5H4B

Crystal structure of Cbln4

> Summary

Summary for 5H4B

Related5H48 5H49 5H4C
DescriptorCerebellin-4, N-ACETYL-D-GLUCOSAMINE (3 entities in total)
Functional Keywordscbln1, cbln4, c1q domain, c1q/tnf superfamily, neurexin, receptor specificity, synaptogenesis, protein binding
Biological sourceMus musculus (Mouse)
Cellular locationSecreted Q8BME9
Total number of polymer chains1
Total molecular weight20839.55
Authors
Zhong, C.,Shen, J.,Zhang, H.,Ding, J. (deposition date: 2016-10-31, release date: 2017-09-13, Last modification date: 2017-09-20)
Primary citation
Zhong, C.,Shen, J.,Zhang, H.,Li, G.,Shen, S.,Wang, F.,Hu, K.,Cao, L.,He, Y.,Ding, J.
Cbln1 and Cbln4 are structurally similar but differ in GluD2 binding interactions
To be published,
Experimental method
X-RAY DIFFRACTION (2.8 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.220405.9%6.6%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5h4b
no rotation
Molmil generated image of 5h4b
rotated about x axis by 90°
Molmil generated image of 5h4b
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5h4b
no rotation
Molmil generated image of 5h4b
rotated about x axis by 90°
Molmil generated image of 5h4b
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5h4b.pdb1.gz [68.07 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ACerebellin-4polymer18620618.31
UniProt (Q8BME9)
Pfam (PF00386)
Mus musculus (Mouse)Cerebellin-like glycoprotein 1
N-ACETYL-D-GLUCOSAMINEnon-polymer221.21
waterwater18.023

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight20618.3
Non-Polymers*Number of molecules1
Total molecular weight221.2
All*Total molecular weight20839.6
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.8 Å)

Cell axes132.357132.357132.357
Cell angles90.0090.0090.00
SpacegroupP 43 3 2
Resolution limits50.00 - 2.80
the highest resolution shell value2.868 - 2.795
R-factor0.2085
R-work0.20724
the highest resolution shell value0.306
R-free0.23282
the highest resolution shell value0.512
RMSD bond length0.014
RMSD bond angle1.299

Data Collection Statistics

Resolution limits50.00 - 2.80
the highest resolution shell value -
Number of reflections10335
Completeness99.9
Redundancy9.3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP6.2298

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
AC13binding site for Mono-Saccharide NAG A 201 bound to ASN A 79
ChainResidue
AGLU73
AASN79
AASN174

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

site_idNumber of ResiduesDetails
NAG_5h4b_A_2017N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
AGLU73-PRO74NAG: N-ACETYL-D-GLUCOSAMINE
AGLU76NAG: N-ACETYL-D-GLUCOSAMINE
AASN79NAG: N-ACETYL-D-GLUCOSAMINE
AGLY173-ASN174NAG: N-ACETYL-D-GLUCOSAMINE
ALEU176NAG: N-ACETYL-D-GLUCOSAMINE

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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
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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