1FI8 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   RAT GRANZYME B [N66Q] COMPLEXED TO ECOTIN [81-84 IEPD]

Authors :   S. M. Waugh, J. L. Harris, R. J. Fletterick, C. S. Craik

Date :   03 Aug 00 (Deposition) - 13 Sep 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Complex (Serine Protease/Inhibitor), Protease Substrate Interactions, Beta Strand Structure, Chymotrypsin Fold, Granzyme B, Ecotin, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Waugh, J. L. Harris, R. Fletterick, C. S. Craik
The Structure Of The Pro-Apoptotic Protease Granzyme B Reveals The Molecular Determinants Of Its Specificity
Nat. Struct. Biol. V. 7 762 2000
PubMed-ID: 10966646 | Reference-DOI: 10.1038/78992
(for further references see the PDB file header)

Molecule 1 - NATURAL KILLER CELL PROTEASE 1
	Chains	:	A, B
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPICZAA
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Other Details	:	CYTOTOXIC LYMPHOCYTE GRANULES
	Synonym	:	GRANZYME B

Molecule 2 - ECOTIN
	Chains	:	C, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTACTAC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 28 - 111
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 3 - ECOTIN
	Chains	:	D, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTACTAC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 112 - 169
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1FI8)

(no "Site" information available for 1FI8)

Asymmetric/Biological Unit

No.	Residues
1	A:42	-	A:58
2	A:136	-	A:201
3	A:168	-	A:182
4	B:42	-	B:58
5	B:136	-	B:201
6	B:168	-	B:182

Asymmetric/Biological Unit

No.	Residues
1	Thr A:224	-	Pro A:225
2	Thr B:224	-	Pro B:225

(no "SAP(SNP)/Variant" information available for 1FI8)

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	GRAB_RAT	21-246	2	A:16-243 B:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	GRAB_RAT	61-66	2	A:53-58 B:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	GRAB_RAT	198-209	2	A:189-200 B:189-200

(no "Exon" information available for 1FI8)

Asymmetric/Biological 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:226
 aligned with GRAB_RAT | P18291 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       
            GRAB_RAT     21 IIGGHEAKPHSRPYMAYLQIMDEYSGSKKCGGFLIREDFVLTAAHCSGSKINVTLGAHNIKEQEKMQQIIPVVKIIPHPAYNSKTISNDIMLLKLKSKAKRSSAVKPLNLPRRNVKVKPGDVCYVAGWGKLGPMGKYSDTLQEVELTVQEDQKCESYLKNYFDKANEICAGDPKIKRASFRGDSGGPLVCKKVAAGIVSYGQNDGSTPRAFTKVSTFLSWIKKTMKK  247
               SCOP domains d1fi8a_ A: Granzyme B                                                                                                                                                                                                               SCOP domains
               CATH domains 1fi8A01     1fi8A02 A:28- 120,A:233-243 Trypsin-like serine proteases                                      1fi8A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     1fi8A02    - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeeee....-..eeeeeeee..eeeehhhhh..eeeeee............eeeeeeeeee.............eeeee..........................eeeeee..............eeeeee..hhhhhhhhh........eeee................eeee..eeeeeeeeee......eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 21-246                                                                                                                                                                                        - PROSITE (1)
                PROSITE (2) ----------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1fi8 A   16 IIGGHEAKPHSRPYMAYLQIMDEYS-SKKCGGFLIREDFVLTAAHCSGSKIQVTLGAHNIKEQEKMQQIIPVVKIIPHPAYNSKTISNDIMLLKLKSKAKRSSAVKPLNLPRRNVKVKPGDVCYVAGWGKLGPMGKYSDTLQEVELTVQEDQKCESYLKNYFDKANEICAGDPKIKRASFRGDSGGPLVCKKVAAGIVSYGQNDGSTPRAFTKVSTFLSWIKKTMKK  244
                                    25        35 || | | 42        52        64   |    73        83        93       103       113       123       133       143     ||154       164      |173       183|    | 191       201  ||   215     ||227       237       
                                               36A| | |                    61| 67A                                                                               149|                171A          184A 188A              204|         221|                    
                                                36B | |                     64                                                                                    151                                                      209          224                    
                                                  37A |                                                                                                                                                                                                        
                                                     39

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with GRAB_RAT | P18291 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       
            GRAB_RAT     21 IIGGHEAKPHSRPYMAYLQIMDEYSGSKKCGGFLIREDFVLTAAHCSGSKINVTLGAHNIKEQEKMQQIIPVVKIIPHPAYNSKTISNDIMLLKLKSKAKRSSAVKPLNLPRRNVKVKPGDVCYVAGWGKLGPMGKYSDTLQEVELTVQEDQKCESYLKNYFDKANEICAGDPKIKRASFRGDSGGPLVCKKVAAGIVSYGQNDGSTPRAFTKVSTFLSWIKKTMKK  247
               SCOP domains d1fi8b_ B: Granzyme B                                                                                                                                                                                                               SCOP domains
               CATH domains 1fi8B01     1fi8B02 B:28-120,B:233-243 Trypsin-like serine proteases                                       1fi8B01 B:16-27,B:121-232 Trypsin-like serine proteases                                                     1fi8B02    - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeeee.....eeeeeeeeee..eeeehhhhh..eeeeee............eeeeeeeeee.............eeeee..........................eeeeee..............eeeeee..hhhhhhhhh........eeee................eeee..eeeeeeeeee......eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 21-246                                                                                                                                                                                        - PROSITE (1)
                PROSITE (2) ----------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1fi8 B   16 IIGGHEAKPHSRPYMAYLQIMDEYSGSKKCGGFLIREDFVLTAAHCSGSKIQVTLGAHNIKEQEKMQQIIPVVKIIPHPAYNSKTISNDIMLLKLKSKAKRSSAVKPLNLPRRNVKVKPGDVCYVAGWGKLGPMGKYSDTLQEVELTVQEDQKCESYLKNYFDKANEICAGDPKIKRASFRGDSGGPLVCKKVAAGIVSYGQNDGSTPRAFTKVSTFLSWIKKTMKK  244
                                    25        35 || |   42        52        64   |    73        83        93       103       113       123       133       143     ||154       164      |173       183|    | 191       201  ||   215     ||227       237       
                                               36A| |                      61| 67A                                                                               149|                171A          184A 188A              204|         221|                    
                                                36B |                       64                                                                                    151                                                      209          224                    
                                                  37A

Chain C from PDB  Type:PROTEIN  Length:78
 aligned with ECOT_ECOLI | P23827 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:84
                                    35        45        55        65        75        85        95       105    
          ECOT_ECOLI     26 PLEKIAPYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDCNLHRLGGKLENKTLEGWGYDYYVFDKVSSPVSTMMACPD  109
               SCOP domains d1fi8.1 C:,D: Ecotin, trypsin inhibitor                                              SCOP domains
               CATH domains 1fi8C00 C:6-84  [code=2.60.40.550, no name de fined]                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh.........eeeeee......hhh.eeeeeeeeee.....-......eeeeee......eeeeee.....ee-----e. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                1fi8 C    6 PLEKIAPYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDC-LHRLGGKLENKTLEGWGYDYYVFDKVSSPIE-----PD   84
                                    15        25        35        45    | | 55        65        75      |  -  | 
                                                                       50 |                            82    83 
                                                                         52

Chain D from PDB  Type:PROTEIN  Length:48
 aligned with ECOT_ECOLI | P23827 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:48
                                   124       134       144       154        
          ECOT_ECOLI    115 KFVTAYLGDAGMLRYNSKLPIVVYTPDNVDVKYRVWKAEEKIDNAVVR  162
               SCOP domains d1fi8.1 C:,D: Ecotin, trypsin inhibitor          SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author .eee..hhhh.eee......eeeeee...eeeeeeeee....ee.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                1fi8 D   95 KFVTAYLGDAGMLRYNSKLPIVVYTPDNVDVKYRVWKAEEKIDNAVVR  142
                                   104       114       124       134

Chain E from PDB  Type:PROTEIN  Length:76
 aligned with ECOT_ECOLI | P23827 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:84
                                    35        45        55        65        75        85        95       105    
          ECOT_ECOLI     26 PLEKIAPYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDCNLHRLGGKLENKTLEGWGYDYYVFDKVSSPVSTMMACPD  109
               SCOP domains d1fi8.2 E:,F: Ecotin, trypsin inhibitor                                              SCOP domains
               CATH domains 1fi8E00 E:6-84  [code=2.60.40.550, no name de fined]                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh.........eeeeee......hhh.eeeeeeeeee.....-......eeeeee......eeeeee--...ee-----e. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                1fi8 E    6 PLEKIAPYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDC-LHRLGGKLENKTLEGWGYDYYVFD--SSPIE-----PD   84
                                    15        25        35        45    | | 55        65        75  |   |  -  | 
                                                                       50 |                     75 78  82    83 
                                                                         52

Chain F from PDB  Type:PROTEIN  Length:48
 aligned with ECOT_ECOLI | P23827 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:48
                                   124       134       144       154        
          ECOT_ECOLI    115 KFVTAYLGDAGMLRYNSKLPIVVYTPDNVDVKYRVWKAEEKIDNAVVR  162
               SCOP domains d1fi8.2 E:,F: Ecotin, trypsin inhibitor          SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author .eee..hhhh.eee......eeeeee...eeeeeeeee....ee.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                1fi8 F   95 KFVTAYLGDAGMLRYNSKLPIVVYTPDNVDVKYRVWKAEEKIDNAVVR  142
                                   104       114       124       134

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Ecotin, trypsin inhibitor (19)

Superfamily: Ecotin, trypsin inhibitor (19)

Family: Ecotin, trypsin inhibitor (19)

Protein domain: Ecotin, trypsin inhibitor (17)

Escherichia coli [TaxId: 562] (17)

1a	d1fi8.1	C:,D:
1b	d1fi8.2	E:,F:

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Eukaryotic proteases (1343)

Protein domain: Granzyme B (3)

Norway rat (Rattus norvegicus) [TaxId: 10116] (1)

2a	d1fi8a_	A:
2b	d1fi8b_	B:

Asymmetric/Biological 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)

Norway rat (Rattus norvegicus) (18)

1a	1fi8A01	A:16-27,A:121-232
1b	1fi8B01	B:16-27,B:121-232
1c	1fi8B02	B:28-120,B:233-243
1d	1fi8A02	A:28-120,A:233-243

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.550, no name defined] (17)

Norway rat (Rattus norvegicus) (1)

2a	1fi8C00	C:6-84
2b	1fi8E00	E:6-84

(no "Pfam Domain" information available for 1FI8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GRAB_RAT | P18291)

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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	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:0010942	positive regulation of cell death	Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
	GO:0060545	positive regulation of necroptotic process	Any process that increases the rate, frequency or extent of a necroptotic process, a necrotic cell death process that results from the activation of endogenous cellular processes, such as signaling involving death domain receptors or Toll-like receptors.
	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:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.

Chain C,D,E,F (ECOT_ECOLI | P23827)

molecular function
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
cellular component
	GO:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric/Biological Unit
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(no "Sites" information available for 1fi8)

	Cis Peptide Bonds
		Thr A:224 - Pro A:225	[ RasMol ]
		Thr B:224 - Pro B:225	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 1FI8)

Description

Compounds

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

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