1PUO

Crystal structure of Fel d 1- the major cat allergen

> Summary

Summary for 1PUO

DescriptorMajor allergen I polypeptide, fused chain 2, chain 1
Functional Keywordscat allergen, uteroglobin, secretoglobin, allergen
Biological sourceFelis catus (domestic cat)
Cellular locationSecreted P30438
Total number of polymer chains2
Total molecular weight38622.7
Authors
Kaiser, L.,Gronlund, H.,Sandalova, T.,Ljunggren, H.G.,van Hage-Hamsten, M.,Achour, A.,Schneider, G. (deposition date: 2003-06-25, release date: 2003-10-14, modification date: 2009-02-24)
Primary citation
Kaiser, L.,Gronlund, H.,Sandalova, T.,Ljunggren, H.G.,van Hage-Hamsten, M.,Achour, A.,Schneider, G.
The crystal structure of the major cat allergen Fel d 1, a member of the secretoglobin family.
J.Biol.Chem., 278:37730-37735, 2003
PubMed: 12851385
DOI: 10.1074/jbc.M304740200
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.85 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.245504.3%6.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1puo
no rotation
Molmil generated image of 1puo
rotated about x axis by 90°
Molmil generated image of 1puo
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BMajor allergen I polypeptide, fused chain 2, chain 1polymer17019075.02
UniProt (P30440)
UniProt (P30438)
Pfam (PF01099)
Pfam (PF09252)
Felis catus (domestic cat)@PDBjAllergen Fel d 1-B, Allergen Fel d 1-A
(4S)-2-METHYL-2,4-PENTANEDIOLnon-polymer118.24
waterwater18.0233

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight38150.0
Non-Polymers*Number of molecules4
Total molecular weight472.7
All*Total molecular weight38622.7
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.85 Å)

Cell axes43.29051.53967.725
Cell angles90.0095.2790.00
SpacegroupP 1 21 1
Resolution limits24.04 - 1.85
the highest resolution shell value1.898 - 1.850
R-factor0.20275
R-work0.20087 (0.20300*)
the highest resolution shell value0.221
R-free0.23731 (0.23900*)
the highest resolution shell value0.238
RMSD bond length0.010
RMSD bond angle1.268 (1.270*)

Data Collection Statistics

Resolution limits24.50 (30.00*) - 1.85
the highest resolution shell value -
Number of reflections25173 (69889*)
Number of measurements25113*
Rmerge_l_obs0.089*
the highest resolution shell value0.460*
Completeness98.4
the highest resolution shell value99.7*
Redundancy2.8
the highest resolution shell value2.7
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP4.8 (7.5*)293 (4*)*
1VAPOR DIFFUSION, HANGING DROP4.8 (7.5*)293 (4*)*
1VAPOR DIFFUSION, HANGING DROP4.8 (7.5*)293 (4*)*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11dropprotein7.5 (mg/ml)
21reservoirTris-HCl20 (mM)pH7.5
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005576cellular_componentextracellular region
A0005496molecular_functionsteroid binding
B0005576cellular_componentextracellular region
B0005496molecular_functionsteroid binding
A0005615cellular_componentextracellular space
B0005615cellular_componentextracellular space
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC16BINDING SITE FOR RESIDUE MPD B 302
ChainResidue
BPHE10
BPHE14
BVAL17
BTYR49
BPHE105
BHOH413

AC26BINDING SITE FOR RESIDUE MPD A 303
ChainResidue
APHE14
AVAL17
ATYR49
AMET64
APHE105
ALEU153

AC35BINDING SITE FOR RESIDUE MPD A 304
ChainResidue
APHE14
APHE15
AALA18
AASN19
AHOH411

AC42BINDING SITE FOR RESIDUE MPD B 305
ChainResidue
BPHE15
BASN19

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

site_idNumber of ResiduesDetails
MPD_1puo_A_30314(4S)-2-METHYL-2,4-PENTANEDIOL binding site
ChainResidueligand
APHE10MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AVAL13-PHE14MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AVAL17MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AMET42MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AILE45MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
ATYR49MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AASP60MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AMET64MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AASP101-VAL102MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
APHE105-LEU106MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
ALEU153MPD: (4S)-2-METHYL-2,4-PENTANEDIOL

MPD_1puo_A_3048(4S)-2-METHYL-2,4-PENTANEDIOL binding site
ChainResidueligand
ATYR11MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
APHE14-PHE15MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AALA18-ASN19MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AARG57-VAL58MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
AGLY61MPD: (4S)-2-METHYL-2,4-PENTANEDIOL

MPD_1puo_B_30212(4S)-2-METHYL-2,4-PENTANEDIOL binding site
ChainResidueligand
BPHE10MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BVAL13-PHE14MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BVAL17MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BMET42MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BILE45MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BTYR49MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BASP60MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BMET64MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BVAL102MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BPHE105MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BLEU153MPD: (4S)-2-METHYL-2,4-PENTANEDIOL

MPD_1puo_B_3057(4S)-2-METHYL-2,4-PENTANEDIOL binding site
ChainResidueligand
BPHE14-PHE15MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BALA18-ASN19MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BARG57-VAL58MPD: (4S)-2-METHYL-2,4-PENTANEDIOL
BGLY61MPD: (4S)-2-METHYL-2,4-PENTANEDIOL

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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
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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