2PKA - JenaLib

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Biological Unit 3 (Jmol Viewer)

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)

Molecule 1 - KALLIKREIN A
	Chains	:	A, X
	EC Number	:	3.4.21.35
	Engineered	:	YES
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

Molecule 2 - KALLIKREIN A
	Chains	:	B, Y
	EC Number	:	3.4.21.35
	Engineered	:	YES
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

		1	2	3	4
Asymmetric Unit	:	A	B	X	Y
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			X	Y
Biological Unit 3 (1x)	:	A	B	X	Y

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	BEN	2	Ligand/Ion	BENZAMIDINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BEN	1	Ligand/Ion	BENZAMIDINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	BEN	1	Ligand/Ion	BENZAMIDINE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	BEN	2	Ligand/Ion	BENZAMIDINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:189 , THR B:190 , THR B:213 , SER B:214 , GLY B:216 , HIS B:217 , CYS B:220 , SER B:226	BINDING SITE FOR RESIDUE BEN B 1
2	AC2	SOFTWARE	ASP 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:226	BINDING SITE FOR RESIDUE BEN Y 1

Asymmetric Unit

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

Asymmetric Unit

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

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	KLK_PIG	8-243	2	A:16-95B X:16-95B
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	KLK_PIG	44-49	2	A:53-58 X:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	KLK_PIG	192-203	2	B:189-200 Y:189-200

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	KLK_PIG	8-243	1	A:16-95B -
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	KLK_PIG	44-49	1	A:53-58 -
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	KLK_PIG	192-203	1	B:189-200 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	KLK_PIG	8-243	1	- X:16-95B
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	KLK_PIG	44-49	1	- X:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	KLK_PIG	192-203	1	- Y: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.	KLK_PIG	8-243	2	A:16-95B X:16-95B
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	KLK_PIG	44-49	2	A:53-58 X:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	KLK_PIG	192-203	2	B:189-200 Y:189-200

(no "Exon" information available for 2PKA)

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 '\|'

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: Kallikrein A (3)

Pig (Sus scrofa) [TaxId: 9823] (3)

1a	d2pka.1	A:,B:
1b	d2pka.2	X:,Y:

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)

Pig (Sus scrofa) (115)

1a	2pkaA00	A:16-95B
1b	2pkaX00	X:16-95B
1c	2pkaB00	B:95Y-246
1d	2pkaY00	Y:95Y-246

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Sus scrofa (Pig) (47)

1a	Trypsin-2pkaY01	Y:95Y-238
1b	Trypsin-2pkaY02	Y:95Y-238
1c	Trypsin-2pkaY03	Y:95Y-238
1d	Trypsin-2pkaY04	Y:95Y-238

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly B:147A - Pro B:147	[ RasMol ]
		Gly Y:147A - Pro Y:147	[ RasMol ]
		Thr B:218 - Pro B:219	[ RasMol ]
		Thr Y:218 - Pro Y:219	[ RasMol ]

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	2pka
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SS Bonds (10, 10)

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