2BDZ - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   MEXICAIN FROM JACARATIA MEXICANA

Authors :   J. A. Gavira, M. C. Oliver-Salvador, L. A. Gonzalez-Ramirez, M. Sorian J. M. Garcia-Ruiz

Date :   21 Oct 05 (Deposition) - 03 Oct 06 (Release) - 09 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Mexicain, Cysteine Protease, Peptidase_c1, Papain-Like, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. Gavira, M. C. Oliver-Salvador, L. A. Gonzalez-Ramirez, M. Soriano-Garcia, J. M. Garcia-Ruiz
Crystallographic Structure Of Mexicain From Jacaratia Mexicana
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - MEXICAIN
	Chains	:	A, B, C, D
	EC Number	:	3.4.22.-
	Organism Scientific	:	JACARATIA MEXICANA
	Organism Taxid	:	309130
	Other Details	:	LATEX

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	E64	4	Ligand/Ion	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	E64	1	Ligand/Ion	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	E64	1	Ligand/Ion	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	E64	1	Ligand/Ion	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	E64	1	Ligand/Ion	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:19 , GLY A:23 , SER A:24 , CYS A:25 , TRP A:26 , ASP A:64 , GLY A:65 , GLY A:66 , VAL A:133 , THR A:157 , ASP A:158 , HIS A:159 , HOH A:1101 , HOH A:1132 , HOH A:1371 , ASN B:180 , GLN D:92 , GLY D:93	BINDING SITE FOR RESIDUE E64 A 501
2	AC2	SOFTWARE	ASN A:180 , GLN B:19 , GLY B:23 , SER B:24 , CYS B:25 , TRP B:26 , ASP B:64 , GLY B:65 , GLY B:66 , THR B:157 , ASP B:158 , HIS B:159 , HOH B:1018 , HOH B:1310 , HOH B:1372	BINDING SITE FOR RESIDUE E64 B 502
3	AC3	SOFTWARE	GLN C:19 , GLY C:23 , SER C:24 , CYS C:25 , TRP C:26 , ASP C:64 , GLY C:65 , GLY C:66 , ASP C:158 , HIS C:159 , HOH C:1068 , HOH C:1258 , HOH C:1347	BINDING SITE FOR RESIDUE E64 C 503
4	AC4	SOFTWARE	LYS A:91 , GLN A:92 , GLY A:93 , GLN D:19 , GLY D:23 , SER D:24 , CYS D:25 , TRP D:26 , ASP D:64 , GLY D:65 , GLY D:66 , VAL D:133 , THR D:157 , ASP D:158 , HIS D:159 , HOH D:1040 , HOH D:1160	BINDING SITE FOR RESIDUE E64 D 504

Asymmetric Unit

No.	Residues
1	A:22	-	A:63
2	A:56	-	A:95
3	A:153	-	A:200
4	B:22	-	B:63
5	B:56	-	B:95
6	B:153	-	B:200
7	C:22	-	C:63
8	C:56	-	C:95
9	C:153	-	C:200
10	D:22	-	D:63
11	D:56	-	D:95
12	D:153	-	D:200

Asymmetric Unit

No.	Residues
1	Asn A:20	-	Pro A:21
2	Gly A:151	-	Pro A:152
3	Asn B:20	-	Pro B:21
4	Gly B:151	-	Pro B:152
5	Asn C:20	-	Pro C:21
6	Gly C:151	-	Pro C:152
7	Asn D:20	-	Pro D:21
8	Gly D:151	-	Pro D:152

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	MEX1_JACME	19-30	4	A:19-30 B:19-30 C:19-30 D:19-30
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	MEX1_JACME	157-167	4	A:157-167 B:157-167 C:157-167 D:157-167

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.	MEX1_JACME	19-30	1	A:19-30 - - -
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	MEX1_JACME	157-167	1	A:157-167 - - -

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.	MEX1_JACME	19-30	1	- B:19-30 - -
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	MEX1_JACME	157-167	1	- B:157-167 - -

Biological Unit 3 (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.	MEX1_JACME	19-30	1	- - C:19-30 -
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	MEX1_JACME	157-167	1	- - C:157-167 -

Biological Unit 4 (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.	MEX1_JACME	19-30	1	- - - D:19-30
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	MEX1_JACME	157-167	1	- - - D:157-167

(no "Exon" information available for 2BDZ)

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:212
 aligned with MEX1_JACME | P84346 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
           MEX1_JACME     1 YPESIDWREKGAVTPVKNQNPCGSCWAFSTVATIEGINKIITGQLISLSEQELLDCEYRSHGCDGGYQTPSLQYVVDNGVHTEREYPYEKKQGRCRAKDKKGPKVYITGYKYVPANDEISLIQAIANQPVSVVTDSRGRGFQFYKGGIYEGPCGTNTDHAVTAVGYGKTYLLLKNSWGPNWGEKGYIRIKRASGRSKGTCGVYTSSFFPIKG 212
               SCOP domains d2bdza_ A: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains 2bdzA00 A:1-212 Cysteine proteinases                                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhhee......................ee...eeeee...hhhhhhhhhhhh.eeeee...hhhhhh....ee.........eeeeeeee...eeeee...........eeeee.......hhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE--------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bdz A   1 YPESIDWREKGAVTPVKNQNPCGSCWAFSTVATIEGINKIITGQLISLSEQELLDCERRSHGCDGGYQTTSLQYVVDNGVHTEREYPYEKKQGRCRAKDKKGPKVYITGYKYVPANDEISLIQAIANQPVSVVTDSRGRGFQFYKGGIYEGPCGTNTDHAVTAVGYGKTYLLLKNSWGPNWGEKGYIRIKRASGRSKGTCGVYTSSFFPIKG 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:212
 aligned with MEX1_JACME | P84346 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
           MEX1_JACME     1 YPESIDWREKGAVTPVKNQNPCGSCWAFSTVATIEGINKIITGQLISLSEQELLDCEYRSHGCDGGYQTPSLQYVVDNGVHTEREYPYEKKQGRCRAKDKKGPKVYITGYKYVPANDEISLIQAIANQPVSVVTDSRGRGFQFYKGGIYEGPCGTNTDHAVTAVGYGKTYLLLKNSWGPNWGEKGYIRIKRASGRSKGTCGVYTSSFFPIKG 212
               SCOP domains d2bdzb_ B: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains 2bdzB00 B:1-212 Cysteine proteinases                                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh................hhhhh........eeee....hhhhhhhhhhhh.eeeee...hhhhhh....ee.........eeeeeeee...eeeee...........eeeee.......hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE--------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bdz B   1 YPESIDWREKGAVTPVKNQNPCGSCWAFSTVATIEGINKIITGQLISLSEQELLDCERRSHGCDGGYQTTSLQYVVDNGVHTEREYPYEKKQGRCRAKDKKGPKVYITGYKYVPANDEISLIQAIANQPVSVVTDSRGRGFQFYKGGIYEGPCGTNTDHAVTAVGYGKTYLLLKNSWGPNWGEKGYIRIKRASGRSKGTCGVYTSSFFPIKG 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain C from PDB  Type:PROTEIN  Length:212
 aligned with MEX1_JACME | P84346 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
           MEX1_JACME     1 YPESIDWREKGAVTPVKNQNPCGSCWAFSTVATIEGINKIITGQLISLSEQELLDCEYRSHGCDGGYQTPSLQYVVDNGVHTEREYPYEKKQGRCRAKDKKGPKVYITGYKYVPANDEISLIQAIANQPVSVVTDSRGRGFQFYKGGIYEGPCGTNTDHAVTAVGYGKTYLLLKNSWGPNWGEKGYIRIKRASGRSKGTCGVYTSSFFPIKG 212
               SCOP domains d2bdzc_ C: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains 2bdzC00 C:1-212 Cysteine proteinases                                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.................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_PROTE--------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bdz C   1 YPESIDWREKGAVTPVKNQNPCGSCWAFSTVATIEGINKIITGQLISLSEQELLDCERRSHGCDGGYQTTSLQYVVDNGVHTEREYPYEKKQGRCRAKDKKGPKVYITGYKYVPANDEISLIQAIANQPVSVVTDSRGRGFQFYKGGIYEGPCGTNTDHAVTAVGYGKTYLLLKNSWGPNWGEKGYIRIKRASGRSKGTCGVYTSSFFPIKG 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain D from PDB  Type:PROTEIN  Length:212
 aligned with MEX1_JACME | P84346 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
           MEX1_JACME     1 YPESIDWREKGAVTPVKNQNPCGSCWAFSTVATIEGINKIITGQLISLSEQELLDCEYRSHGCDGGYQTPSLQYVVDNGVHTEREYPYEKKQGRCRAKDKKGPKVYITGYKYVPANDEISLIQAIANQPVSVVTDSRGRGFQFYKGGIYEGPCGTNTDHAVTAVGYGKTYLLLKNSWGPNWGEKGYIRIKRASGRSKGTCGVYTSSFFPIKG 212
               SCOP domains d2bdzd_ D: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains 2bdzD00 D:1-212 Cysteine proteinases                                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh................hhhhh........eeee....hhhhhhhhhhhh.eeeee...hhhhhh....ee.........eeeeeeee...eeeee...........eeeee.......hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE--------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bdz D   1 YPESIDWREKGAVTPVKNQNPCGSCWAFSTVATIEGINKIITGQLISLSEQELLDCERRSHGCDGGYQTTSLQYVVDNGVHTEREYPYEKKQGRCRAKDKKGPKVYITGYKYVPANDEISLIQAIANQPVSVVTDSRGRGFQFYKGGIYEGPCGTNTDHAVTAVGYGKTYLLLKNSWGPNWGEKGYIRIKRASGRSKGTCGVYTSSFFPIKG 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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)

Jacaratia mexicana [TaxId: 309130] (1)

1a	d2bdza_	A:
1b	d2bdzb_	B:
1c	d2bdzc_	C:
1d	d2bdzd_	D:

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)

Jacaratia mexicana. Organism_taxid: 309130. (1)

1a	2bdzA00	A:1-212
1b	2bdzB00	B:1-212
1c	2bdzC00	C:1-212
1d	2bdzD00	D:1-212

(no "Pfam Domain" information available for 2BDZ)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (MEX1_JACME | P84346)

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: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
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	Cis Peptide Bonds
		Asn A:20 - Pro A:21	[ RasMol ]
		Asn B:20 - Pro B:21	[ RasMol ]
		Asn C:20 - Pro C:21	[ RasMol ]
		Asn D:20 - Pro D:21	[ RasMol ]
		Gly A:151 - Pro A:152	[ RasMol ]
		Gly B:151 - Pro B:152	[ RasMol ]
		Gly C:151 - Pro C:152	[ RasMol ]
		Gly D:151 - Pro D:152	[ RasMol ]

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Access by PDB/NDB ID
	2bdz
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	3.4.22.-
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(no "Entries Sharing at Least One Protein Chain" available for 2BDZ)

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (12, 12)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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