5H49

Crystal structure of Cbln1

> Summary

Summary for 5H49

Related5H48 5H4B 5H4C
DescriptorCerebellin-1, N-ACETYL-D-GLUCOSAMINE (3 entities in total)
Functional Keywordscbln1, c1q domain, c1q/tnf superfamily, synaptogenesis, protein binding
Biological sourceRattus norvegicus (Rat)
Cellular locationSecreted  P63182
Total number of polymer chains3
Total molecular weight61478.16
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 outliers0.3101301.5%6.4%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5h49
no rotation
Molmil generated image of 5h49
rotated about x axis by 90°
Molmil generated image of 5h49
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, CCerebellin-1polymer18420419.03
UniProt (P63182)
Pfam (PF00386)
Rattus norvegicus (Rat)Precerebellin
N-ACETYL-D-GLUCOSAMINEnon-polymer221.21
waterwater18.022

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight61257.0
Non-Polymers*Number of molecules1
Total molecular weight221.2
All*Total molecular weight61478.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.8 Å)

Cell axes91.63891.638151.046
Cell angles90.0090.0090.00
SpacegroupP 43 21 2
Resolution limits50.00 - 2.80
the highest resolution shell value2.877 - 2.804
R-factor0.27318
R-work0.27142
the highest resolution shell value0.306
R-free0.30696
the highest resolution shell value0.385
RMSD bond length0.004
RMSD bond angle1.004

Data Collection Statistics

Resolution limits50.00 - 2.80
the highest resolution shell value -
Number of reflections16418
Completeness99.8
Redundancy6.4

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP298

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
AC15binding site for Mono-Saccharide NAG A 201 bound to ASN A 79
ChainResidue
AGLU73
APRO74
AGLU76
AASN79
BSER59

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

site_idNumber of ResiduesDetails
NAG_5h49_A_2018N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
AGLU73-GLU76NAG: N-ACETYL-D-GLUCOSAMINE
AASN79NAG: N-ACETYL-D-GLUCOSAMINE
AASN175-MET177NAG: 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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