5EZL

Crystal Structure of Fab c12

> Summary

Summary for 5EZL

DescriptorFab c12
Functional Keywordsmalaria inhibitory antibody, fab, immune system, cyrpa
Biological sourceMus musculus (mouse)
Total number of polymer chains4
Total molecular weight95178.86
Authors
Favuzza, P.,Pluschke, G.,Rudolph, M.G. (deposition date: 2015-11-26, release date: 2017-01-11)
Primary citation
Favuzza, P.,Pluschke, G.,Benz, J.,Rudolph, M.G.
Crystal Structure of Fab c12
To be published,
Experimental method
X-RAY DIFFRACTION (2.43 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.237303.3%0.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

More Biological unit images

Molmil generated image of 5ezl
no rotation
Molmil generated image of 5ezl
rotated about x axis by 90°
Molmil generated image of 5ezl
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 (5ezl.pdb1.gz [143.9 KB])
Coordinate files for Biological unit (5ezl.pdb2.gz [144.51 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, HFab c12polymer22223676.52
Mus musculus (mouse)
B, LFab c12polymer21323581.12
Mus musculus (mouse)
N-ACETYL-D-GLUCOSAMINEnon-polymer221.23
waterwater18.0190

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight94515.2
Non-Polymers*Number of molecules3
Total molecular weight663.6
All*Total molecular weight95178.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.43 Å)

Cell axes101.420108.90097.400
Cell angles90.0097.7590.00
SpacegroupC 1 2 1
Resolution limits48.20 - 2.43
the highest resolution shell value -
R-factor0.1898
R-work0.18680
R-free0.24520

Data Collection Statistics

Resolution limits48.20 - 2.43
the highest resolution shell value -
Number of reflections39274
Rmerge_l_obs0.148
the highest resolution shell value1.411
Completeness99.3
Redundancy3.4
the highest resolution shell value3.5
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP7295

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
AC14binding site for Poly-Saccharide residues NAG A 301 through NAG A 302 bound to ASN A 33
ChainResidue
AASN33
AGLN96
AHOH401
AHOH422

AC23binding site for Mono-Saccharide NAG H 301 bound to ASN H 33
ChainResidue
HSER31
HASN33
HHOH424

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

site_idNumber of ResiduesDetails
NAG_5ezl_A_3014N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
ASER31-ASN33NAG: N-ACETYL-D-GLUCOSAMINE
AGLN96NAG: N-ACETYL-D-GLUCOSAMINE

NAG_5ezl_A_3021N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
AGLN96NAG: N-ACETYL-D-GLUCOSAMINE

NAG_5ezl_H_3014N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
HSER31-ASN33NAG: N-ACETYL-D-GLUCOSAMINE
HGLN96NAG: 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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