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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CHYMASE WITH BENZIMIDAZOLONE INHIBITOR
 
Authors :  K. C. Qian, N. A. Farrow, A. K. Padyana
Date :  13 May 11  (Deposition) - 20 Jul 11  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Y. Lo, P. A. Nemoto, J. M. Kim, M. H. Hao, K. C. Qian, N. A. Farrow, D. R. Albaugh, D. M. Fowler, R. D. Schneiderman, E. Michael August, L. Martin, M. Hill-Drzewi, S. S. Pullen, H. Takahashi, S. De Lombaert
Benzimidazolone As Potent Chymase Inhibitor: Modulation Of Reactive Metabolite Formation In The Hydrophobic (P(1)) Region.
Bioorg. Med. Chem. Lett. V. 21 4533 2011
PubMed-ID: 21733690  |  Reference-DOI: 10.1016/J.BMCL.2011.05.126

(-) Compounds

Molecule 1 - CHYMASE
    ChainsA
    EC Number3.4.21.39
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentUNP RESIDUES 22-247
    GeneCMA1, CYH, CYM
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymALPHA-CHYMASE, MAST CELL PROTEASE I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
10BB1Ligand/Ion4-{3-[(4-METHYL-1-BENZOTHIOPHEN-3-YL)METHYL]-2-OXO-2,3-DIHYDRO-1H-BENZIMIDAZOL-1-YL}BUTANOIC ACID
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:59 , THR A:61 , GLU A:62 , THR A:140 , HOH A:341BINDING SITE FOR RESIDUE NAG A 227
2AC2SOFTWAREASN A:82 , SER A:84 , THR A:85 , HOH A:357BINDING SITE FOR RESIDUE NAG A 228
3AC3SOFTWAREHIS A:10 , GLU A:64 , GLU A:71 , LYS A:96BINDING SITE FOR RESIDUE ZN A 229
4AC4SOFTWAREHIS A:45 , ALA A:177 , PHE A:178 , SER A:182 , VAL A:196 , SER A:197 , GLY A:199 , ARG A:200BINDING SITE FOR RESIDUE 0BB A 230

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:30 -A:46
2A:123 -A:188
3A:154 -A:167

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:110 -Pro A:111
2Pro A:205 -Pro A:206

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011770G46RCMA1_HUMANPolymorphism5246AG25R
2UniProtVAR_011771H66RCMA1_HUMANPolymorphism5247AH45R
3UniProtVAR_029190R98HCMA1_HUMANPolymorphism13306252AR77H

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CMA1_HUMAN22-245  1A:1-224
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CMA1_HUMAN62-67  1A:41-46
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CMA1_HUMAN197-208  1A:176-187

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002503781ENSE00001144725chr14:24977471-2497738488CMA1_HUMAN1-20200--
1.2aENST000002503782aENSE00001144738chr14:24976712-24976562151CMA1_HUMAN20-70511A:1-4949
1.3ENST000002503783ENSE00000586440chr14:24975810-24975675136CMA1_HUMAN70-115461A:49-9446
1.4aENST000002503784aENSE00000654524chr14:24975488-24975234255CMA1_HUMAN116-200851A:95-17985
1.5bENST000002503785bENSE00001816406chr14:24974865-24974561305CMA1_HUMAN201-247471A:180-22647

(-) 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:226
 aligned with CMA1_HUMAN | P23946 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:226
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      
          CMA1_HUMAN     22 IIGGTECKPHSRPYMAYLEIVTSNGPSKFCGGFLIRRNFVLTAAHCAGRSITVTLGAHNITEEEDTWQKLEVIKQFRHPKYNTSTLHHDIMLLKLKEKASLTLAVGTLPFPSQFNFVPPGRMCRVAGWGRTGVLKPGSDTLQEVKLRLMDPQACSHFRDFDHNLQLCVGNPRKTKSAFKGDSGGPLLCAGVAQGIVSYGRSDAKPPAVFTRISHYRPWINQILQAN  247
               SCOP domains d3s0na_ A: Chymase (mast cell protease I)                                                                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeeeee..eeeeeeeeeeee..eeeehhhhh..eeeeee............eeeeeeeeee.............eeeee..........................eeeeee..............eeeeeeeehhhhhh.........eeee................eeee..eeeeeeee........eeeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------R-------------------R-------------------------------H----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:1-224 UniProt: 22-245                                                                                                                                                                                       -- PROSITE (1)
                PROSITE (2) ----------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2a  PDB: A:1-49 UniProt: 20-70            ---------------------------------------------Exon 1.4a  PDB: A:95-179 UniProt: 116-200                                            Exon 1.5b  PDB: A:180-226 UniProt: 201-247      Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------Exon 1.3  PDB: A:49-94 UniProt: 70-115        ------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                3s0n A    1 IIGGTECKPHSRPYMAYLEIVTSNGPSKFCGGFLIRRNFVLTAAHCAGRSITVTLGAHNITEEEDTWQKLEVIKQFRHPKYNTSTLHHDIMLLKLKEKASLTLAVGTLPFPSQKNFVPPGRMCRVAGWGRTGVLKPGSDTLQEVKLRLMDPQACSHFRDFDHNLQLCVGNPRKTKSAFKGDSGGPLLCAGAAQGIVSYGRSDAKPPAVFTRISHYQPWINQILQAN  226
                                    10        20 |||    30        40        50        60        70        80        90       100       110       120       130       140       150       160 |     170||     180       190       200       210       220      
                                               22A||                                                                                                                                      162B     171A|                                                      
                                                23B|                                                                                                                                                172B                                                      
                                                 24C                                                                                                                                                                                                          

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S0N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S0N)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CMA1_HUMAN | P23946)
molecular function
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    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:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    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:0002003    angiotensin maturation    The process leading to the attainment of the full functional capacity of angiotensin by conversion of renin substrate into mature angiotensin in the blood.
    GO:0071333    cellular response to glucose stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    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:0050720    interleukin-1 beta biosynthetic process    The chemical reactions and pathways resulting in the formation of interleukin-1 beta.
    GO:0030901    midbrain development    The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles).
    GO:0006518    peptide metabolic process    The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CMA1_HUMAN | P239461klt 1nn6 1pjp 1t31 2hvx 3n7o 4afq 4afs 4afu 4afz 4ag1 4ag2 4k2y 4k5z 4k60 4k69 4kp0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3S0N)