1S4V - JenaLib

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Title :   THE 2.0 A CRYSTAL STRUCTURE OF THE KDEL-TAILED CYSTEINE ENDOPEPTIDASE FUNCTIONING IN PROGRAMMED CELL DEATH OF RICINUS COMMUNIS ENDOSPERM

Authors :   M. E. Than, M. Helm, D. J. Simpson, F. Lottspeich, R. Huber, C. Gietl

Date :   19 Jan 04 (Deposition) - 16 Mar 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Kdel Er Retention Signal, Endosperm, Ricinosomes, Seed Germination, Senescence, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Than, M. Helm, D. J. Simpson, F. Lottspeich, R. Huber, C. Gietl
The 2. 0 A Crystal Structure And Substrate Specificity Of Th Kdel-Tailed Cysteine Endopeptidase Functioning In Programme Cell Death Of Ricinus Communis Endosperm.
J. Mol. Biol. V. 336 1103 2004
PubMed-ID: 15037072 | Reference-DOI: 10.1016/J.JMB.2003.12.075

Molecule 1 - CYSTEINE ENDOPEPTIDASE
	Chains	:	A, B
	Organism Common	:	CASTOR BEAN
	Organism Scientific	:	RICINUS COMMUNIS
	Organism Taxid	:	3988
	Tissue	:	ENDOSPERM

Molecule 2 - DVA-LEU-LYS-0QE PEPTIDE
	Chains	:	C, D
	Organism Common	:	CASTOR BEAN
	Organism Scientific	:	RICINUS COMMUNIS
	Organism Taxid	:	3988
	Tissue	:	ENDOSPERM

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	0QE	2	Mod. Amino Acid	CHLOROMETHANE
2	DVA	2	Mod. Amino Acid	D-VALINE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	0QE	1	Mod. Amino Acid	CHLOROMETHANE
2	DVA	1	Mod. Amino Acid	D-VALINE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	0QE	1	Mod. Amino Acid	CHLOROMETHANE
2	DVA	1	Mod. Amino Acid	D-VALINE
3	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:15 , SER A:16 , SER A:48 , HOH A:335 , HOH A:368	BINDING SITE FOR RESIDUE SO4 A 401
2	AC2	SOFTWARE	GLN A:20 , GLY A:24 , SER A:25 , CYS A:26 , TRP A:27 , GLY A:67 , GLY A:68 , GLU A:114 , ASP A:161 , HIS A:162 , HOH A:289 , HOH A:307 , HOH A:370	BINDING SITE FOR CHAIN C OF DVA-LEU-LYS-0QE PEPTIDE
3	AC3	SOFTWARE	GLN B:20 , GLY B:24 , SER B:25 , CYS B:26 , TRP B:27 , GLY B:67 , GLY B:68 , ASP B:161 , HIS B:162 , HOH B:334	BINDING SITE FOR CHAIN D OF DVA-LEU-LYS-0QE PEPTIDE

Asymmetric Unit

No.	Residues
1	A:23	-	A:65
2	A:57	-	A:98
3	A:156	-	A:208
4	B:23	-	B:65
5	B:57	-	B:98
6	B:156	-	B:208

Asymmetric Unit

No.	Residues
1	Gly A:154	-	Ser A:155
2	Gly B:154	-	Ser B:155

(no "SAP(SNP)/Variant" information available for 1S4V)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CYSEP_RICCO	144-155	2	A:20-31 B:20-31
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CYSEP_RICCO	284-294	2	A:160-170 B:160-170
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	CYSEP_RICCO	302-321	2	A:178-197 B:178-197

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CYSEP_RICCO	144-155	1	A:20-31 -
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CYSEP_RICCO	284-294	1	A:160-170 -
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	CYSEP_RICCO	302-321	1	A:178-197 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CYSEP_RICCO	144-155	1	- B:20-31
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CYSEP_RICCO	284-294	1	- B:160-170
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	CYSEP_RICCO	302-321	1	- B:178-197

(no "Exon" information available for 1S4V)

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:224
 aligned with CYSEP_RICCO | O65039 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:224
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344    
          CYSEP_RICCO   125 TVPASVDWRKKGAVTSVKDQGQCGSCWAFSTIVAVEGINQIKTNKLVSLSEQELVDCDTDQNQGCNGGLMDYAFEFIKQRGGITTEANYPYEAYDGTCDVSKENAPAVSIDGHENVPENDENALLKAVANQPVSVAIDAGGSDFQFYSEGVFTGSCGTELDHGVAIVGYGTTIDGTKYWTVKNSWGPEWGEKGYIRMERGISDKEGLCGIAMEASYPIKKSSNN 348
               SCOP domains d1s4va_ A: Vignain (bean endopeptidase)                                                                                                                                                                                          SCOP domains
               CATH domains 1s4vA00 A:1-224 Cysteine proteinases                                                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..................hhhhhhhhhhhhhhhhhh.......hhhhhhh............hhhhhhhhhhh...................hhhh........eeee.....hhhhhhhhhh..eeeee....hhhh................eeeeeeeeee.....eeeeee...........eeeee................eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------THIOL_PROTEA--------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE-------THIOL_PROTEASE_ASN  --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s4v A   1 TVPASVDWRKKGAVTSVKDQGQCGSCWAFSTIVAVEGINQIKTNKLVSLSEQELVDCDTDQNQGCNGGLMDYAFEFIKQRGGITTEANYPYEAYDGTCDVSKENAPAVSIDGHENVPENDENALLKAVANQPVSVAIDAGGSDFQFYSEGVFTGSCGTELDHGVAIVGYGTTIDGTKYWTVKNSWGPEWGEKGYIRMERGISDKEGLCGIAMEASYPIKKSSNN 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:226
 aligned with CYSEP_RICCO | O65039 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:226
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344      
          CYSEP_RICCO   125 TVPASVDWRKKGAVTSVKDQGQCGSCWAFSTIVAVEGINQIKTNKLVSLSEQELVDCDTDQNQGCNGGLMDYAFEFIKQRGGITTEANYPYEAYDGTCDVSKENAPAVSIDGHENVPENDENALLKAVANQPVSVAIDAGGSDFQFYSEGVFTGSCGTELDHGVAIVGYGTTIDGTKYWTVKNSWGPEWGEKGYIRMERGISDKEGLCGIAMEASYPIKKSSNNPS 350
               SCOP domains d1s4vb_ B: Vignain (bean endopeptidase)                                                                                                                                                                                            SCOP domains
               CATH domains 1s4vB00 B:1-226 Cysteine proteinases                                                                                                                                                                                               CATH domains
           Pfam domains (1) -Peptidase_C1-1s4vB01 B:2-218                                                                                                                                                                                             -------- Pfam domains (1)
           Pfam domains (2) -Peptidase_C1-1s4vB02 B:2-218                                                                                                                                                                                             -------- Pfam domains (2)
         Sec.struct. author .....ee..................hhhhhhhhhhhhhhhhhh.......hhhhhhh............hhhhhhhhhhh...................hhhh........eeee.....hhhhhhhhhh..eeeee....hhhh................eeeeeeeeee.....eeeeee...........eeeee................eeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------THIOL_PROTEA--------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE-------THIOL_PROTEASE_ASN  ----------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s4v B   1 TVPASVDWRKKGAVTSVKDQGQCGSCWAFSTIVAVEGINQIKTNKLVSLSEQELVDCDTDQNQGCNGGLMDYAFEFIKQRGGITTEANYPYEAYDGTCDVSKENAPAVSIDGHENVPENDENALLKAVANQPVSVAIDAGGSDFQFYSEGVFTGSCGTELDHGVAIVGYGTTIDGTKYWTVKNSWGPEWGEKGYIRMERGISDKEGLCGIAMEASYPIKKSSNNPS 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain C from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 1s4v C 501 xLKx 504
                            |  |
                          501-DVA
                             504-0QE

Chain D from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 1s4v D 501 xLKx 504
                            |  |
                            |  |
                          501-DVA
                             504-0QE

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(

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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: Vignain (bean endopeptidase) (1)

Castor bean (Ricinus communis) [TaxId: 3988] (1)

1a	d1s4va_	A:
1b	d1s4vb_	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)

Castor bean (Ricinus communis) (1)

1a	1s4vB00	B:1-226
1b	1s4vA00	A:1-224

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_CA (169)

Family: Peptidase_C1 (81)

Ricinus communis (Castor bean) (1)

1a	Peptidase_C1-1s4vB01	B:2-218
1b	Peptidase_C1-1s4vB02	B:2-218

Asymmetric Unit(hide GO term definitions)

Chain A,B (CYSEP_RICCO | O65039)

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.
	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:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.

Asymmetric Unit
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		Gly B:154 - Ser B:155	[ RasMol ]

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	1s4v
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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 5)

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SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

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