1P9H - JenaLib

Title :   CRYSTAL STRUCTURE OF THE COLLAGEN-BINDING DOMAIN OF YERSINIA ADHESIN YADA

Authors :   H. Nummelin, M. C. Merckel, M. Skurnik, A. Goldman

Date :   12 May 03 (Deposition) - 23 Mar 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Collagen-Binding, Left-Handed Beta-Roll, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Nummelin, M. C. Merckel, J. C. Leo, H. Lankinen, M. Skurnik, A. Goldman
The Yersinia Adhesin Yada Collagen-Binding Domain Structure Is A Novel Left-Handed Parallel Beta-Roll.
Embo J. V. 23 701 2004
PubMed-ID: 14765110 | Reference-DOI: 10.1038/SJ.EMBOJ.7600100

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_YADA1_YEREN_002 *	L	49	Q	YADA1_YEREN	---	---	A	L	49	Q
2	UniProt	VAR_YADA1_YEREN_003 *	A	65	C	YADA1_YEREN	---	---	A	A	65	C
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_YADA1_YEREN_002 *	L	49	Q	YADA1_YEREN	---	---	A	L	49	Q
2	UniProt	VAR_YADA1_YEREN_003 *	A	65	C	YADA1_YEREN	---	---	A	A	65	C
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (0, 0)

Exons (0, 0)

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:179
 aligned with YADA1_YEREN | P31489 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:189
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
          YADA1_YEREN    32 PNLTAVQISPNADPALGLEYPVRPPVPGAGGLNASAKGIHSIAIGATAEAAKGAAVAVGAGSIATGVNSVAIGPLSKALGDSAVTYGAASTAQKDGVAIGARASTSDTGVAVGFNSKADAKNSVAIGHSSHVAANHGYSIAIGDRSKTDRENSVSIGHESLNRQLTHLAAGTKDTDAVNVAQLKKEIEK 220
               SCOP domains d1p9ha_ A: Adhesin Y          adA, collagen-binding domain                                                                                                                                    SCOP domains
               CATH domains 1p9hA00 A:32-220 Alk          aline Protease, subunit P, domain 1                                                                                                                             CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------Hep_Hag-1p9hA02 A:135-162   -------------------------------HIM-1p9hA01 A:194-214------ Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------Hep_Hag-1p9hA03 A:135-162   ---------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....eee............----------....ee.....eee....ee.....eee....ee.....eee....ee.....eee....ee....eee....ee....eee....ee.....eee....ee.......eee...........ee.......................hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------Q---------------C----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p9h A  32 PNLTAVQISPNADPALGLEY----------GLNASAKGIHSIAIGATAEAAKGAAVAVGAGSIATGVNSVAIGPLSKALGDSAVTYGAASTAQKDGVAIGARASTSDTGVAVGFNSKADAKNSVAIGHSSHVAANHGYSIAIGDRSKTDRENSVSIGHESLNRQLTHLAAGTKDTDAVNVAQLKKEIEK 220
                                    41        51         -|       71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
                                              51         62

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)

CATH Domains (1, 1)

Pfam Domains (2, 3)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A (YADA1_YEREN | P31489)

molecular function
	GO:0005518	collagen binding	Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019867	outer membrane	The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

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	Ligands, Modified Residues, Ions
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	Sites
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	Cis Peptide Bonds
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Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1p9h
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