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Description

Title :   CRYSTAL STRUCTURE OF THE FUNCTIONAL DOMAIN OF THE MAJOR GRASS POLLEN ALLERGEN PHL P 5B

Authors :   K. R. Rajashankar, A. Bufe, W. Weber, S. Eschenburg, B. Lindner, C. Betz

Date :   28 Feb 02 (Deposition) - 28 Feb 03 (Release) - 08 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.98

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Grass Pollen Allergen, Phl P 5B, Allergy, Allergen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Rajashankar, A. Bufe, W. Weber, S. Eschenburg, B. Lindner, C. Betze
Structure Of The Functional Domain Of The Major Grass-Polle Allergen Phlp 5B.
Acta Crystallogr. , Sect. D V. 58 1175 2002
PubMed-ID: 12077438 | Reference-DOI: 10.1107/S0907444902007254
(for further references see the PDB file header)

Compounds

Molecule 1 - POLLEN ALLERGEN PHL P 5B
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMALC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	TIMOTHY GRASS
	Organism Scientific	:	PHLEUM PRATENSE
	Organism Taxid	:	15957
	Synonym	:	PHL P VB

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:173 , ALA A:177 , LYS A:180 , GLN A:226 , GLU A:233 , HOH A:253 , HOH A:254 , HOH A:256 , HOH A:306	BINDING SITE FOR RESIDUE PO4 A 252
2	AC2	SOFTWARE	THR A:170 , ALA A:177 , HOH A:253 , HOH A:263	BINDING SITE FOR RESIDUE MG A 350

SS Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	A:205	-	A:205

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1L3P)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1L3P)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 1L3P)

Exons (0, 0)

(no "Exon" information available for 1L3P)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:102
 aligned with MPA5B_PHLPR | Q40963 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:102
                                   159       169       179       189       199       209       219       229       239       249  
          MPA5B_PHLPR   150 IPAGELQIIDKIDAAFKVAATAAATAPADDKFTVFEAAFNKAIKESTGGAYDTYKCIPSLEAAVKQAYAATVAAAPQVKYAVFEAALTKAITAMSEVQKVSQ 251
               SCOP domains d1l3pa_ A: Functional domain of pollen allergen Phl P 5b                                               SCOP domains
               CATH domains 1l3pA00 A:150-251  [code=1.20.120.320, no name defined]                                                CATH domains
               Pfam domains Pollen_allerg_2-1l3pA01 A:150-251                                                                      Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1l3p A 150 IPAGELQIIDKIDAAFKVAATAAATAPADDKFTVFEAAFNKAIKETTGGAYDTYKCIPSLEAAVKQAYAATVAAAPQVKYAVFEAALTKAITAMSEVQKVSQ 251
                                   159       169       179       189       199       209       219       229       239       249

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Four-helical up-and-down bundle (308)

Superfamily: Group V grass pollen allergen (2)

Family: Group V grass pollen allergen (2)

Protein domain: Functional domain of pollen allergen Phl P 5b (1)

Timothy grass (Phleum pratense) [TaxId: 15957] (1)

d1l3pa_

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Four Helix Bundle (Hemerythrin (Met), subunit A) (300)

Homologous Superfamily: [code=1.20.120.320, no name defined] (2)

Timothy grass (Phleum pratense) (2)

1l3pA00

A:150-251

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Pollen_allerg_2] (2)

Family: Pollen_allerg_2 (2)

Phleum pratense (Common timothy) (2)

Pollen_allerg_2-1l3pA01

A:150-251

Gene Ontology (2, 2)

Asymmetric Unit(hide GO term definitions)

Chain A (MPA5B_PHLPR | Q40963)

molecular function
	GO:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

Classification and Annotation

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