3LXS - JenaLib

Asymmetric Unit (26, 26)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:19 , GLY A:23 , CYS A:25 , TRP A:26 , CYS A:63 , SER A:64 , GLY A:65 , GLY A:66 , LEU A:67 , MET A:145 , LEU A:160 , ASP A:161 , HIS A:162 , TRP A:184 , GLU A:208 , EDO A:227 , HOH A:247 , HOH A:355 , ASP C:161 , 4MC C:216	BINDING SITE FOR RESIDUE 4MC A 216
02	AC2	SOFTWARE	LYS A:17 , ASP A:18 , GLU A:50 , HOH A:298 , HOH A:463	BINDING SITE FOR RESIDUE EDO A 221
03	AC3	SOFTWARE	TRP A:7 , ARG A:10 , LEU A:40 , HOH A:389 , TRP C:7 , ARG C:10 , PHE C:39 , LEU C:40	BINDING SITE FOR RESIDUE EDO A 222
04	AC4	SOFTWARE	ASP A:18 , GLN A:19 , GLY A:20 , HOH A:480	BINDING SITE FOR RESIDUE EDO A 225
05	AC5	SOFTWARE	4MC A:216 , HOH A:232 , HOH A:372 , 4MC C:216	BINDING SITE FOR RESIDUE EDO A 227
06	AC6	SOFTWARE	TYR A:147 , GLY A:149 , VAL A:151 , MET A:152 , HOH A:485 , HOH A:488	BINDING SITE FOR RESIDUE EDO A 230
07	AC7	SOFTWARE	HIS A:43 , PRO A:44 , HOH A:386 , HOH A:407 , HOH A:415 , HOH A:448 , PRO C:2 , ALA C:3 , HOH C:348	BINDING SITE FOR RESIDUE SO4 A 217
08	AC8	SOFTWARE	PRO A:2 , ALA A:3 , HOH A:307 , HOH A:442 , HOH A:457 , HIS C:43 , PRO C:44	BINDING SITE FOR RESIDUE SO4 A 218
09	AC9	SOFTWARE	THR A:102 , THR A:103 , SER A:104 , THR A:111 , HOH A:368 , EDO C:236	BINDING SITE FOR RESIDUE SO4 A 219
10	BC1	SOFTWARE	ARG A:195 , HOH A:336 , HOH A:405 , ASN C:80	BINDING SITE FOR RESIDUE SO4 A 220
11	BC2	SOFTWARE	ASP A:161 , 4MC A:216 , EDO A:227 , GLN C:19 , GLY C:23 , CYS C:25 , TRP C:26 , CYS C:63 , GLY C:65 , GLY C:66 , LEU C:67 , MET C:145 , LEU C:160 , ASP C:161 , HIS C:162 , TRP C:184 , GLU C:208 , HOH C:412	BINDING SITE FOR RESIDUE 4MC C 216
12	BC3	SOFTWARE	LYS C:17 , GLU C:86 , HOH C:247 , HOH C:371	BINDING SITE FOR RESIDUE EDO C 223
13	BC4	SOFTWARE	ALA C:127 , TRP C:128 , HOH C:367 , HOH C:386 , HOH C:473	BINDING SITE FOR RESIDUE EDO C 224
14	BC5	SOFTWARE	CYS A:155 , VAL A:156 , SER A:157 , HOH A:256 , HOH A:294 , HOH A:419 , PRO C:100	BINDING SITE FOR RESIDUE EDO C 225
15	BC6	SOFTWARE	GLU A:122 , GLY A:199 , ASN A:201 , LYS A:206 , HOH A:305 , GLY C:105 , THR C:107 , HOH C:267	BINDING SITE FOR RESIDUE EDO C 226
16	BC7	SOFTWARE	ALA A:9 , SO4 C:218 , HOH C:349	BINDING SITE FOR RESIDUE EDO C 227
17	BC8	SOFTWARE	ASN C:79 , ASN C:80 , ALA C:82 , TYR C:84	BINDING SITE FOR RESIDUE EDO C 228
18	BC9	SOFTWARE	LEU C:45 , HOH C:320	BINDING SITE FOR RESIDUE EDO C 229
19	CC1	SOFTWARE	ALA C:1 , ALA C:123 , ALA C:126 , ASP C:171 , LYS C:198	BINDING SITE FOR RESIDUE EDO C 230
20	CC2	SOFTWARE	LYS C:198 , GLY C:199 , HOH C:263 , HOH C:318 , HOH C:397	BINDING SITE FOR RESIDUE EDO C 232
21	CC3	SOFTWARE	PHE A:39 , ALA C:9	BINDING SITE FOR RESIDUE EDO C 233
22	CC4	SOFTWARE	TRP A:38 , HIS A:43 , VAL A:214 , SO4 A:219 , HOH A:300 , ALA C:1	BINDING SITE FOR RESIDUE EDO C 236
23	CC5	SOFTWARE	ASP C:18 , GLN C:19 , GLY C:20	BINDING SITE FOR RESIDUE EDO C 238
24	CC6	SOFTWARE	HOH A:253 , HOH A:364 , THR C:102 , THR C:103 , SER C:104	BINDING SITE FOR RESIDUE SO4 C 217
25	CC7	SOFTWARE	ARG A:10 , HOH A:236 , HIS C:43 , PRO C:44 , EDO C:227 , HOH C:306 , HOH C:328 , HOH C:359 , HOH C:433	BINDING SITE FOR RESIDUE SO4 C 218
26	CC8	SOFTWARE	GLY C:150 , ARG C:195 , HOH C:261 , HOH C:366	BINDING SITE FOR RESIDUE SO4 C 221

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 14)

Asymmetric Unit (7, 14)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CYSP_TRYCR_009 *	S	146	G	CYSP_TRYCR	---	---	A/C	S	24	G
2	UniProt	VAR_CYSP_TRYCR_010 *	S	186	G	CYSP_TRYCR	---	---	A/C	S	64	G
3	UniProt	VAR_CYSP_TRYCR_011 *	A	204	G	CYSP_TRYCR	---	---	A/C	A	82	G
4	UniProt	VAR_CYSP_TRYCR_012 *	V	286	F	CYSP_TRYCR	---	---	A/C	V	164	F
5	UniProt	VAR_CYSP_TRYCR_013 *	V	286	L	CYSP_TRYCR	---	---	A/C	V	164	L
6	UniProt	VAR_CYSP_TRYCR_014 *	T	308	A	CYSP_TRYCR	---	---	A/C	T	186	A
7	UniProt	VAR_CYSP_TRYCR_015 *	E	313	D	CYSP_TRYCR	---	---	A/C	E	191	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CYSP_TRYCR_009 *	S	146	G	CYSP_TRYCR	---	---	A	S	24	G
2	UniProt	VAR_CYSP_TRYCR_010 *	S	186	G	CYSP_TRYCR	---	---	A	S	64	G
3	UniProt	VAR_CYSP_TRYCR_011 *	A	204	G	CYSP_TRYCR	---	---	A	A	82	G
4	UniProt	VAR_CYSP_TRYCR_012 *	V	286	F	CYSP_TRYCR	---	---	A	V	164	F
5	UniProt	VAR_CYSP_TRYCR_013 *	V	286	L	CYSP_TRYCR	---	---	A	V	164	L
6	UniProt	VAR_CYSP_TRYCR_014 *	T	308	A	CYSP_TRYCR	---	---	A	T	186	A
7	UniProt	VAR_CYSP_TRYCR_015 *	E	313	D	CYSP_TRYCR	---	---	A	E	191	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CYSP_TRYCR_009 *	S	146	G	CYSP_TRYCR	---	---	C	S	24	G
2	UniProt	VAR_CYSP_TRYCR_010 *	S	186	G	CYSP_TRYCR	---	---	C	S	64	G
3	UniProt	VAR_CYSP_TRYCR_011 *	A	204	G	CYSP_TRYCR	---	---	C	A	82	G
4	UniProt	VAR_CYSP_TRYCR_012 *	V	286	F	CYSP_TRYCR	---	---	C	V	164	F
5	UniProt	VAR_CYSP_TRYCR_013 *	V	286	L	CYSP_TRYCR	---	---	C	V	164	L
6	UniProt	VAR_CYSP_TRYCR_014 *	T	308	A	CYSP_TRYCR	---	---	C	T	186	A
7	UniProt	VAR_CYSP_TRYCR_015 *	E	313	D	CYSP_TRYCR	---	---	C	E	191	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (3, 6)

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.	CYSP_TRYCR	141-152	2	A:19-30 C:19-30
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CYSP_TRYCR	282-292	2	A:160-170 C:160-170
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	CYSP_TRYCR	299-318	2	A:177-196 C:177-196

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.	CYSP_TRYCR	141-152	1	A:19-30 -
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CYSP_TRYCR	282-292	1	A:160-170 -
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	CYSP_TRYCR	299-318	1	A:177-196 -

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.	CYSP_TRYCR	141-152	1	- C:19-30
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	CYSP_TRYCR	282-292	1	- C:160-170
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	CYSP_TRYCR	299-318	1	- C:177-196

Exons (0, 0)

Sequences/Alignments

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:215
 aligned with CYSP_TRYCR | P25779 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:215
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332     
           CYSP_TRYCR   123 APAAVDWRARGAVTAVKDQGQCGSCWAFSAIGNVECQWFLAGHPLTNLSEQMLVSCDKTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVMTSCVSEQLDHGVLLVGYNDSAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVVG 337
               SCOP domains d3lxsa_ A: Cruzain                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.................hhhhhhhhhhhhhhhhhh.......hhhhhhhhh...hhhhh.hhhhhhhhhhhhh..eee.......................eeee..eeee...hhhhhhhhhhhhh.eeeee.hhhhh.....ee.........eeeeeeeee......eeeee...........eeeee...hhhhh...eeeee.. Sec.struct. author
             SAPs(SNPs) (1) -----------------------G---------------------------------------G-----------------G---------------------------------------------------------------------------------F---------------------A----D------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------L--------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------THIOL_PROTEA---------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  ------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lxs A   1 APAAVDWRARGAVTAVKDQGQCGSCWAFSAIGNVECQWFLAGHPLTNLSEQMLVSCDKTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVMTSCVSEQLDHGVLLVGYNDSAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVVG 215
                                    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:215
 aligned with CYSP_TRYCR | P25779 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:215
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332     
           CYSP_TRYCR   123 APAAVDWRARGAVTAVKDQGQCGSCWAFSAIGNVECQWFLAGHPLTNLSEQMLVSCDKTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVMTSCVSEQLDHGVLLVGYNDSAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVVG 337
               SCOP domains d3lxsc_ C: Cruzain                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Peptidase_C1-3lxsC01 C:1-213                                                                                                                                                                                         -- Pfam domains (1)
           Pfam domains (2) Peptidase_C1-3lxsC02 C:1-213                                                                                                                                                                                         -- Pfam domains (2)
         Sec.struct. author ...eee.................hhhhhhhhhhhhhhhhhh.......hhhhhhhhh...hhhhh.hhhhhhhhhhhhh..eee.hhhh..................eeee..eeee...hhhhhhhhhhhhh.eeeee...........ee.........eeeeeeeee......eeeee...........eeeee...hhhhh...eeeee.. Sec.struct. author
             SAPs(SNPs) (1) -----------------------G---------------------------------------G-----------------G---------------------------------------------------------------------------------F---------------------A----D------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------L--------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------THIOL_PROTEA---------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  ------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lxs C   1 APAAVDWRARGAVTAVKDQGQCGSCWAFSAIGNVECQWFLAGHPLTNLSEQMLVSCDKTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVMTSCVSEQLDHGVLLVGYNDSAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVVG 215
                                    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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0 ; only for superseded entry 2EFM: 1,2)

Pfam Domains (1, 2)

Gene Ontology (5, 5)

Asymmetric Unit(hide GO term definitions)

Chain A,C (CYSP_TRYCR | P25779)

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.

Visualization

Interactive Views

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
		4MC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]
		CC5	[ RasMol ]	+environment [ RasMol ]
		CC6	[ RasMol ]	+environment [ RasMol ]
		CC7	[ RasMol ]	+environment [ RasMol ]
		CC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3lxs)

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

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3lxs
		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
	CYSP_TRYCR \| P25779
		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)
	3.4.22.51
		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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 26)

Sites (26, 26)