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(-) Description

Title :  REFINED 2 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF PORCINE PANCREATIC KALLIKREIN A, A SPECIFIC TRYPSIN-LIKE SERINE PROTEINASE. CRYSTALLIZATION, STRUCTURE DETERMINATION, CRYSTALLOGRAPHIC REFINEMENT, STRUCTURE AND ITS COMPARISON WITH BOVINE TRYPSIN
 
Authors :  W. Bode, Z. Chen
Date :  21 May 84  (Deposition) - 19 Jul 84  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,X,Y
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  X,Y  (1x)
Biol. Unit 3:  A,B,X,Y  (1x)
Keywords :  Serine Proteinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Bode, Z. Chen, K. Bartels, C. Kutzbach, G. Schmidt-Kastner, H. Bartunik
Refined 2 A X-Ray Crystal Structure Of Porcine Pancreatic Kallikrein A, A Specific Trypsin-Like Serine Proteinase. Crystallization, Structure Determination, Crystallographic Refinement, Structure And Its Comparison With Bovine Trypsin.
J. Mol. Biol. V. 164 237 1983
PubMed-ID: 6551452  |  Reference-DOI: 10.1016/0022-2836(83)90077-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KALLIKREIN A
    ChainsA, X
    EC Number3.4.21.35
    EngineeredYES
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823
 
Molecule 2 - KALLIKREIN A
    ChainsB, Y
    EC Number3.4.21.35
    EngineeredYES
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABXY
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  XY
Biological Unit 3 (1x)ABXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1BEN2Ligand/IonBENZAMIDINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1BEN2Ligand/IonBENZAMIDINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:189 , THR B:190 , THR B:213 , SER B:214 , GLY B:216 , HIS B:217 , CYS B:220 , SER B:226BINDING SITE FOR RESIDUE BEN B 1
2AC2SOFTWAREASP Y:189 , THR Y:190 , SER Y:195 , THR Y:213 , SER Y:214 , GLY Y:216 , HIS Y:217 , CYS Y:220 , SER Y:226BINDING SITE FOR RESIDUE BEN Y 1

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:22 -B:157
2A:42 -A:58
3B:136 -B:201
4B:168 -B:182
5B:191 -B:220
6X:22 -Y:157
7X:42 -X:58
8Y:136 -Y:201
9Y:168 -Y:182
10Y:191 -Y:220

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly B:147A-Pro B:147
2Thr B:218 -Pro B:219
3Gly Y:147A-Pro Y:147
4Thr Y:218 -Pro Y:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PKA)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK_PIG8-243
 
  2A:16-95B
X:16-95B
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK_PIG44-49
 
  2A:53-58
X:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK_PIG192-203
 
  2B:189-200
Y:189-200
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK_PIG8-243
 
  1A:16-95B
-
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK_PIG44-49
 
  1A:53-58
-
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK_PIG192-203
 
  1B:189-200
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK_PIG8-243
 
  1-
X:16-95B
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK_PIG44-49
 
  1-
X:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK_PIG192-203
 
  1-
Y:189-200
Biological Unit 3 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK_PIG8-243
 
  2A:16-95B
X:16-95B
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK_PIG44-49
 
  2A:53-58
X:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK_PIG192-203
 
  2B:189-200
Y:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 2PKA)

(-) 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:80
 aligned with KLK_PIG | P00752 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:80
                                    17        27        37        47        57        67        77        87
             KLK_PIG      8 IIGGRECEKNSHPWQVAIYHYSSFQCGGVLVNPKWVLTAAHCKNDNYEVWLGRHNLFENENTAQFFGVTADFPHPGFNLS   87
               SCOP domains d2pka.1 A:,B: Kallikrein A                                                       SCOP domains
               CATH domains 2pkaA00 A:16-95B Trypsin-like serine proteases                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee..eeeeeeeeee.eeeeehhhhh.....eeee...........eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-95B UniProt: 8-243                                        PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI-------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------- Transcript
                2pka A   16 IIGGRECEKNSHPWQVAIYHYSSFQCGGVLVNPKWVLTAAHCKNDNYEVWLGRHNLFENENTAQFFGVTADFPHPGFNLS  95B
                                    25        35||      46        56        66||      77        87       95B
                                               36|                           67|                        95A|
                                                38                            69                         95B

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with KLK_PIG | P00752 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:152
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244  
             KLK_PIG     95 ADGKDYSHDLMLLRLQSPAKITDAVKVLELPTQEPELGSTCEASGWGSIEPGPDBFEFPDEIQCVQLTLLQNTFCABAHPBKVTESMLCAGYLPGGKDTCMGDSGGPLICNGMWQGITSWGHTPCGSANKPSIYTKLIFYLDWINDTITENP  246
               SCOP domains d2pka.1 A:,B: Kallikrein A                                                                                                                               SCOP domains
               CATH domains 2pkaB00 B:95Y-246 Trypsin-like serine proteases                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee.....................eeeeeeee.................eeeeeeeehhhhhhhhh........eeee.............eeeeee..eeeeeeee...........eeeehhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: - UniProt: 8-243                                                                                                                   --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2pka B  95Y ADGKDYSHDLMLLRLQSPAKITDAVKVLELPTQEPELGSTCEASGWGSIEPGPDDFEFPDEIQCVQLTLLQNTFCADAHPDKVTESMLCAGYLPGGKDTCMGDSGGPLICNGMWQGITSWGHTPCGSANKPSIYTKLIFYLDWIDDTITENP  246
                            ||     103       113       123 ||  ||135       145 | |   153       163       173       183|    | 191       201 ||    215     | 224       234       244  
                            ||                           125|  ||           147A |                                 184A 188A             203|         221A                          
                          95Y|                            127  ||             148A                                                        208                                       
                           95Z                               130|                                                                                                                   
                                                              132                                                                                                                   

Chain X from PDB  Type:PROTEIN  Length:80
 aligned with KLK_PIG | P00752 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:80
                                    17        27        37        47        57        67        77        87
             KLK_PIG      8 IIGGRECEKNSHPWQVAIYHYSSFQCGGVLVNPKWVLTAAHCKNDNYEVWLGRHNLFENENTAQFFGVTADFPHPGFNLS   87
               SCOP domains d2pka.2 X:,Y: Kallikrein A                                                       SCOP domains
               CATH domains 2pkaX00 X:16-95B Trypsin-like serine proteases                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee..eeeeeeeeee.eeeeehhhhh.....eeee...........eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: X:16-95B UniProt: 8-243                                        PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI-------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------- Transcript
                2pka X   16 IIGGRECEKNSHPWQVAIYHYSSFQCGGVLVNPKWVLTAAHCKNDNYEVWLGRHNLFENENTAQFFGVTADFPHPGFNLS  95B
                                    25        35||      46        56        66||      77        87       95B
                                               36|                           67|                        95A|
                                                38                            69                         95B

Chain Y from PDB  Type:PROTEIN  Length:152
 aligned with KLK_PIG | P00752 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:152
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244  
             KLK_PIG     95 ADGKDYSHDLMLLRLQSPAKITDAVKVLELPTQEPELGSTCEASGWGSIEPGPDBFEFPDEIQCVQLTLLQNTFCABAHPBKVTESMLCAGYLPGGKDTCMGDSGGPLICNGMWQGITSWGHTPCGSANKPSIYTKLIFYLDWINDTITENP  246
               SCOP domains d2pka.2 X:,Y: Kallikrein A                                                                                                                               SCOP domains
               CATH domains 2pkaY00 Y:95Y-246 Trypsin-like serine proteases                                                                                                          CATH domains
           Pfam domains (1) Trypsin-2pkaY01 Y:95Y-238                                                                                                                       -------- Pfam domains (1)
           Pfam domains (2) Trypsin-2pkaY02 Y:95Y-238                                                                                                                       -------- Pfam domains (2)
           Pfam domains (3) Trypsin-2pkaY03 Y:95Y-238                                                                                                                       -------- Pfam domains (3)
           Pfam domains (4) Trypsin-2pkaY04 Y:95Y-238                                                                                                                       -------- Pfam domains (4)
         Sec.struct. author .........eeeeeee.....................eeeeeeee.................eeeeeeeehhhhhhhhh........eeee.............eeeeee..eeeeeeee...........eeeehhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: - UniProt: 8-243                                                                                                                   --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2pka Y  95Y ADGKDYSHDLMLLRLQSPAKITDAVKVLELPTQEPELGSTCEASGWGSIEPGPDDFEFPDEIQCVQLTLLQNTFCADAHPDKVTESMLCAGYLPGGKDTCMGDSGGPLICNGMWQGITSWGHTPCGSANKPSIYTKLIFYLDWIDDTITENP  246
                            ||     103       113       123 ||  ||135       145 | |   153       163       173       183|    | 191       201 ||    215     | 224       234       244  
                            ||                           125|  ||           147A |                                 184A 188A             203|         221A                          
                          95Y|                            127  ||             148A                                                        208                                       
                           95Z                               130|                                                                                                                   
                                                              132                                                                                                                   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Family: Trypsin (679)
1aTrypsin-2pkaY01Y:95Y-238
1bTrypsin-2pkaY02Y:95Y-238
1cTrypsin-2pkaY03Y:95Y-238
1dTrypsin-2pkaY04Y:95Y-238

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,X,Y   (KLK_PIG | P00752)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KLK_PIG | P007521hia 2kai

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2PKA)