2PNS - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   1.9 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A PLANT CYSTEINE PROTEASE ERVATAMIN-C REFINEMENT WITH CDNA DERIVED AMINO ACID SEQUENCE

Authors :   R. Ghosh, P. Guha Thakurta, S. Biswas, C. Chakrabarti, J. K. Dattagupt

Date :   25 Apr 07 (Deposition) - 19 Jun 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Papain-Like Fold, Thermostable, Plant Cysteine Protease, Ervatamin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Ghosh, J. K. Dattagupta, S. Biswas
A Thermostable Cysteine Protease Precursor From A Tropical Plant Contains An Unusual C-Terminal Propeptide: Cdna Cloning, Sequence Comparison And Molecular Modeling Studies
Biochem. Biophys. Res. Commun. V. 362 965 2007
PubMed-ID: 17767923 | Reference-DOI: 10.1016/J.BBRC.2007.08.098

Molecule 1 - ERVATAMIN-C, A PAPAIN-LIKE PLANT CYSTEINE PROTEASE
	Chains	:	A, B
	EC Number	:	3.4.22.-
	Organism Scientific	:	TABERNAEMONTANA DIVARICATA
	Organism Taxid	:	52861
	Other Details	:	TROPICAL FLOWERING PLANT

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION
2	THJ	2	Ligand/Ion	THIOSULFATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION
2	THJ	1	Ligand/Ion	THIOSULFATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	PO4	-1	Ligand/Ion	PHOSPHATE ION
2	THJ	1	Ligand/Ion	THIOSULFATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:113 , HIS B:113 , HOH B:733	BINDING SITE FOR RESIDUE PO4 A 300
2	AC2	SOFTWARE	GLN A:19 , CYS A:22 , GLY A:23 , SER A:24 , CYS A:25 , TRP A:26 , GLY A:65 , GLY A:66 , HOH A:708 , HOH A:718	BINDING SITE FOR RESIDUE THJ A 601
3	AC3	SOFTWARE	GLN B:19 , GLY B:23 , SER B:24 , CYS B:25 , TRP B:26 , HIS B:157 , HOH B:720	BINDING SITE FOR RESIDUE THJ B 602

Asymmetric Unit

No.	Residues
1	A:22	-	A:63
2	A:56	-	A:96
3	A:114	-	A:193
4	A:151	-	A:196
5	B:22	-	B:63
6	B:56	-	B:96
7	B:114	-	B:193
8	B:151	-	B:196

Asymmetric Unit

No.	Residues
1	Gly A:149	-	Pro A:150
2	Gly B:149	-	Pro B:150

(no "SAP(SNP)/Variant" information available for 2PNS)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	ERVC_TABDI	19-30	2	A:19-30 B:19-30
2	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	ERVC_TABDI	168-187	2	A:168-187 B:168-187

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	ERVC_TABDI	19-30	1	A:19-30 -
2	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	ERVC_TABDI	168-187	1	A:168-187 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	ERVC_TABDI	19-30	1	- B:19-30
2	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	ERVC_TABDI	168-187	1	- B:168-187

(no "Exon" information available for 2PNS)

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:208
 aligned with ERVC_TABDI | P83654 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
           ERVC_TABDI     1 LPEQIDWRKKGAVTPVKNQGSCGSCWAFSTVSTVESINQIRTGNLISLSEQELVDCDKKNHGCLGGAFVFAYQYIINNGGIDTQANYPYKAVQGPCQAASKVVSIDGYNGVPFCNEXALKQAVAVQPSTVAIDASSAQFQQYSSGIFSGPCGTKLNHGVTIVGYQANYWIVRNSWGRYWGEKGYIRMLRVGGCGLCGIARLPYYPTKA 208
               SCOP domains d2pnsa_ A: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2pnsA00 A:1-208 Cysteine proteinases                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh...........................eeee....hhhhhhhhhhhh.eeeee...hhhhhh....ee.........eeeeeeee...eeeee...........eeeee.....hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA-----------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTEASE_ASN  --------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pns A   1 LPEQIDWRKKGAVTPVKNQGKCGSCWAFSTVSTVESINQIRTGNLISLSEQQLVDCNKKNHGCKGGAFVYAYQYIIDNGGIDTEANYPYKAVQGPCRAAKKVVRIDGYKGVPHCNENALKKAVASQPSVVAIDASSKQFQHYKSGIFSGPCGTKLNHGVVIVGYWKDYWIVRNSWGRYWGEQGYIRMKRVGGCGLCGIARLPYYPTKA 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain B from PDB  Type:PROTEIN  Length:208
 aligned with ERVC_TABDI | P83654 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
           ERVC_TABDI     1 LPEQIDWRKKGAVTPVKNQGSCGSCWAFSTVSTVESINQIRTGNLISLSEQELVDCDKKNHGCLGGAFVFAYQYIINNGGIDTQANYPYKAVQGPCQAASKVVSIDGYNGVPFCNEXALKQAVAVQPSTVAIDASSAQFQQYSSGIFSGPCGTKLNHGVTIVGYQANYWIVRNSWGRYWGEKGYIRMLRVGGCGLCGIARLPYYPTKA 208
               SCOP domains d2pnsb_ B: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2pnsB00 B:1-208 Cysteine proteinases                                                                                                                                                                             CATH domains
           Pfam domains (1) Peptidase_C1-2pnsB01 B:1-206                                                                                                                                                                                  -- Pfam domains (1)
           Pfam domains (2) Peptidase_C1-2pnsB02 B:1-206                                                                                                                                                                                  -- Pfam domains (2)
         Sec.struct. author ....ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh...........................eeee....hhhhhhhhhhhh.eeeee...hhhhhh....ee.........eeeeeeeee..eeeee...........eeeee.....hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA-----------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTEASE_ASN  --------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pns B   1 LPEQIDWRKKGAVTPVKNQGKCGSCWAFSTVSTVESINQIRTGNLISLSEQQLVDCNKKNHGCKGGAFVYAYQYIIDNGGIDTEANYPYKAVQGPCRAAKKVVRIDGYKGVPHCNENALKKAVASQPSVVAIDASSKQFQHYKSGIFSGPCGTKLNHGVVIVGYWKDYWIVRNSWGRYWGEQGYIRMKRVGGCGLCGIARLPYYPTKA 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Cysteine proteinases (392)

Superfamily: Cysteine proteinases (392)

Family: Papain-like (200)

Protein domain: automated matches (30)

Tabernaemontana divaricata [TaxId: 52861] (3)

1a	d2pnsa_	A:
1b	d2pnsb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Cathepsin B; Chain A (207)

Homologous Superfamily: Cysteine proteinases (207)

TabeRNAemontana divaricata. Organism_taxid: 52861. (2)

1a	2pnsA00	A:1-208
1b	2pnsB00	B:1-208

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_CA (169)

Family: Peptidase_C1 (81)

Tabernaemontana divaricata (Crepe jasmine) (Ervatamia coronaria) (2)

1a	Peptidase_C1-2pnsB01	B:1-206
1b	Peptidase_C1-2pnsB02	B:1-206

Asymmetric Unit(hide GO term definitions)

Chain A,B (ERVC_TABDI | P83654)

molecular function
	GO:0004197	cysteine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-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.
	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.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
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: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 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
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		THJ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:149 - Pro A:150	[ RasMol ]
		Gly B:149 - Pro B:150	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2pns
		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
	ERVC_TABDI \| P83654
		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)
	3.4.22.-
		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

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
	ERVC_TABDI \| P83654
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ERVC_TABDI \| P83654	:	1o0e

1o0e	SAME PROTEIN, AMINO ACID SEQUENCE DETERMINED FROM ELECTRON DENSITY

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (8, 8)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File