1OP8 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN GRANZYME A

Authors :   C. Hink-Schauer, E. Estebanez-Perpina, W. Bode, D. Jenne

Date :   05 Mar 03 (Deposition) - 01 Jul 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Granzyme A, Serine Proteinase, Apoptosis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Hink-Schauer, E. Estebanez-Perpina, F. Kurschus, W. Bode, D. Jenne
Crystal Structure Of The Apoptosis-Inducing Human Granzyme A Dimer
Nat. Struct. Biol. V. 10 535 2003
PubMed-ID: 12819770 | Reference-DOI: 10.1038/NSB945
(for further references see the PDB file header)

Molecule 1 - GRANZYME A
	Chains	:	A, B, C, D, E, F
	EC Number	:	3.4.21.78
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 12)

No.	Name	Count	Type	Full Name
1	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 4)

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

Biological Unit 3 (1, 3)

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

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY F:19 , ASN F:20 , GLU F:21 , ARG F:156	BINDING SITE FOR RESIDUE SO4 F 1001
02	AC2	SOFTWARE	ILE A:17 , GLY A:18 , GLY A:19 , THR A:144 , HIS A:145 , ARG A:156 , HOH A:1023	BINDING SITE FOR RESIDUE SO4 A 1003
03	AC3	SOFTWARE	ASN B:20 , GLU B:21 , ARG B:156	BINDING SITE FOR RESIDUE SO4 B 1005
04	AC4	SOFTWARE	ILE C:16 , ILE C:17 , GLY C:18 , GLY C:19 , THR C:144 , HIS C:145 , ARG C:156 , HOH C:1017	BINDING SITE FOR RESIDUE SO4 C 1006
05	AC5	SOFTWARE	ARG C:27 , HOH C:1119 , SER F:185 , LEU F:186 , ARG F:187 , HOH F:1027	BINDING SITE FOR RESIDUE SO4 C 1008
06	AC6	SOFTWARE	SER B:185 , LEU B:186 , ARG B:187 , HOH B:1092 , ARG E:27	BINDING SITE FOR RESIDUE SO4 B 1009
07	AC7	SOFTWARE	ARG A:27 , THR D:161 , SER D:185 , LEU D:186 , ARG D:187	BINDING SITE FOR RESIDUE SO4 A 1010
08	AC8	SOFTWARE	ASN D:20 , GLU D:21 , ARG D:156	BINDING SITE FOR RESIDUE SO4 D 1015
09	AC9	SOFTWARE	ILE F:17 , GLY F:18 , HIS F:145 , ASN F:146 , ARG F:156	BINDING SITE FOR RESIDUE SO4 F 1019
10	BC1	SOFTWARE	ILE E:17 , GLY E:18 , GLY E:19 , THR E:144 , HIS E:145 , ARG E:156	BINDING SITE FOR RESIDUE SO4 E 1020
11	BC2	SOFTWARE	GLY D:18 , GLY D:19 , THR D:144 , HIS D:145 , ASN D:146 , ARG D:156 , HOH D:1088	BINDING SITE FOR RESIDUE SO4 D 1022
12	BC3	SOFTWARE	ILE B:17 , GLY B:18 , HIS B:145 , HOH B:1075	BINDING SITE FOR RESIDUE SO4 B 1023

Asymmetric Unit

No.	Residues
1	A:42	-	A:58
2	A:93	-	B:93
3	A:136	-	A:201
4	A:168	-	A:182
5	A:191	-	A:220
6	B:42	-	B:58
7	B:136	-	B:201
8	B:168	-	B:182
9	B:191	-	B:220
10	C:42	-	C:58
11	C:93	-	D:93
12	C:136	-	C:201
13	C:168	-	C:182
14	C:191	-	C:220
15	D:42	-	D:58
16	D:136	-	D:201
17	D:168	-	D:182
18	D:191	-	D:220
19	E:42	-	E:58
20	E:93	-	F:93
21	E:136	-	E:201
22	E:168	-	E:182
23	E:191	-	E:220
24	F:42	-	F:58
25	F:136	-	F:201
26	F:168	-	F:182
27	F:191	-	F:220

Asymmetric Unit

No.	Residues
1	Asn A:173B	-	Pro A:174
2	Asn B:173B	-	Pro B:174
3	Asn C:173B	-	Pro C:174
4	Asn D:173B	-	Pro D:174
5	Asn E:173B	-	Pro E:174
6	Asn F:173B	-	Pro F:174

Asymmetric Unit (1, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024291	M	121	T	GRAA_HUMAN	Polymorphism	3104233	A/B/C/D/E/F	T	109	T

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

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024291	M	121	T	GRAA_HUMAN	Polymorphism	3104233	A/B	T	109	T

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

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024291	M	121	T	GRAA_HUMAN	Polymorphism	3104233	C/D	T	109	T

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

Biological Unit 3 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024291	M	121	T	GRAA_HUMAN	Polymorphism	3104233	E/F	T	109	T

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

Asymmetric Unit (3, 18)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	GRAA_HUMAN	29-259	6	A:16-243 B:16-243 C:16-243 D:16-243 E:16-243 F:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	GRAA_HUMAN	65-70	6	A:53-58 B:53-58 C:53-58 D:53-58 E:53-58 F:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	GRAA_HUMAN	206-217	6	A:189-200 B:189-200 C:189-200 D:189-200 E:189-200 F:189-200

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	GRAA_HUMAN	29-259	2	A:16-243 B:16-243 - - - -
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	GRAA_HUMAN	65-70	2	A:53-58 B:53-58 - - - -
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	GRAA_HUMAN	206-217	2	A:189-200 B:189-200 - - - -

Biological Unit 2 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	GRAA_HUMAN	29-259	2	- - C:16-243 D:16-243 - -
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	GRAA_HUMAN	65-70	2	- - C:53-58 D:53-58 - -
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	GRAA_HUMAN	206-217	2	- - C:189-200 D:189-200 - -

Biological Unit 3 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	GRAA_HUMAN	29-259	2	- - - - E:16-243 F:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	GRAA_HUMAN	65-70	2	- - - - E:53-58 F:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	GRAA_HUMAN	206-217	2	- - - - E:189-200 F:189-200

Asymmetric Unit (4, 24)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000274306	1	ENSE00001127870	chr5:54398476-54398580	105	GRAA_HUMAN	1-24	24	0	-	-
1.2	ENST00000274306	2	ENSE00000971463	chr5:54401302-54401446	145	GRAA_HUMAN	24-72	49	6	A:16-60 (gaps) B:16-60 (gaps) C:16-60 (gaps) D:16-60 (gaps) E:16-60 (gaps) F:16-60 (gaps)	45 45 45 45 45 45
1.3	ENST00000274306	3	ENSE00000971464	chr5:54403622-54403763	142	GRAA_HUMAN	72-119	48	6	A:60-107 B:60-107 C:60-107 D:60-107 E:60-107 F:60-107	48 48 48 48 48 48
1.4	ENST00000274306	4	ENSE00000971465	chr5:54403953-54404222	270	GRAA_HUMAN	120-209	90	6	A:108-192 (gaps) B:108-192 (gaps) C:108-192 (gaps) D:108-192 (gaps) E:108-192 (gaps) F:108-192 (gaps)	91 91 91 91 91 91
1.5	ENST00000274306	5	ENSE00001127864	chr5:54405849-54406080	232	GRAA_HUMAN	210-262	53	6	A:193-246 (gaps) B:193-246 (gaps) C:193-246 (gaps) D:193-246 (gaps) E:193-246 (gaps) F:193-246 (gaps)	57 57 57 57 57 57

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:234
 aligned with GRAA_HUMAN | P12544 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:234
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    
          GRAA_HUMAN     29 IIGGNEVTPHSRPYMVLLSLDRKTICAGALIAKDWVLTAAHCNLNKRSQVILGAHSITREEPTKQIMLVKKEFPYPCYDPATREGDLKLLQLMEKAKINKYVTILHLPKKGDDVKPGTMCQVAGWGRTHNSASWSDTLREVNITIIDRKVCNDRNHYNFNPVIGMNMVCAGSLRGGRDSCNGDSGSPLLCEGVFRGVTSFGLENKCGDPRGPGVYILLSKKHLNWIIMTIKGAV  262
               SCOP domains d1op8a_ A: Granzyme A                                                                                                                                                                                                                      SCOP domains
               CATH domains 1op8A01     1op8A02 A:28-120,A:233-246 Trypsin-like serine proteases                                    1op8A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                            -1op8A02        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeee.....eeeeeeee..eeee..........eeee............eee.eeeeee.............eeeee..........................eeeeee..............eeeeeeeehhhhhh..............eeeee...............eeee..eeeeeeee............eeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 29-259                                                                                                                                                                                             --- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:16-60 (gaps) UniProt: 24-72-----------------------------------------------Exon 1.4  PDB: A:108-192 (gaps) UniProt: 120-209                                          Exon 1.5  PDB: A:193-246 (gaps) UniProt: 210-262      Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: A:60-107 UniProt: 72-119         ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1op8 A   16 IIGGNEVTPHSRPYMVLLSLDRKTICAGALIAKDWVLTAAHCNLNKRSQVILGAHSITREEPTKQIMLVKKEFPYPCYDPATREGDLKLLQLTEKAKINKYVTILHLPKKGDDVKPGTMCQVAGWGRTHNSASWSDTLREVNITIIDRKVCNDRNHYNFNPVIGMNMVCAGSLRGGRDSCNGDSGSPLLCEGVFRGVTSFGLENKCGDPRGPGVYILLSKKHLNWIIMTIKGAV  246
                                    25        35|       46        56        66        76        86        96       106       116       126       136       146  ||   157       167   || 173B       183     ||191       201||     215   |  223A      232A       242    
                                              35|                                                                                                             149|                170A|   ||            188A|           202|        218A  223A      232A              
                                               37                                                                                                              151                 170B   ||             188B            207                                          
                                                                                                                                                                                       173A|                                                                          
                                                                                                                                                                                        173B

Chain B from PDB  Type:PROTEIN  Length:234
 aligned with GRAA_HUMAN | P12544 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:234
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    
          GRAA_HUMAN     29 IIGGNEVTPHSRPYMVLLSLDRKTICAGALIAKDWVLTAAHCNLNKRSQVILGAHSITREEPTKQIMLVKKEFPYPCYDPATREGDLKLLQLMEKAKINKYVTILHLPKKGDDVKPGTMCQVAGWGRTHNSASWSDTLREVNITIIDRKVCNDRNHYNFNPVIGMNMVCAGSLRGGRDSCNGDSGSPLLCEGVFRGVTSFGLENKCGDPRGPGVYILLSKKHLNWIIMTIKGAV  262
               SCOP domains d1op8b_ B: Granzyme A                                                                                                                                                                                                                      SCOP domains
               CATH domains 1op8B01     1op8B02 B:28-120,B:233-246 Trypsin-like serine proteases                                    1op8B01 B:16-27,B:121-232 Trypsin-like serine proteases                                                            -1op8B02        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeee.....eeeeeeee..eeee..........eeee............eee.eeeeee.............eeeee..........................eeeeee..............eeeeee..hhhhhhh.............eeee................eeee..eeeeeeee............eeeee.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 29-259                                                                                                                                                                                             --- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: B:16-60 (gaps) UniProt: 24-72-----------------------------------------------Exon 1.4  PDB: B:108-192 (gaps) UniProt: 120-209                                          Exon 1.5  PDB: B:193-246 (gaps) UniProt: 210-262      Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: B:60-107 UniProt: 72-119         ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1op8 B   16 IIGGNEVTPHSRPYMVLLSLDRKTICAGALIAKDWVLTAAHCNLNKRSQVILGAHSITREEPTKQIMLVKKEFPYPCYDPATREGDLKLLQLTEKAKINKYVTILHLPKKGDDVKPGTMCQVAGWGRTHNSASWSDTLREVNITIIDRKVCNDRNHYNFNPVIGMNMVCAGSLRGGRDSCNGDSGSPLLCEGVFRGVTSFGLENKCGDPRGPGVYILLSKKHLNWIIMTIKGAV  246
                                    25        35|       46        56        66        76        86        96       106       116       126       136       146  ||   157       167   || 173B       183     ||191       201||     215   |  223A      232A       242    
                                              35|                                                                                                             149|                170A|   ||            188A|           202|        218A  223A      232A              
                                               37                                                                                                              151                 170B   ||             188B            207                                          
                                                                                                                                                                                       173A|                                                                          
                                                                                                                                                                                        173B

Chain C from PDB  Type:PROTEIN  Length:234
 aligned with GRAA_HUMAN | P12544 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:234
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    
          GRAA_HUMAN     29 IIGGNEVTPHSRPYMVLLSLDRKTICAGALIAKDWVLTAAHCNLNKRSQVILGAHSITREEPTKQIMLVKKEFPYPCYDPATREGDLKLLQLMEKAKINKYVTILHLPKKGDDVKPGTMCQVAGWGRTHNSASWSDTLREVNITIIDRKVCNDRNHYNFNPVIGMNMVCAGSLRGGRDSCNGDSGSPLLCEGVFRGVTSFGLENKCGDPRGPGVYILLSKKHLNWIIMTIKGAV  262
               SCOP domains d1op8c_ C: Granzyme A                                                                                                                                                                                                                      SCOP domains
               CATH domains 1op8C01     1op8C02 C:28-120,C:233-246 Trypsin-like serine proteases                                    1op8C01 C:16-27,C:121-232 Trypsin-like serine proteases                                                            -1op8C02        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeee.....eeeeeeee..eeee..........eeee............eee.eeeeee.............eeeee..........................eeeeee..............eeeeeeee..hhhhh.............eeeee...............eeee..eeeeeeee............eeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: C:16-243 UniProt: 29-259                                                                                                                                                                                             --- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: C:16-60 (gaps) UniProt: 24-72-----------------------------------------------Exon 1.4  PDB: C:108-192 (gaps) UniProt: 120-209                                          Exon 1.5  PDB: C:193-246 (gaps) UniProt: 210-262      Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: C:60-107 UniProt: 72-119         ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1op8 C   16 IIGGNEVTPHSRPYMVLLSLDRKTICAGALIAKDWVLTAAHCNLNKRSQVILGAHSITREEPTKQIMLVKKEFPYPCYDPATREGDLKLLQLTEKAKINKYVTILHLPKKGDDVKPGTMCQVAGWGRTHNSASWSDTLREVNITIIDRKVCNDRNHYNFNPVIGMNMVCAGSLRGGRDSCNGDSGSPLLCEGVFRGVTSFGLENKCGDPRGPGVYILLSKKHLNWIIMTIKGAV  246
                                    25        35|       46        56        66        76        86        96       106       116       126       136       146  ||   157       167   || 173B       183     ||191       201||     215   |  223A      232A       242    
                                              35|                                                                                                             149|                170A|   ||            188A|           202|        218A  223A      232A              
                                               37                                                                                                              151                 170B   ||             188B            207                                          
                                                                                                                                                                                       173A|                                                                          
                                                                                                                                                                                        173B

Chain D from PDB  Type:PROTEIN  Length:234
 aligned with GRAA_HUMAN | P12544 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:234
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    
          GRAA_HUMAN     29 IIGGNEVTPHSRPYMVLLSLDRKTICAGALIAKDWVLTAAHCNLNKRSQVILGAHSITREEPTKQIMLVKKEFPYPCYDPATREGDLKLLQLMEKAKINKYVTILHLPKKGDDVKPGTMCQVAGWGRTHNSASWSDTLREVNITIIDRKVCNDRNHYNFNPVIGMNMVCAGSLRGGRDSCNGDSGSPLLCEGVFRGVTSFGLENKCGDPRGPGVYILLSKKHLNWIIMTIKGAV  262
               SCOP domains d1op8d_ D: Granzyme A                                                                                                                                                                                                                      SCOP domains
               CATH domains 1op8D01     1op8D02 D:28-120,D:233-246 Trypsin-like serine proteases                                    1op8D01 D:16-27,D:121-232 Trypsin-like serine proteases                                                            -1op8D02        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeee.....eeeeeeee..eeee..........eeee............eee.eeeeee.............eeeee..........................eeeeee..............eeeeeeee..hhhhh.............eeeee...............eeee..eeeeeeee............eeeee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: D:16-243 UniProt: 29-259                                                                                                                                                                                             --- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: D:16-60 (gaps) UniProt: 24-72-----------------------------------------------Exon 1.4  PDB: D:108-192 (gaps) UniProt: 120-209                                          Exon 1.5  PDB: D:193-246 (gaps) UniProt: 210-262      Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: D:60-107 UniProt: 72-119         ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1op8 D   16 IIGGNEVTPHSRPYMVLLSLDRKTICAGALIAKDWVLTAAHCNLNKRSQVILGAHSITREEPTKQIMLVKKEFPYPCYDPATREGDLKLLQLTEKAKINKYVTILHLPKKGDDVKPGTMCQVAGWGRTHNSASWSDTLREVNITIIDRKVCNDRNHYNFNPVIGMNMVCAGSLRGGRDSCNGDSGSPLLCEGVFRGVTSFGLENKCGDPRGPGVYILLSKKHLNWIIMTIKGAV  246
                                    25        35|       46        56        66        76        86        96       106       116       126       136       146  ||   157       167   || 173B       183     ||191       201||     215   |  223A      232A       242    
                                              35|                                                                                                             149|                170A|   ||            188A|           202|        218A  223A      232A              
                                               37                                                                                                              151                 170B   ||             188B            207                                          
                                                                                                                                                                                       173A|                                                                          
                                                                                                                                                                                        173B

Chain E from PDB  Type:PROTEIN  Length:234
 aligned with GRAA_HUMAN | P12544 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:234
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    
          GRAA_HUMAN     29 IIGGNEVTPHSRPYMVLLSLDRKTICAGALIAKDWVLTAAHCNLNKRSQVILGAHSITREEPTKQIMLVKKEFPYPCYDPATREGDLKLLQLMEKAKINKYVTILHLPKKGDDVKPGTMCQVAGWGRTHNSASWSDTLREVNITIIDRKVCNDRNHYNFNPVIGMNMVCAGSLRGGRDSCNGDSGSPLLCEGVFRGVTSFGLENKCGDPRGPGVYILLSKKHLNWIIMTIKGAV  262
               SCOP domains d1op8e_ E: Granzyme A                                                                                                                                                                                                                      SCOP domains
               CATH domains 1op8E01     1op8E02 E:28-120,E:233-246 Trypsin-like serine proteases                                    1op8E01 E:16-27,E:121-232 Trypsin-like serine proteases                                                            -1op8E02        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeee.....eeeeeeee..eeee..........eeee............eee.eeeeee.............eeeee..........................eeeeee..............eeeeee..hhhhhh..............eeee................eeee..eeeeeeee............eeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: E:16-243 UniProt: 29-259                                                                                                                                                                                             --- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: E:16-60 (gaps) UniProt: 24-72-----------------------------------------------Exon 1.4  PDB: E:108-192 (gaps) UniProt: 120-209                                          Exon 1.5  PDB: E:193-246 (gaps) UniProt: 210-262      Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: E:60-107 UniProt: 72-119         ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1op8 E   16 IIGGNEVTPHSRPYMVLLSLDRKTICAGALIAKDWVLTAAHCNLNKRSQVILGAHSITREEPTKQIMLVKKEFPYPCYDPATREGDLKLLQLTEKAKINKYVTILHLPKKGDDVKPGTMCQVAGWGRTHNSASWSDTLREVNITIIDRKVCNDRNHYNFNPVIGMNMVCAGSLRGGRDSCNGDSGSPLLCEGVFRGVTSFGLENKCGDPRGPGVYILLSKKHLNWIIMTIKGAV  246
                                    25        35|       46        56        66        76        86        96       106       116       126       136       146  ||   157       167   || 173B       183     ||191       201||     215   |  223A      232A       242    
                                              35|                                                                                                             149|                170A|   ||            188A|           202|        218A  223A      232A              
                                               37                                                                                                              151                 170B   ||             188B            207                                          
                                                                                                                                                                                       173A|                                                                          
                                                                                                                                                                                        173B

Chain F from PDB  Type:PROTEIN  Length:234
 aligned with GRAA_HUMAN | P12544 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:234
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    
          GRAA_HUMAN     29 IIGGNEVTPHSRPYMVLLSLDRKTICAGALIAKDWVLTAAHCNLNKRSQVILGAHSITREEPTKQIMLVKKEFPYPCYDPATREGDLKLLQLMEKAKINKYVTILHLPKKGDDVKPGTMCQVAGWGRTHNSASWSDTLREVNITIIDRKVCNDRNHYNFNPVIGMNMVCAGSLRGGRDSCNGDSGSPLLCEGVFRGVTSFGLENKCGDPRGPGVYILLSKKHLNWIIMTIKGAV  262
               SCOP domains d1op8f_ F: Granzyme A                                                                                                                                                                                                                      SCOP domains
               CATH domains 1op8F01     1op8F02 F:28-120,F:233-246 Trypsin-like serine proteases                                    1op8F01 F:16-27,F:121-232 Trypsin-like serine proteases                                                            -1op8F02        CATH domains
           Pfam domains (1) Trypsin-1op8F01 F:16-238                                                                                                                                                                                                          -------- Pfam domains (1)
           Pfam domains (2) Trypsin-1op8F02 F:16-238                                                                                                                                                                                                          -------- Pfam domains (2)
           Pfam domains (3) Trypsin-1op8F03 F:16-238                                                                                                                                                                                                          -------- Pfam domains (3)
           Pfam domains (4) Trypsin-1op8F04 F:16-238                                                                                                                                                                                                          -------- Pfam domains (4)
           Pfam domains (5) Trypsin-1op8F05 F:16-238                                                                                                                                                                                                          -------- Pfam domains (5)
           Pfam domains (6) Trypsin-1op8F06 F:16-238                                                                                                                                                                                                          -------- Pfam domains (6)
         Sec.struct. author ....ee........eeeee.....eeeeeeee..eeeee.........eeee............eee.eeeeee............eeeeee..........................eeeeee..............eeeeeeeehhhhhhh.............eeeee...............eeee..eeeeeeee............eeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: F:16-243 UniProt: 29-259                                                                                                                                                                                             --- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: F:16-60 (gaps) UniProt: 24-72-----------------------------------------------Exon 1.4  PDB: F:108-192 (gaps) UniProt: 120-209                                          Exon 1.5  PDB: F:193-246 (gaps) UniProt: 210-262      Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: F:60-107 UniProt: 72-119         ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1op8 F   16 IIGGNEVTPHSRPYMVLLSLDRKTICAGALIAKDWVLTAAHCNLNKRSQVILGAHSITREEPTKQIMLVKKEFPYPCYDPATREGDLKLLQLTEKAKINKYVTILHLPKKGDDVKPGTMCQVAGWGRTHNSASWSDTLREVNITIIDRKVCNDRNHYNFNPVIGMNMVCAGSLRGGRDSCNGDSGSPLLCEGVFRGVTSFGLENKCGDPRGPGVYILLSKKHLNWIIMTIKGAV  246
                                    25        35|       46        56        66        76        86        96       106       116       126       136       146  ||   157       167   || 173B       183     ||191       201||     215   |  223A      232A       242    
                                              35|                                                                                                             149|                170A|   ||            188A|           202|        218A  223A      232A              
                                               37                                                                                                              151                 170B   ||             188B            207                                          
                                                                                                                                                                                       173A|                                                                          
                                                                                                                                                                                        173B

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: Granzyme A (2)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d1op8a_	A:
1b	d1op8b_	B:
1c	d1op8c_	C:
1d	d1op8d_	D:
1e	d1op8e_	E:
1f	d1op8f_	F:

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)

Human (Homo sapiens) (615)

1a	1op8A01	A:16-27,A:121-232
1b	1op8B01	B:16-27,B:121-232
1c	1op8C01	C:16-27,C:121-232
1d	1op8D01	D:16-27,D:121-232
1e	1op8E01	E:16-27,E:121-232
1f	1op8F01	F:16-27,F:121-232
1g	1op8A02	A:28-120,A:233-246
1h	1op8B02	B:28-120,B:233-246
1i	1op8C02	C:28-120,C:233-246
1j	1op8D02	D:28-120,D:233-246
1k	1op8E02	E:28-120,E:233-246
1l	1op8F02	F:28-120,F:233-246

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Homo sapiens (Human) (339)

1a	Trypsin-1op8F01	F:16-238
1b	Trypsin-1op8F02	F:16-238
1c	Trypsin-1op8F03	F:16-238
1d	Trypsin-1op8F04	F:16-238
1e	Trypsin-1op8F05	F:16-238
1f	Trypsin-1op8F06	F:16-238

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (GRAA_HUMAN | P12544)

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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	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:0043392	negative regulation of DNA binding	Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
	GO:0032078	negative regulation of endodeoxyribonuclease activity	Any process that stops or reduces the rate of endodeoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
	GO:0051354	negative regulation of oxidoreductase activity	Any process that stops or reduces the rate of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0051603	proteolysis involved in cellular protein catabolic process	The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
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.
	GO:0001772	immunological synapse	An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric Unit
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	1op8
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(no "Related Entries Specified in the PDB File" available for 1OP8)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 12)

Sites (12, 12)

SS Bonds (27, 27)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 6)

PROSITE Motifs (3, 18)

Exons (4, 24)

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