1RN7 - JenaLib

Title :   STRUCTURE OF HUMAN CYSTATIN D

Authors :   M. Alvarez-Fernandez, Y. H. Liang, M. Abrahamson, X. D. Su

Date :   30 Nov 03 (Deposition) - 18 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Inhibitor Of Cysteine Peptidases, Cystatin D, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Alvarez-Fernandez, Y. H. Liang, M. Abrahamson, X. D. Su
Crystal Structure Of Human Cystatin D, A Cysteine Peptidase Inhibitor With Restricted Inhibition Profile.
J. Biol. Chem. V. 280 18221 2005
PubMed-ID: 15728581 | Reference-DOI: 10.1074/JBC.M411914200
(for further references see the PDB file header)

Compounds

Molecule 1 - CYSTATIN D
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHD389
	Expression System Strain	:	MC1061
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Tissue	:	PAROTID GLAND

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (3, 3)

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000304710	1	ENSE00001131256	chr20:23860387-23860083	305	CYTD_HUMAN	1-77	77	1	A:11-57	47
1.2	ENST00000304710	2	ENSE00001592538	chr20:23858255-23858142	114	CYTD_HUMAN	78-115	38	1	A:58-95	38
1.3	ENST00000304710	3	ENSE00001131251	chr20:23856908-23856572	337	CYTD_HUMAN	116-142	27	1	A:96-122	27

Sequences/Alignments

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:112
 aligned with CYTD_HUMAN | P28325 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:112
                                    40        50        60        70        80        90       100       110       120       130       140  
           CYTD_HUMAN    31 AGGIHATDLNDKSVQCALDFAISEYNKVINKDEYYSRPLQVMAAYQQIVGGVNYYFNVKFGRTTCTKSQPNLDNCPFNDQPKLKEEEFCSFQINEVPWEDKISILNYKCRKV 142
               SCOP domains d1rn7a_ A: Cystatin D                                                                                            SCOP domains
               CATH domains 1rn7A00 A:11-122  [code=3.10.450.10, no name defined]                                                            CATH domains
               Pfam domains -Cystatin-1rn7A01 A:12-108                                                                        -------------- Pfam domains
         Sec.struct. author ....eee...hhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee...................eeeeeeeeeeehhhheeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------R------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------CYSTATIN      ----------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:11-57 UniProt: 1-77           Exon 1.2  PDB: A:58-95 UniProt: 78-115Exon 1.3  PDB: A:96-122     Transcript 1
                 1rn7 A  11 AGGIHATDLNDKSVQRALDFAISEYNKVINKDEYYSRPLQVMAAYQQIVGGVNYYFNVKFGRTTCTKSQPNLDNCPFNDQPKLKEEEFCSFQINEVPWEDKISILNYKCRKV 122
                                    20        30        40        50        60        70        80        90       100       110       120

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 (1, 1)

Gene Ontology (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CYTD_HUMAN | P28325)

molecular function
	GO:0004869	cysteine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces 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:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
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: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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1rn7)

	Sites
(no "Sites" information available for 1rn7)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1rn7)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1rn7
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CYTD_HUMAN \| P28325
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	CYTD_HUMAN \| P28325
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description