1YVB - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   THE PLASMODIUM FALCIPARUM CYSTEINE PROTEASE FALCIPAIN-2

Authors :   S. X. Wang

Date :   15 Feb 05 (Deposition) - 28 Mar 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Cysteine Protease-Inhibitor Complex, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. X. Wang, K. C. Pandey, J. R. Somoza, P. S. Sijwali, T. Kortemme, L. S. Brinen, R. J. Fletterick, P. J. Rosenthal, J. H. Mckerrow
Structural Basis For Unique Mechanisms Of Folding And Hemoglobin Binding By A Malarial Protease.
Proc. Natl. Acad. Sci. Usa V. 103 11503 2006
PubMed-ID: 16864794 | Reference-DOI: 10.1073/PNAS.0600489103

Molecule 1 - FALCIPAIN 2
	Chains	:	A
	EC Number	:	3.4.22.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE30
	Expression System Strain	:	M15 PREP4
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AF239801
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	36329
	Strain	:	3D7

Molecule 2 - CYSTATIN
	Chains	:	I
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Synonym	:	EGG-WHITE CYSTATIN

		1	2
Asymmetric/Biological Unit	:	A	I

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:114 , ASN A:115 , THR I:70 , HIS I:84 , ASP I:85 , GLU I:86 , MET I:89	BINDING SITE FOR RESIDUE GOL A 1001

Asymmetric/Biological Unit

No.	Residues
1	A:22	-	A:63
2	A:56	-	A:95
3	A:81	-	A:100
4	A:153	-	A:200
5	I:71	-	I:81
6	I:95	-	I:115

Asymmetric/Biological Unit

No.	Residues
1	Leu I:78	-	Gln I:79

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYSTATIN	PS00287	Cysteine proteases inhibitors signature.	CYT_CHICK	75-88	1	I:52-65

(no "Exon" information available for 1YVB)

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:241
 aligned with Q9N6S8_PLAFA | Q9N6S8 from UniProtKB/TrEMBL  Length:484

    Alignment length:241
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483 
        Q9N6S8_PLAFA    244 QMNYEEVIKKYRGEENFDHAAYDWRLHSGVTPVKDQKNCGSCWAFSSIGSVESQYAIRKNKLITLSEQELVDCSFKNYGCNGGLINNAFEDMIELGGICPDGDYPYVSDAPNLCNIDRCTEKYGIKNYLSVPDNKLKEALRFLGPISISVAVSDDFAFYKEGIFDGECGDQLNHAVMLVGFGMKEIVNPLTKKGEKHYYYIIKNSWGQQWGERGFINIETDESGLMRKCGLGTDAFIPLIE  484
               SCOP domains d1yvba1 A:0-212 Falcipain 2                                                                                                                                                                                                                       SCOP domains
               CATH domains 1yvbA00 A:0-212 Cysteine proteinases                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh........ee.hhh.............hhhhhhhhhhhhhhhhhhh......hhhhhhhhh...hhhhh.hhhhhhhhhhhhh..............................eeee....hhhhhhhhh..eeeee..hhhhhh....ee.........eeeeeeeeeeeeee......eeeeeeeeee...........eeeeee......hhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yvb A    0 QMNYEEVIKKYRGEENFDHAAYDWRLHSGVTPVKDQKNCGSCWAFSSIGSVESQYAIRKNKLITLSEQELVDCSFKNYGCNGGLINNAFEDMIELGGICPDGDYPYVSDAPNLCNIDRCTEKYGIKNYLSVPDNKLKEALRFLGPISISVAVSDDFAFYKEGIFDGECGDQLNHAVMLVGFGMKEIVNPLTKKGEKHYYYIIKNSWGQQWGERGFINIETDESGLMRKCGLGTDAFIPLIE  212
                             |||||||0I|||||||  3        13        23        33        43        53        63        73      | 82        91       101       111   ||  122   ||  134    || 145       155       165    ||169F|||||||171       181       191       201       211 
                            0A|||||||0J||||||                                                                             79A         90A                      115|      126|       139|                         169A|||||169J||||                                           
                             0B|||||||0K|||||                                                                                                                   117       129        141                          169B|||||169K|||                                           
                              0C|||||| 0L||||                                                                                                                                                                      169C|||||169L||                                           
                               0D|||||  0M|||                                                                                                                                                                       169D|||||169M|                                           
                                0E||||   0N||                                                                                                                                                                        169E|||| 169N                                           
                                 0F|||    0O|                                                                                                                                                                         169F|||                                                
                                  0G||     0P                                                                                                                                                                          169G||                                                
                                   0H|                                                                                                                                                                                  169H|                                                
                                    0I                                                                                                                                                                                   169I

Chain I from PDB  Type:PROTEIN  Length:111
 aligned with CYT_CHICK | P01038 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:111
                                    38        48        58        68        78        88        98       108       118       128       138 
           CYT_CHICK     29 RLLGAPVPVDENDEGLQRALQFAMAEYNRASNDKYSSRVVRVISAKRQLVSGIKYILQVEIGRTTCPKSSGDLQSCEFHDEPEMAKYTTCTFVVYSIPWLNQIKLLESKCQ  139
               SCOP domains d1yvbi_ I: automated matches                                                                                    SCOP domains
               CATH domains 1yvbI00 I:6-116  [code=3.10.450.10, no name defined]                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....hhhhhhhhhhhhhhhhhhh.....eeeeee...eeee...eeeeeeeeeee........................eeeeeeeeeehhhheeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------CYSTATIN      --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                1yvb I    6 RLLGAPVPVDENDEGLQRALQFAMAEYNRASNDKYSSRVVRVISAKRQLVSGIKYILQVEIGRTTCPKSSGDLQSCEFHDEPEMAKYTTCTFVVYSIPWLNQIKLLESKCQ  116
                                    15        25        35        45        55        65        75        85        95       105       115

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) (23004)

Fold: Cystatin-like (403)

Superfamily: Cystatin/monellin (68)

Family: Cystatins (31)

Protein domain: automated matches (3)

Chicken (Gallus gallus) [TaxId: 9031] (1)

d1yvbi_

Fold: Cysteine proteinases (392)

Superfamily: Cysteine proteinases (392)

Family: Papain-like (200)

Protein domain: Falcipain 2 (5)

Malaria parasite (Plasmodium falciparum) [TaxId: 5833] (5)

d1yvba1

A:0-212

(no "Pfam Domain" information available for 1YVB)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q9N6S8_PLAFA | Q9N6S8)

molecular function
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	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.

Chain I (CYT_CHICK | P01038)

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.
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: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.

Asymmetric/Biological Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Leu I:78 - Gln I:79	[ RasMol ]

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	1yvb
		Family and Domain Information	:	ProDom \| SYSTERS
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
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	CYT_CHICK \| P01038
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	Q9N6S8_PLAFA \| Q9N6S8
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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	3.4.22.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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	(no 'MIM ID' available)
		Disease Information	:	OMIM

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

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	CYT_CHICK \| P01038
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	Q9N6S8_PLAFA \| Q9N6S8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	CYT_CHICK \| P01038	:	1a67 1a90 1cew
	Q9N6S8_PLAFA \| Q9N6S8	:	2oul
UniProtKB/TrEMBL
	Q9N6S8_PLAFA \| Q9N6S8	:	2ghu 3bpf 3pnr

1aim	CRUZAIN
1atk	HUMAN CATHEPSIN K
1pe6	PAPAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (6, 6)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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Related Entries

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Related Entries Specified in the PDB File