResidueDetails
GARG45

SWS_FT_FI221Phosphatidylinositol 3-phosphate; via amide nitrogen and carbonyl oxygen. {ECO:0000250}.
ChainResidueDetails
HTHR47

SWS_FT_FI231Phosphatidylinositol 3-phosphate. {ECO:0000250}.
ChainResidueDetails
HARG85

SWS_FT_FI241Phosphatidylinositol 3-phosphate. {ECO:0000305}.
ChainResidueDetails
HARG45

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb5gw1.ent.gz (509.23 KB)
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all (no-compress)pdb5gw1.ent (1.91 MB)
header onlypdb5gw1.ent.gz (14.23 KB)
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PDBx/mmCIF5gw1.cif.gz (584.29 KB)
PDBMLall5gw1.xml.gz (797.16 KB)
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no-atom5gw1-noatom.xml.gz (44.54 KB)
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ext-atom5gw1-extatom.xml.gz (262.08 KB)
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PDBMLplusall5gw1-plus.xml.gz (798.86 KB)
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no-atom5gw1-plus-noatom.xml.gz (46.24 KB)
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add only5gw1-add.xml.gz (1.7 KB)
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RDF5gw1.rdf.gz (91.8 KB)
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Structure factorsr5gw1sf.ent.gz (2.02 MB)
Biological unit (PDB format)5gw1.pdb1.gz (126.19 KB) (A,B)
*author and software defined assembly, 2 molecule(s) (dimeric)
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5gw1.pdb2.gz (128.01 KB) (C,D)
*author and software defined assembly, 2 molecule(s) (dimeric)
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5gw1.pdb3.gz (127.23 KB) (E,F)
*author and software defined assembly, 2 molecule(s) (dimeric)
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5gw1.pdb4.gz (124.52 KB) (G,H)
*author and software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF5gw1​_validation.pdf.gz (307.89 KB)
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PDF-full5gw1​_full​_validation.pdf.gz (343.89 KB)
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XML5gw1​_validation.xml.gz (48.55 KB)
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PNG5gw1​_multipercentile​_validation.png.gz (158.39 KB)
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SVG5gw1​_multipercentile​_validation.svg.gz (943 B)
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Sequence (fasta)5gw1​_seq.txt
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