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(-) Description

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)

(-) Compounds

Molecule 1 - GRANZYME A
    ChainsA, B, C, D, E, F
    EC Number3.4.21.78
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB    
Biological Unit 2 (1x)  CD  
Biological Unit 3 (1x)    EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY F:19 , ASN F:20 , GLU F:21 , ARG F:156BINDING SITE FOR RESIDUE SO4 F 1001
02AC2SOFTWAREILE A:17 , GLY A:18 , GLY A:19 , THR A:144 , HIS A:145 , ARG A:156 , HOH A:1023BINDING SITE FOR RESIDUE SO4 A 1003
03AC3SOFTWAREASN B:20 , GLU B:21 , ARG B:156BINDING SITE FOR RESIDUE SO4 B 1005
04AC4SOFTWAREILE C:16 , ILE C:17 , GLY C:18 , GLY C:19 , THR C:144 , HIS C:145 , ARG C:156 , HOH C:1017BINDING SITE FOR RESIDUE SO4 C 1006
05AC5SOFTWAREARG C:27 , HOH C:1119 , SER F:185 , LEU F:186 , ARG F:187 , HOH F:1027BINDING SITE FOR RESIDUE SO4 C 1008
06AC6SOFTWARESER B:185 , LEU B:186 , ARG B:187 , HOH B:1092 , ARG E:27BINDING SITE FOR RESIDUE SO4 B 1009
07AC7SOFTWAREARG A:27 , THR D:161 , SER D:185 , LEU D:186 , ARG D:187BINDING SITE FOR RESIDUE SO4 A 1010
08AC8SOFTWAREASN D:20 , GLU D:21 , ARG D:156BINDING SITE FOR RESIDUE SO4 D 1015
09AC9SOFTWAREILE F:17 , GLY F:18 , HIS F:145 , ASN F:146 , ARG F:156BINDING SITE FOR RESIDUE SO4 F 1019
10BC1SOFTWAREILE E:17 , GLY E:18 , GLY E:19 , THR E:144 , HIS E:145 , ARG E:156BINDING SITE FOR RESIDUE SO4 E 1020
11BC2SOFTWAREGLY D:18 , GLY D:19 , THR D:144 , HIS D:145 , ASN D:146 , ARG D:156 , HOH D:1088BINDING SITE FOR RESIDUE SO4 D 1022
12BC3SOFTWAREILE B:17 , GLY B:18 , HIS B:145 , HOH B:1075BINDING SITE FOR RESIDUE SO4 B 1023

(-) SS Bonds  (27, 27)

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

(-) Cis Peptide Bonds  (6, 6)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 6)

Asymmetric Unit (1, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024291M121TGRAA_HUMANPolymorphism3104233A/B/C/D/E/FT109T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024291M121TGRAA_HUMANPolymorphism3104233A/BT109T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024291M121TGRAA_HUMANPolymorphism3104233C/DT109T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024291M121TGRAA_HUMANPolymorphism3104233E/FT109T

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

(-) PROSITE Motifs  (3, 18)

Asymmetric Unit (3, 18)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.GRAA_HUMAN29-259
 
 
 
 
 
  6A:16-243
B:16-243
C:16-243
D:16-243
E:16-243
F:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.GRAA_HUMAN65-70
 
 
 
 
 
  6A:53-58
B:53-58
C:53-58
D:53-58
E:53-58
F:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.GRAA_HUMAN206-217
 
 
 
 
 
  6A:189-200
B:189-200
C:189-200
D:189-200
E:189-200
F:189-200
Biological Unit 1 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.GRAA_HUMAN29-259
 
 
 
 
 
  2A:16-243
B:16-243
-
-
-
-
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.GRAA_HUMAN65-70
 
 
 
 
 
  2A:53-58
B:53-58
-
-
-
-
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.GRAA_HUMAN206-217
 
 
 
 
 
  2A:189-200
B:189-200
-
-
-
-
Biological Unit 2 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.GRAA_HUMAN29-259
 
 
 
 
 
  2-
-
C:16-243
D:16-243
-
-
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.GRAA_HUMAN65-70
 
 
 
 
 
  2-
-
C:53-58
D:53-58
-
-
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.GRAA_HUMAN206-217
 
 
 
 
 
  2-
-
C:189-200
D:189-200
-
-
Biological Unit 3 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.GRAA_HUMAN29-259
 
 
 
 
 
  2-
-
-
-
E:16-243
F:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.GRAA_HUMAN65-70
 
 
 
 
 
  2-
-
-
-
E:53-58
F:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.GRAA_HUMAN206-217
 
 
 
 
 
  2-
-
-
-
E:189-200
F:189-200

(-) Exons   (4, 24)

Asymmetric Unit (4, 24)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002743061ENSE00001127870chr5:54398476-54398580105GRAA_HUMAN1-24240--
1.2ENST000002743062ENSE00000971463chr5:54401302-54401446145GRAA_HUMAN24-72496A: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
1.3ENST000002743063ENSE00000971464chr5:54403622-54403763142GRAA_HUMAN72-119486A:60-107
B:60-107
C:60-107
D:60-107
E:60-107
F:60-107
48
48
48
48
48
48
1.4ENST000002743064ENSE00000971465chr5:54403953-54404222270GRAA_HUMAN120-209906A: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
1.5ENST000002743065ENSE00001127864chr5:54405849-54406080232GRAA_HUMAN210-262536A: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

(-) 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: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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 6)

Asymmetric Unit

(-) CATH Domains  (1, 12)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a1op8A01A:16-27,A:121-232
1b1op8B01B:16-27,B:121-232
1c1op8C01C:16-27,C:121-232
1d1op8D01D:16-27,D:121-232
1e1op8E01E:16-27,E:121-232
1f1op8F01F:16-27,F:121-232
1g1op8A02A:28-120,A:233-246
1h1op8B02B:28-120,B:233-246
1i1op8C02C:28-120,C:233-246
1j1op8D02D:28-120,D:233-246
1k1op8E02E:28-120,E:233-246
1l1op8F02F:28-120,F:233-246

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Family: Trypsin (679)
1aTrypsin-1op8F01F:16-238
1bTrypsin-1op8F02F:16-238
1cTrypsin-1op8F03F:16-238
1dTrypsin-1op8F04F:16-238
1eTrypsin-1op8F05F:16-238
1fTrypsin-1op8F06F:16-238

(-) Gene Ontology  (18, 18)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GRAA_HUMAN | P125441hf1 1orf

(-) Related Entries Specified in the PDB File

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