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(-) Description

Title :  HUMAN BETA-TRYPTASE CO-CRYSTAL STRUCTURE WITH [(1,1,3,3-TETRAMETHYLDISILOXANE-1,3-DIYL)DI-1-BENZOTHIENE-4,2-DIYL]BIS({4-[3-(AMINOMETHYL)PHENYL]PIPERIDIN-1-YL}METHANONE)
 
Authors :  A. White, A. J. Stein, R. Suto
Date :  13 Sep 13  (Deposition) - 18 Mar 15  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Coferon, Alpha-Hydroxyketone, Small Molecule Inhibitor, Drug Discovery, Self-Assembly, Crystal Catalysis, Silanol, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. F. Giardina, M. Pingle, K. W. Foreman, D. S. Werner, D. E. Bergstrom, F. Barany, L. D. Arnold
Target-Directed Self-Assembly Of Homodimeric Drugs
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRYPTASE ALPHA/BETA-1
    ChainsA, B
    EC Number3.4.21.59
    EngineeredYES
    Expression SystemKOMAGATAELLA PASTORIS
    Expression System CommonPICHIA PASTORIS
    Expression System Taxid4922
    FragmentUNP RESIDUES 31-275
    GeneTPS1, TPS2, TPSAB1, TPSB1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTRYPTASE-1, TRYPTASE I, TRYPTASE ALPHA-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB
Biological Unit 2 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric Unit (5, 11)
No.NameCountTypeFull Name
12AV1Ligand/Ion[(1,1,3,3-TETRAMETHYLDISILOXANE-1,3-DIYL)DI-1-BENZOTHIENE-4,2-DIYL]BIS({4-[3-(AMINOMETHYL)PHENYL]PIPERIDIN-1-YL}METHANONE)
2CL2Ligand/IonCHLORIDE ION
3MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4PGE2Ligand/IonTRIETHYLENE GLYCOL
5SO45Ligand/IonSULFATE ION
Biological Unit 1 (4, 18)
No.NameCountTypeFull Name
12AV2Ligand/Ion[(1,1,3,3-TETRAMETHYLDISILOXANE-1,3-DIYL)DI-1-BENZOTHIENE-4,2-DIYL]BIS({4-[3-(AMINOMETHYL)PHENYL]PIPERIDIN-1-YL}METHANONE)
2CL-1Ligand/IonCHLORIDE ION
3MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4PGE4Ligand/IonTRIETHYLENE GLYCOL
5SO410Ligand/IonSULFATE ION
Biological Unit 2 (4, 9)
No.NameCountTypeFull Name
12AV1Ligand/Ion[(1,1,3,3-TETRAMETHYLDISILOXANE-1,3-DIYL)DI-1-BENZOTHIENE-4,2-DIYL]BIS({4-[3-(AMINOMETHYL)PHENYL]PIPERIDIN-1-YL}METHANONE)
2CL-1Ligand/IonCHLORIDE ION
3MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4PGE2Ligand/IonTRIETHYLENE GLYCOL
5SO45Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:138 , TRP A:236 , HOH A:460 , HOH A:530BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWAREHIS A:74 , GLN A:221 , GLY A:222 , SER A:224BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREGLN A:35 , LYS A:179 , ARG A:217BINDING SITE FOR RESIDUE CL A 303
04AC4SOFTWAREVAL A:50 , PHE A:58 , LYS A:81 , ASP A:82 , ALA A:85 , HOH A:544BINDING SITE FOR RESIDUE PGE A 304
05AC5SOFTWARETHR A:115 , GLN A:117 , ASP A:218 , SER A:219 , CYS A:220 , GLN A:221 , SER A:224 , TRP A:244 , GLY A:245 , GLU A:246 , GLY A:247 , GLY A:255 , HOH A:408 , GLN B:117 , ASP B:218 , SER B:219 , CYS B:220 , SER B:224 , VAL B:242 , TRP B:244 , GLY B:245 , GLU B:246 , GLY B:247 , CYS B:248 , HOH B:413BINDING SITE FOR RESIDUE 2AV B 301
06AC6SOFTWAREHIS B:74 , GLN B:221 , GLY B:222 , SER B:224BINDING SITE FOR RESIDUE SO4 B 302
07AC7SOFTWAREHIS A:136 , GLU B:128 , HIS B:186 , ARG B:203 , MES B:307BINDING SITE FOR RESIDUE SO4 B 303
08AC8SOFTWAREASN B:214 , THR B:215 , ARG B:216BINDING SITE FOR RESIDUE SO4 B 304
09AC9SOFTWAREASN B:185BINDING SITE FOR RESIDUE CL B 305
10BC1SOFTWAREVAL B:50 , PHE B:58 , LYS B:81 , ASP B:82 , ALA B:85 , HOH B:504BINDING SITE FOR RESIDUE PGE B 306
11BC2SOFTWARELYS A:132 , HIS A:136 , HOH A:468 , ARG B:203 , ARG B:206 , ASP B:207 , SO4 B:303BINDING SITE FOR RESIDUE MES B 307

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:59 -A:75
2A:155 -A:230
3A:188 -A:211
4A:220 -A:248
5B:59 -B:75
6B:155 -B:230
7B:188 -B:211
8B:220 -B:248

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:77 -Pro A:78
2Pro A:171 -Pro A:172
3Gly B:77 -Pro B:78
4Pro B:171 -Pro B:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MPX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MPX)

(-) Exons   (0, 0)

(no "Exon" information available for 4MPX)

(-) 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:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhh.....hhh.eeee............eeeeeeee.............eeeee...........................eeeee................eeeee.eehhhhhhhhhhh..............eeee..............eeeeee..eeeeeeeeee..........eeeee...hhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mpx A  31 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVP 272
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270  

Chain B from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhh.....hhh.eeee............eeeeeeee.............eeeee..........................eeeeee................eeeeeeeehhhhhhhhhhh..............eeee..............eeeeee..eeeeeeeeee..........eeeee...hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mpx B  31 IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPK 273
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   

   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  (0, 0)

(no "SCOP Domain" information available for 4MPX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MPX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MPX)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRYB1_HUMAN | Q156611lto 2f9n 2f9o 2f9p 2za5 2zeb 2zec 4a6l 4mpu 4mpv 4mpw 4mqa 5f03

(-) Related Entries Specified in the PDB File

4mpu 4mpv 4mpw 4mqa