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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   DIMERIC BOVINE TISSUE-EXTRACTED DECORIN, CRYSTAL FORM 2

Authors :   P. G. Scott, P. A. Mcewan, C. M. Dodd, E. M. Bergmann, P. N. Bishop, J. Bell

Date :   09 Sep 04 (Deposition) - 02 Nov 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B

Keywords :   Proteoglycan; Leucine-Rich Repeat, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. G. Scott, P. A. Mcewan, C. M. Dodd, E. M. Bergmann, P. N. Bishop, J. Bella
Crystal Structure Of The Dimeric Protein Core Of Decorin, The Archetypal Small Leucine-Rich Repeat Proteoglycan
Proc. Natl. Acad. Sci. Usa V. 101 15633 2004
PubMed-ID: 15501918 | Reference-DOI: 10.1073/PNAS.0402976101
(for further references see the PDB file header)

Molecule 1 - DECORIN
	Chains	:	A, B
	Organ	:	SKIN
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Other Details	:	PROTEIN WAS EXTRACTED FROM CALF SKIN UNDER DENATURING CONDITIONS AND REFOLDED
	Synonym	:	BONE PROTEOGLYCAN II; PG-S2

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 7)

No.	Name	Count	Type	Full Name
1	NAG	7	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:155 , PRO A:156 , ASP A:180 , ASN A:182 , TRP A:308 , NAG A:410 , HOH A:618 , HOH A:632 , HOH A:649 , HOH A:774	BINDING SITE FOR RESIDUE NAG A 400
2	AC2	SOFTWARE	TRP A:308 , ILE A:310 , GLN A:311 , NAG A:400	BINDING SITE FOR RESIDUE NAG A 410
3	AC3	SOFTWARE	ASN A:233	BINDING SITE FOR RESIDUE NAG A 401
4	AC4	SOFTWARE	ASN A:274 , HOH A:746 , HOH A:761	BINDING SITE FOR RESIDUE NAG A 402
5	AC5	SOFTWARE	ASN B:155 , PRO B:156 , ASN B:182 , HOH B:737	BINDING SITE FOR RESIDUE NAG B 403
6	AC6	SOFTWARE	ASN B:164 , ASN B:274 , NAG B:415 , HOH B:742	BINDING SITE FOR RESIDUE NAG B 405
7	AC7	SOFTWARE	ASN B:164 , NAG B:405 , HOH B:742	BINDING SITE FOR RESIDUE NAG B 415

Asymmetric/Biological Unit

No.	Residues
1	A:25	-	A:31
2	A:29	-	A:38
3	A:284	-	A:317
4	B:25	-	B:31
5	B:29	-	B:38
6	B:284	-	B:317

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

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

Asymmetric/Biological Unit (1, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	PGS2_BOVIN	83-104 107-128 131-152 153-173 223-243 247-268 271-293 294-315	16	A:53-74 B:53-74 A:77-98 B:77-98 A:101-122 B:101-122 A:123-143 B:123-143 A:193-213 B:193-213 A:217-238 B:217-238 A:241-263 B:241-263 A:264-285 B:264-285

Asymmetric/Biological Unit (7, 14)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000004562	1	ENSBTAE00000300120	chr5:23762660-23762470	191	PGS2_BOVIN	-	0	0	-	-
1.3	ENSBTAT00000004562	3	ENSBTAE00000036594	chr5:23758480-23758234	247	PGS2_BOVIN	1-72	72	2	A:22-42 B:22-42	21 21
1.4	ENSBTAT00000004562	4	ENSBTAE00000036606	chr5:23746370-23746258	113	PGS2_BOVIN	72-109	38	2	A:42-79 B:42-79	38 38
1.5	ENSBTAT00000004562	5	ENSBTAE00000036610	chr5:23739602-23739389	214	PGS2_BOVIN	110-181	72	2	A:80-151 B:80-151	72 72
1.6	ENSBTAT00000004562	6	ENSBTAE00000036614	chr5:23738587-23738474	114	PGS2_BOVIN	181-219	39	2	A:151-189 B:151-189	39 39
1.7	ENSBTAT00000004562	7	ENSBTAE00000036619	chr5:23732791-23732698	94	PGS2_BOVIN	219-250	32	2	A:189-220 B:189-220	32 32
1.8	ENSBTAT00000004562	8	ENSBTAE00000036625	chr5:23728847-23728709	139	PGS2_BOVIN	250-296	47	2	A:220-266 B:220-266	47 47
1.9b	ENSBTAT00000004562	9b	ENSBTAE00000036725	chr5:23724466-23723438	1029	PGS2_BOVIN	297-360	64	2	A:267-326 B:267-326	60 60

Asymmetric/Biological 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:305
 aligned with PGS2_BOVIN | P21793 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:305
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351     
           PGS2_BOVIN    52 GPVCPFRCQCHLRVVQCSDLGLEKVPKDLPPDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQGLPPSLTELHLDGNKITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPHLRELHLNNNKLVKVPGGLADHKYIQVVYLHNNNISAIGSNDFCPPGYNTKKASYSGVSLFSNPVQYWEIQPSTFRCVYVRAAVQL 356
               SCOP domains d1xeca_ A: Decorin                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1xecA00 A:22-326 Ribonuclease Inhibitor                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eee..................eee.......ee............eee.......ee............eee..................eee.........hhhhh.......eee......hhhhh............eee..................eee.......ee............eee.......ee...hhhhh....eee....................eee...........................eee......hhhhhhhhhhh...hhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------LRR  PDB: A:53-74     --LRR  PDB: A:77-98     --LRR  PDB: A:101-122   LRR  PDB: A:123-143  -------------------------------------------------LRR  PDB: A:193-213  ---LRR  PDB: A:217-238   --LRR  PDB: A:241-263    LRR  PDB: A:264-285   ----------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:22-4-------------------------------------Exon 1.5  PDB: A:80-151 UniProt: 110-181                                -------------------------------------Exon 1.7  PDB: A:189-220        ----------------------------------------------Exon 1.9b  PDB: A:267-326 UniProt: 297-360 [INCOMPLETE]      Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.4  PDB: A:42-79 UniProt: 72-109-----------------------------------------------------------------------Exon 1.6  PDB: A:151-189               ------------------------------Exon 1.8  PDB: A:220-266 UniProt: 250-296      ------------------------------------------------------------ Transcript 1 (2)
                 1xec A  22 GPVCPFRCQCHLRVVQCSDLGLEKVPKDLPPDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQGLPPSLTELHLDGNKITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPHLRELHLNNNKLVKVPGGLADHKYIQVVYLHNNNISAIGSNDFCPPGYNTKKASYSGVSLFSNPVQYWEIQPSTFRCVYVRAAVQL 326
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321

Chain B from PDB  Type:PROTEIN  Length:305
 aligned with PGS2_BOVIN | P21793 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:305
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351     
           PGS2_BOVIN    52 GPVCPFRCQCHLRVVQCSDLGLEKVPKDLPPDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQGLPPSLTELHLDGNKITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPHLRELHLNNNKLVKVPGGLADHKYIQVVYLHNNNISAIGSNDFCPPGYNTKKASYSGVSLFSNPVQYWEIQPSTFRCVYVRAAVQL 356
               SCOP domains d1xecb_ B: Decorin                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1xecB00 B:22-326 Ribonuclease Inhibitor                                                                                                                                                                                                                                                                           CATH domains
           Pfam domains (1) --LRRNT-1xecB05 B:24-51       --------------------------------------------------------------------------------------------------------------------------------------------LRR_8-1xecB01 B:192-252                                      -------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --LRRNT-1xecB06 B:24-51       --------------------------------------------------------------------------------------------------------------------------------------------LRR_8-1xecB02 B:192-252                                      -------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_8-1xecB03 B:192-252                                      -------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_8-1xecB04 B:192-252                                      -------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ........eee..eee..................eee.....................eee.....................eee..................eee.........hhhhh.......eee......hhhhh............eee..................eee.......eehhhhhh......eee.......ee...hhhhh....eee....................eee...........................eee......hhhhhhhhhhh...hhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------LRR  PDB: B:53-74     --LRR  PDB: B:77-98     --LRR  PDB: B:101-122   LRR  PDB: B:123-143  -------------------------------------------------LRR  PDB: B:193-213  ---LRR  PDB: B:217-238   --LRR  PDB: B:241-263    LRR  PDB: B:264-285   ----------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:22-4-------------------------------------Exon 1.5  PDB: B:80-151 UniProt: 110-181                                -------------------------------------Exon 1.7  PDB: B:189-220        ----------------------------------------------Exon 1.9b  PDB: B:267-326 UniProt: 297-360 [INCOMPLETE]      Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.4  PDB: B:42-79 UniProt: 72-109-----------------------------------------------------------------------Exon 1.6  PDB: B:151-189               ------------------------------Exon 1.8  PDB: B:220-266 UniProt: 250-296      ------------------------------------------------------------ Transcript 1 (2)
                 1xec B  22 GPVCPFRCQCHLRVVQCSDLGLEKVPKDLPPDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQGLPPSLTELHLDGNKITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPHLRELHLNNNKLVKVPGGLADHKYIQVVYLHNNNISAIGSNDFCPPGYNTKKASYSGVSLFSNPVQYWEIQPSTFRCVYVRAAVQL 326
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) (112)

Superfamily: L domain-like (93)

Family: Ngr ectodomain-like (21)

Protein domain: Decorin (3)

Cow (Bos taurus) [TaxId: 9913] (3)

1a	d1xeca_	A:
1b	d1xecb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Horseshoe (92)

Topology: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) (73)

Homologous Superfamily: Ribonuclease Inhibitor (73)

Cattle (Bos taurus) (5)

1a	1xecA00	A:22-326
1b	1xecB00	B:22-326

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: LRR (77)

Family: LRR_8 (41)

Bos taurus (Bovine) (2)

1a	LRR_8-1xecB01	B:192-252
1b	LRR_8-1xecB02	B:192-252
1c	LRR_8-1xecB03	B:192-252
1d	LRR_8-1xecB04	B:192-252

Clan: no clan defined [family: LRRNT] (22)

Family: LRRNT (22)

Bos taurus (Bovine) (2)

2a	LRRNT-1xecB05	B:24-51
2b	LRRNT-1xecB06	B:24-51

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PGS2_BOVIN | P21793)

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%).
	GO:0050840	extracellular matrix binding	Interacting selectively and non-covalently with a component of the extracellular matrix.
	GO:0005539	glycosaminoglycan binding	Interacting selectively and non-covalently with any glycan (polysaccharide) containing a substantial proportion of aminomonosaccharide residues.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004860	protein kinase inhibitor activity	Stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein.
biological process
	GO:0019221	cytokine-mediated signaling pathway	A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0046426	negative regulation of JAK-STAT cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of the JAK-STAT signaling pathway activity.
	GO:0006469	negative regulation of protein kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
	GO:0019800	peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan	The formation of a cross-link between peptide chains mediated by a chondroitin 4-sulfate glycosaminoglycan that originates from a typical O-glycosidic link to serine of one chain; the other chain is esterified, via the alpha-carbon of its C-terminal Asp, to C-6 of an internal N-acetylgalactosamine of the glycosaminoglycan chain.
	GO:0010508	positive regulation of autophagy	Any process that activates, maintains or increases the rate of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

Asymmetric/Biological Unit
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UniProtKB/Swiss-Prot
	PGS2_BOVIN \| P21793	:	1xcd 1xku

1xcd	DIMERIC TISSUE-EXTRACTED BOVINE DECORIN, CRYSTAL FORM 1
1xku	DIMERIC RECOMBINANT BOVINE DECORIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 7)

Sites (7, 7)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (7, 14)

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