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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   NMR STRUCTURE OF THE NTR DOMAIN FROM HUMAN PCOLCE1

Authors :   E. Liepinsh, L. Banyai, G. Pintacuda, M. Trexler, L. Patthy, G. Otting

Date :   14 Mar 03 (Deposition) - 15 Jul 03 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Beta Barrel, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Liepinsh, L. Banyai, G. Pintacuda, M. Trexler, L. Patthy, G. Otting
Nmr Structure Of The Netrin-Like Domain (Ntr) Of Human Type I Procollagen C-Proteinase Enhancer Defines Structural Consensus Of Ntr Domains And Assesses Potential Proteinase Inhibitory Activity And Ligand Binding.
J. Biol. Chem. V. 278 25982 2003
PubMed-ID: 12670942 | Reference-DOI: 10.1074/JBC.M302734200
(for further references see the PDB file header)

Molecule 1 - PROCOLLAGEN C-PROTEINASE ENHANCER PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	NTR DOMAIN
	Gene	:	PCOLCE
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1UAP)

(no "Site" information available for 1UAP)

NMR Structure

No.	Residues
1	A:30	-	A:98
2	A:34	-	A:101
3	A:45	-	A:149

NMR Structure

No.	Model	Residues
1	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20	Cys A:101	-	Pro A:102

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NTR	PS50189	NTR domain profile.	PCOC1_HUMAN	318-437	1	A:30-149

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000223061	1a	ENSE00001861120	chr7:100199800-100200174	375	PCOC1_HUMAN	1-32	32	0	-	-
1.2b	ENST00000223061	2b	ENSE00000710693	chr7:100201053-100201161	109	PCOC1_HUMAN	32-68	37	0	-	-
1.3c	ENST00000223061	3c	ENSE00000710691	chr7:100201582-100201840	259	PCOC1_HUMAN	69-155	87	0	-	-
1.4e	ENST00000223061	4e	ENSE00000710690	chr7:100202714-100202838	125	PCOC1_HUMAN	155-196	42	0	-	-
1.4m	ENST00000223061	4m	ENSE00000710689	chr7:100203299-100203435	137	PCOC1_HUMAN	197-242	46	0	-	-
1.6c	ENST00000223061	6c	ENSE00000710688	chr7:100204039-100204253	215	PCOC1_HUMAN	242-314	73	1	A:24-26	3
1.7	ENST00000223061	7	ENSE00001131240	chr7:100205075-100205146	72	PCOC1_HUMAN	314-338	25	1	A:26-50	25
1.8c	ENST00000223061	8c	ENSE00000710686	chr7:100205260-100205430	171	PCOC1_HUMAN	338-395	58	1	A:50-107	58
1.9b	ENST00000223061	9b	ENSE00001871599	chr7:100205560-100205798	239	PCOC1_HUMAN	395-449	55	1	A:107-154	48

NMR Structure

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:131
 aligned with PCOC1_HUMAN | Q15113 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:131
                                   321       331       341       351       361       371       381       391       401       411       421       431       441 
          PCOC1_HUMAN   312 APDAPTCPKQCRRTGTLQSNFCASSLVVTATVKSMVREPGEGLAVTVSLIGAYKTGGLDLPSPPTGASLKFYVPCKQCPPMKKGVSYLLMGQVEENRGPVLPPESFVVLHRPNQDQILTNLSKRKCPSQPV 442
               SCOP domains d1uapa_ A: Procollagen c-proteinase enhancer protein PCOLCE                                                                         SCOP domains
               CATH domains 1uapA00 A:24-154  [code=2.40.50.120, no name defined]                                                                               CATH domains
               Pfam domains ------------------NTR-1uapA01 A:42-146                                                                                     -------- Pfam domains
         Sec.struct. author ...............hhhhhhhhh.eeeeeeeeeeee.....eeeee...eeeee.............eeeee............eeeeeeeee...eee.....eeee.hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------NTR  PDB: A:30-149 UniProt: 318-437                                                                                     ----- PROSITE
           Transcript 1 (1) 1.6-----------------------Exon 1.8c  PDB: A:50-107 UniProt: 338-395                 ----------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.7  PDB: A:26-50   --------------------------------------------------------Exon 1.9b  PDB: A:107-154 UniProt: 395-449       Transcript 1 (2)
                 1uap A  24 SPDAPTCPKQCRRTGTLQSNFCASSLVVTATVKSMVREPGEGLAVTVSLIGAYKTGGLDLPSPPTGASLKFYVPCKQCPPMKKGVSYLLMGQVEENRGPVLPPESFVVLHRPNQDQILTNLSKRKCPSQPV 154
                                    33        43        53        63        73        83        93       103       113       123       133       143       153

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: OB-fold (1179)

Superfamily: TIMP-like (22)

Family: Netrin-like domain (NTR/C345C module) (4)

Protein domain: Procollagen c-proteinase enhancer protein PCOLCE (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d1uapa_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: [code=2.40.50.120, no name defined] (16)

Human (Homo sapiens) (12)

1uapA00

A:24-154

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIMP-like (15)

Family: NTR (13)

Homo sapiens (Human) (13)

NTR-1uapA01

A:42-146

NMR Structure(hide GO term definitions)

Chain A (PCOC1_HUMAN | Q15113)

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:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	GO:0016504	peptidase activator activity	Binds to and increases the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	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).
biological process
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0010952	positive regulation of peptidase activity	Any process that increases the frequency, rate or extent of peptidase activity, the hydrolysis of peptide bonds within proteins.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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.

NMR Structure
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	Cis Peptide Bonds
		Cys A:101 - Pro A:102	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (3, 3)

Cis Peptide Bonds (1, 20)

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Exons (4, 4)

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