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(-) Description

Title :  HUMAN TRYPTASE WITH 2-AMINO BENZIMIDAZOLE
 
Authors :  J. R. Somoza
Date :  17 Jan 06  (Deposition) - 07 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Serine Protease, Drug Design, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Mcgrath, P. A. Sprengeler, B. Hirschbein, J. R. Somoza, I. Lehoux, J. W. Janc, E. Gjerstad, M. Graupe, A. Estiarte, C. Venkataramani, Y. Liu, R. Yee, J. D. Ho, M. J. Green, C. -S. Lee, L. Liu, V. Tai, J. Spencer, D. Sperandio, B. A. Katz
Structure-Guided Design Of Peptide-Based Tryptase Inhibitors.
Biochemistry V. 45 5964 2006
PubMed-ID: 16681368  |  Reference-DOI: 10.1021/BI060173M
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPTASE BETA-2
    Chains: A, B, C, D
    EC Number: 3.4.21.59
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Taxid: 4922
    Gene: TPSB2, TPS2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRYPTASE-2, TRYPTASE II

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
12704Ligand/Ion2H-BENZOIMIDAZOL-2-YLAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:189 , SER A:190 , CYS A:191 , GLN A:192 , SER A:195 , GLY A:216 , GLY A:219 , GLY A:226 , HOH A:1093BINDING SITE FOR RESIDUE 270 A 1000
2AC2SOFTWAREASP B:189 , SER B:190 , CYS B:191 , GLN B:192 , SER B:195 , GLY B:216 , GLY B:219 , GLY B:226 , HOH B:1039BINDING SITE FOR RESIDUE 270 B 1001
3AC3SOFTWAREASP C:189 , SER C:190 , CYS C:191 , GLN C:192 , SER C:195 , GLY C:216 , GLY C:219 , GLY C:226 , HOH C:1090BINDING SITE FOR RESIDUE 270 C 1002
4AC4SOFTWAREASP D:189 , SER D:190 , CYS D:191 , SER D:195 , TRP D:215 , GLY D:216 , GLY D:219 , GLY D:226BINDING SITE FOR RESIDUE 270 D 1003

(-) SS Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:136 -A:201
3A:168 -A:182
4A:191 -A:220
5B:42 -B:58
6B:136 -B:201
7B:168 -B:182
8B:191 -B:220
9C:42 -C:58
10C:136 -C:201
11C:168 -C:182
12C:191 -C:220
13D:42 -D:58
14D:136 -D:201
15D:168 -D:182
16D:191 -D:220

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gly A:60 -Pro A:60A
2Pro A:152A-Pro A:152B
3Gly B:60 -Pro B:60A
4Pro B:152A-Pro B:152B
5Gly C:60 -Pro C:60A
6Pro C:152A-Pro C:152B
7Gly D:60 -Pro D:60A
8Pro D:152A-Pro D:152B

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 12)

Asymmetric/Biological Unit (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TRYB2_HUMAN31-272
 
 
 		  4A:16-243
B:16-243
C:16-243
D:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TRYB2_HUMAN70-75
 
 
 		  4A:53-58
B:53-58
C:53-58
D:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TRYB2_HUMAN218-229
 
 
 		  4A:189-200
B:189-200
C:189-200
D:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 2FPZ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:243
 aligned with TRYB2_HUMAN | P20231 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:243
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   
         TRYB2_HUMAN     31 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVNVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK  273
               SCOP domains d2fpza_ A: beta-Tryptase                                                                                                                                                                                                                            SCOP domains
               CATH domains 2fpzA01     2fpzA02 A:28-120,A:233-244 Trypsin-like serine proteases                                         2fpzA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                                   2fpzA02      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhhh....hhh.eeee............eeeeeeee.............eeeee..........................eeeeee................eeeeeeeehhhhhhhhhhh..............eeee..............eeeeee..eeeeeeeeee..........eeeee...hhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 31-272                                                                                                                                                                                                        - PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fpz A   16 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK  244
                                    25        35  ||    43        53       60C||      68      ||81        91       101       111       121       131       141     ||152||     160       170   |||173G||     181       191       201       211     |221A       231       241   
                                                37A|                     60A||||             75|                                                                 147|   ||                  173A||||||||                                         217|  |                       
                                                 37B                      60B|||              79                                                                  149   ||                   173B|||||||                                          219  |                       
                                                                           60C||                                                                                     152A|                    173C||||||                                            221A                       
                                                                            60D|                                                                                      152B                     173D|||||                                                                       
                                                                             60E                                                                                                                173E||||                                                                       
                                                                                                                                                                                                 173F|||                                                                       
                                                                                                                                                                                                  173G||                                                                       
                                                                                                                                                                                                   173H|                                                                       
                                                                                                                                                                                                    173I                                                                       


Chain B from PDB  Type:PROTEIN  Length:243
 aligned with TRYB2_HUMAN | P20231 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:243
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   
         TRYB2_HUMAN     31 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVNVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK  273
               SCOP domains d2fpzb_ B: beta-Tryptase                                                                                                                                                                                                                            SCOP domains
               CATH domains 2fpzB01     2fpzB02 B:28-120,B:233-244 Trypsin-like serine proteases                                         2fpzB01 B:16-27,B:121-232 Trypsin-like serine proteases                                                                   2fpzB02      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhh.....hhh.eeee............eeeeeeee.............eeeee...........................eeeee................eeeee.eehhhhhhhhhhh..............eeee..............eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 31-272                                                                                                                                                                                                        - PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fpz B   16 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK  244
                                    25        35  ||    43        53       60C||      68      ||81        91       101       111       121       131       141     ||152||     160       170   |||173G||     181       191       201       211     |221A       231       241   
                                                37A|                     60A||||             75|                                                                 147|   ||                  173A||||||||                                         217|  |                       
                                                 37B                      60B|||              79                                                                  149   ||                   173B|||||||                                          219  |                       
                                                                           60C||                                                                                     152A|                    173C||||||                                            221A                       
                                                                            60D|                                                                                      152B                     173D|||||                                                                       
                                                                             60E                                                                                                                173E||||                                                                       
                                                                                                                                                                                                 173F|||                                                                       
                                                                                                                                                                                                  173G||                                                                       
                                                                                                                                                                                                   173H|                                                                       
                                                                                                                                                                                                    173I                                                                       


Chain C from PDB  Type:PROTEIN  Length:243
 aligned with TRYB2_HUMAN | P20231 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:243
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   
         TRYB2_HUMAN     31 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVNVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK  273
               SCOP domains d2fpzc_ C: beta-Tryptase                                                                                                                                                                                                                            SCOP domains
               CATH domains 2fpzC01     2fpzC02 C:28-120,C:233-244 Trypsin-like serine proteases                                         2fpzC01 C:16-27,C:121-232 Trypsin-like serine proteases                                                                   2fpzC02      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhh.....hhh.eeee............eeeeeeee.............eeeee..........................eeeeee................eeeeeeeehhhhhhhhhhh..............eeee..............eeeee....eeeeeeeee..........eeeee...hhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: C:16-243 UniProt: 31-272                                                                                                                                                                                                        - PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fpz C   16 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK  244
                                    25        35  ||    43        53       60C||      68      ||81        91       101       111       121       131       141     ||152||     160       170   |||173G||     181       191       201       211     |221A       231       241   
                                                37A|                     60A||||             75|                                                                 147|   ||                  173A||||||||                                         217|  |                       
                                                 37B                      60B|||              79                                                                  149   ||                   173B|||||||                                          219  |                       
                                                                           60C||                                                                                     152A|                    173C||||||                                            221A                       
                                                                            60D|                                                                                      152B                     173D|||||                                                                       
                                                                             60E                                                                                                                173E||||                                                                       
                                                                                                                                                                                                 173F|||                                                                       
                                                                                                                                                                                                  173G||                                                                       
                                                                                                                                                                                                   173H|                                                                       
                                                                                                                                                                                                    173I                                                                       


Chain D from PDB  Type:PROTEIN  Length:243
 aligned with TRYB2_HUMAN | P20231 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:243
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   
         TRYB2_HUMAN     31 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVNVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK  273
               SCOP domains d2fpzd_ D: beta-Tryptase                                                                                                                                                                                                                            SCOP domains
               CATH domains 2fpzD01     2fpzD02 D:28-120,D:233-244 Trypsin-like serine proteases                                         2fpzD01 D:16-27,D:121-232 Trypsin-like serine proteases                                                                   2fpzD02      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhhh....hhh.eeee............eeeeeeee.............eeeee...........................eeeee................eeeee.eehhhhhhhhhhh..............eeee..............eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: D:16-243 UniProt: 31-272                                                                                                                                                                                                        - PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fpz D   16 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK  244
                                    25        35  ||    43        53       60C||      68      ||81        91       101       111       121       131       141     ||152||     160       170   |||173G||     181       191       201       211     |221A       231       241   
                                                37A|                     60A||||             75|                                                                 147|   ||                  173A||||||||                                         217|  |                       
                                                 37B                      60B|||              79                                                                  149   ||                   173B|||||||                                          219  |                       
                                                                           60C||                                                                                     152A|                    173C||||||                                            221A                       
                                                                            60D|                                                                                      152B                     173D|||||                                                                       
                                                                             60E                                                                                                                173E||||                                                                       
                                                                                                                                                                                                 173F|||                                                                       
                                                                                                                                                                                                  173G||                                                                       
                                                                                                                                                                                                   173H|                                                                       
                                                                                                                                                                                                    173I
   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, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 8)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Beta Barrel (4804)
(-)
Topology: Thrombin, subunit H (1535)
(-)
Homologous Superfamily: Trypsin-like serine proteases (1488)
(-)
Human (Homo sapiens) (615)
1a2fpzA02A:28-120,A:233-244
1b2fpzA01A:16-27,A:121-232
1c2fpzB01B:16-27,B:121-232
1d2fpzC01C:16-27,C:121-232
1e2fpzD01D:16-27,D:121-232
1f2fpzB02B:28-120,B:233-244
1g2fpzC02C:28-120,C:233-244
1h2fpzD02D:28-120,D:233-244

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FPZ)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (TRYB2_HUMAN | P20231)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.

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  2fpz
    Family and Domain Information: ProDom | SYSTERS
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  TRYB2_HUMAN | P20231
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  3.4.21.59
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRYB2_HUMAN | P20231: 1a0l 1aao 2bm2 2fs8 2fs9 2fww 2fxr 2gdd 2za5 3v7t

(-) Related Entries Specified in the PDB File

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