3FZZ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF GRC

Authors :   A. M. Buckle, D. Kaiserman, J. C. Whisstock

Date :   27 Jan 09 (Deposition) - 17 Mar 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Hydrolase, Cytolysis, Protease, Serine Protease, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Kaiserman, A. M. Buckle, P. Van Damme, J. A. Irving, R. H. P. Law, A. Y. Matthews, T. Bashtannyk-Puhalovich, C. Langendorf, P. Thompson, J. Vandekerckhove, K. Gevaert, J. C. Whisstock, P. I. Bir
Structure Of Granzyme C Reveals An Unusual Mechanism Of Protease Autoinhibition
Proc. Natl. Acad. Sci. Usa V. 106 5587 2009
PubMed-ID: 19299505 | Reference-DOI: 10.1073/PNAS.0811968106

Molecule 1 - GRANZYME C
	Chains	:	A, B
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	CYTOTOXIC CELL PROTEASE 2, CCP2, B10

		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 (1, 7)

No.	Name	Count	Type	Full Name
1	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:122 , ARG A:123	BINDING SITE FOR RESIDUE SO4 A 2
2	AC2	SOFTWARE	PRO A:158 , LYS A:159 , THR A:160	BINDING SITE FOR RESIDUE SO4 A 4
3	AC3	SOFTWARE	ARG A:132 , ARG A:133	BINDING SITE FOR RESIDUE SO4 A 6
4	AC4	SOFTWARE	ARG A:132 , ARG A:212 , ARG B:132 , ARG B:212	BINDING SITE FOR RESIDUE SO4 B 1
5	AC5	SOFTWARE	THR B:122 , ARG B:123	BINDING SITE FOR RESIDUE SO4 B 3
6	AC6	SOFTWARE	PRO B:158 , LYS B:159 , THR B:160	BINDING SITE FOR RESIDUE SO4 B 5
7	AC7	SOFTWARE	ARG B:132 , ARG B:133	BINDING SITE FOR RESIDUE SO4 B 7

Asymmetric Unit

No.	Residues
1	A:50	-	A:66
2	A:143	-	A:210
3	A:174	-	A:189
4	B:50	-	B:66
5	B:143	-	B:210
6	B:174	-	B:189

Asymmetric Unit

No.	Residues
1	Asp A:224	-	Gly A:225
2	Ala A:227	-	Pro A:228
3	Val B:43	-	Gly B:44
4	Asp B:224	-	Gly B:225
5	Ala B:227	-	Pro B:228

(no "SAP(SNP)/Variant" information available for 3FZZ)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	GRAC_MOUSE	21-246	2	A:21-246 B:21-246
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	GRAC_MOUSE	61-66	2	A:61-66 B:61-66

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	GRAC_MOUSE	21-246	1	A:21-246 -
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	GRAC_MOUSE	61-66	1	A:61-66 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	GRAC_MOUSE	21-246	1	- B:21-246
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	GRAC_MOUSE	61-66	1	- B:61-66

(no "Exon" information available for 3FZZ)

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:227
 aligned with GRAC_MOUSE | P08882 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:227
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
           GRAC_MOUSE    21 IIGGNEISPHSRPYMAYYEFLKVGGKKMFCGGFLVRDKFVLTAAHCKGSSMTVTLGAHNIKAKEETQQIIPVAKAIPHPDYNPDDRSNDIMLLKLVRNAKRTRAVRPLNLPRRNAHVKPGDECYVAGWGKVTPDGEFPKTLHEVKLTVQKDQVCESQFQSSYNRANEICVGDSKIKGASFEEDSGGPLVCKRAAAGIVSYGQTDGSAPQVFTRVLSFVSWIKKTMKH 247
               SCOP domains d3fzza_ A: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains 3fzzA01     3fzzA02 A:33-127,A:236-247 Trypsin-like serine proteases                                       3fzzA01 A:21-32,A:128-235 Trypsin-like serine proteases                                                     3fzzA02      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeeee.....eeeeeeeeee..eeee......eeeeeee............eeeeeeeeee.............eeeee..........................eeeeee..............eeeeee..hhhhhhhhhh.......eeee................eeee..eeeeeeee........eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:21-246 UniProt: 21-246                                                                                                                                                                                        - PROSITE (1)
                PROSITE (2) ----------------------------------------TRYPSI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fzz A  21 IIGGNEISPHSRPYMAYYEFLKVGGKKMFCGGFLVRDKFVLTAAHCKGRSMTVTLGAHNIKAKEETQQIIPVAKAIPHPDYNPDDRSNDIMLLKLVRNAKRTRAVRPLNLPRRNAHVKPGDECYVAGWGKVTPDGEFPKTLHEVKLTVQKDQVCESQFQSSYNRANEICVGDSKIKGASFEEDSGGPLVCKRAAAGIVSYGQTDGSAPQVFTRVLSFVSWIKKTMKH 247
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with GRAC_MOUSE | P08882 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:227
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
           GRAC_MOUSE    21 IIGGNEISPHSRPYMAYYEFLKVGGKKMFCGGFLVRDKFVLTAAHCKGSSMTVTLGAHNIKAKEETQQIIPVAKAIPHPDYNPDDRSNDIMLLKLVRNAKRTRAVRPLNLPRRNAHVKPGDECYVAGWGKVTPDGEFPKTLHEVKLTVQKDQVCESQFQSSYNRANEICVGDSKIKGASFEEDSGGPLVCKRAAAGIVSYGQTDGSAPQVFTRVLSFVSWIKKTMKH 247
               SCOP domains d3fzzb_ B: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains 3fzzB01     3fzzB02 B:33-127,B:236-247 Trypsin-like serine proteases                                       3fzzB01 B:21-32,B:128-235 Trypsin-like serine proteases                                                     3fzzB02      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeeee.....eeeeeeeeee..eeee......eeeeeee............eeeeeeeeee.............eeeee..........................eeeeee..............eeeeee..hhhhhhhhhh.......eeee................eeee..eeeeeeee........eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:21-246 UniProt: 21-246                                                                                                                                                                                        - PROSITE (1)
                PROSITE (2) ----------------------------------------TRYPSI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fzz B  21 IIGGNEISPHSRPYMAYYEFLKVGGKKMFCGGFLVRDKFVLTAAHCKGRSMTVTLGAHNIKAKEETQQIIPVAKAIPHPDYNPDDRSNDIMLLKLVRNAKRTRAVRPLNLPRRNAHVKPGDECYVAGWGKVTPDGEFPKTLHEVKLTVQKDQVCESQFQSSYNRANEICVGDSKIKGASFEEDSGGPLVCKRAAAGIVSYGQTDGSAPQVFTRVLSFVSWIKKTMKH 247
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

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: All beta proteins (24004)

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Eukaryotic proteases (1343)

Protein domain: automated matches (162)

Mouse (Mus musculus) [TaxId: 10090] (2)

1a	d3fzza_	A:
1b	d3fzzb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Mouse (Mus musculus) (6)

1a	3fzzA01	A:21-32,A:128-235
1b	3fzzA02	A:33-127,A:236-247
1c	3fzzB02	B:33-127,B:236-247
1d	3fzzB01	B:21-32,B:128-235

(no "Pfam Domain" information available for 3FZZ)

Asymmetric Unit(hide GO term definitions)

Chain A,B (GRAC_MOUSE | P08882)

molecular function
	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.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0016485	protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:227 - Pro A:228	[ RasMol ]
		Ala B:227 - Pro B:228	[ RasMol ]
		Asp A:224 - Gly A:225	[ RasMol ]
		Asp B:224 - Gly B:225	[ RasMol ]
		Val B:43 - Gly B:44	[ RasMol ]

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	3fzz
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	GRAC_MOUSE \| P08882
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	3.4.21.-
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	GRAC_MOUSE \| P08882	:	3g01

(no "Related Entries Specified in the PDB File" available for 3FZZ)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 7)

Sites (7, 7)

SS Bonds (6, 6)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

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