5EZO

Crystal Structure of PfCyRPA in complex with an invasion-inhibitory antibody Fab.

> Summary

Summary for 5EZO

DescriptorPfCyRPA, c12 FAB, c12 Fab
Functional Keywordsmalaria inhibitory antibody, fab, immune system, cyrpa
Biological sourceHomo sapiens (Human)
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Total number of polymer chains3
Total molecular weight87180.41
Authors
Favuzza, P.,Pluschke, G.,Rudolph, M.G. (deposition date: 2015-11-26, release date: 2017-01-11, modification date: 2017-02-15)
Primary citation
Favuzza, P.,Pluschke, G.,Benz, J.,Rudolph, M.G.
Crystal Structure of PfCyRPA
To be published,
Experimental method
X-RAY DIFFRACTION (3.63 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.32990.5%7.5%1.1%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

> Structural details

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains3
Total molecular weight86573.8
Non-Polymers*Number of molecules3
Total molecular weight606.6
All*Total molecular weight87180.4
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (3.63 Å)

Cell axes95.80144.681121.336
Cell angles90.00108.0390.00
SpacegroupP 1 21 1
Resolution limits43.00 - 3.63
the highest resolution shell value -
R-factor0.2763
R-work0.27370
R-free0.33000

Data Collection Statistics

Resolution limits43.00 - 3.63
the highest resolution shell value -
Number of reflections11401
Rmerge_l_obs0.497
the highest resolution shell value2.673
Completeness99.1
Redundancy3.3
the highest resolution shell value3.3
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP7.5295

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
AC12binding site for Poly-Saccharide residues NAG H 501 through FUC H 503 bound to ASN H 37
ChainResidue
HASN37
HTYR98

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

site_idNumber of ResiduesDetails
NAG_5ezo_H_5013N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
HSER35NAG: N-ACETYL-D-GLUCOSAMINE
HASN37NAG: N-ACETYL-D-GLUCOSAMINE
HGLN100NAG: N-ACETYL-D-GLUCOSAMINE

FUC_5ezo_H_5034ALPHA-L-FUCOSE binding site
ChainResidueligand
HSER89FUC: ALPHA-L-FUCOSE
HLYS94FUC: ALPHA-L-FUCOSE
HTYR98FUC: ALPHA-L-FUCOSE
HGLN100FUC: ALPHA-L-FUCOSE

NAG_5ezo_H_5021N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
HGLN100NAG: 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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