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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH FRAGMENT INHIBITOR 6-CHLORO-2,3-DIHYDRO-1H-ISOINDOL-1-ONE
 
Authors :  B. K. Collins, A. K. Padyana
Date :  15 Apr 13  (Deposition) - 29 May 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine Protease, Glycosylated, Mast Cells, Secreted, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Taylor, A. K. Padyana, A. Abeywardane, S. Liang, M. H. Hao, S. De Lombaert, J. Proudfoot, B. S. Farmer, X. Li, B. Collins, L. Martin, D. R. Albaugh, M. Hill-Drzewi, S. S. Pullen, H. Takahashi
Discovery Of Potent, Selective Chymase Inhibitors Via Fragment Linking Strategies.
J. Med. Chem. V. 56 4465 2013
PubMed-ID: 23659209  |  Reference-DOI: 10.1021/JM400138Z
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHYMASE
    Chains: A
    EC Number: 3.4.21.39
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PDEST1393
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 22-247
    Gene: CMA1, CYH, CYM
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-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, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
11P71Ligand/Ion6-CHLORO-2,3-DIHYDRO-1H-ISOINDOL-1-ONE
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:72 , THR A:74 , GLU A:75 , THR A:154 , HOH A:923 , HOH A:966BINDING SITE FOR RESIDUE NAG A 701
2AC2SOFTWAREHIS A:25 , GLU A:78 , GLU A:84 , LYS A:109 , HOH A:982BINDING SITE FOR RESIDUE ZN A 702
3AC3SOFTWARESER A:189 , ALA A:190 , PHE A:191 , SER A:195 , SER A:214 , GLY A:216 , ARG A:217 , ALA A:226 , HOH A:974 , HOH A:981 , HOH A:993BINDING SITE FOR RESIDUE 1P7 A 703

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:136 -A:201
3A:168 -A:182

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:224 -Pro A:225

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K5Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K5Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4K5Z)

(-) 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:220
                                                                                                                                                                                                                                                             
               SCOP domains d4k5za_ 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........eeeeehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k5z A   16 IIGGTECKPHSRPYMAYLEIVTSNGPSKFCGGFLIRRNFVLTAAHCAGRSITVTLGAHNITEEEDTWQKLEVIKQFRHPKYNTSTLHHDIMLLKLKEKASLTLAVGTLPFVPPGRMCRVAGWGRTGVLKPGSDTLQEVKLRLMDPQACSHFRDFDHNLQLCVGNPRKTKSAFKGDSGGPLLCAGAAQGIVSYGRSDAKPPAVFTRISHYQPWINQILQAN  245
                                    25        35 |||    42        52        63        73 ||  |  83        93       103       113       123|      139       150       160       172     | 181    || 189       199  ||   213       225       235       245
                                               36A||                       61|          75|  |                                         123|               148|                169|  177A     185A|              202|           221|                     
                                                36B|                        63           77  |                                          130                150                 172            185B               207            224                     
                                                 36C                                       79A
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K5Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K5Z)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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    Pro A:224 - Pro A:225   [ RasMol ]  
 

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  CMA1_HUMAN | P23946
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 Related Entries

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

UniProtKB/Swiss-Prot
        CMA1_HUMAN | P23946: 1klt 1nn6 1pjp 1t31 2hvx 3n7o 3s0n 4afq 4afs 4afu 4afz 4ag1 4ag2 4k2y 4k60 4k69 4kp0

(-) Related Entries Specified in the PDB File

3s0n HUMAN CHYMASE BOUND TO BENZIMIDAZOLONE INHIBITOR
4k2y HUMAN CHYMASE IN COMPLEX WITH FRAGMENT INHIBITOR 6-CHLORO- 1,3-DIHYDRO-2H-INDOL-2-ONE
4k60 HUMAN CHYMASE IN COMPLEX WITH FRAGMENT 6-BROMO-1,3-DIHYDRO- 2H-INDOL-2-ONE
4k69 HUMAN CHYMASE IN COMPLEX WITH FRAGMENT LINKED BENZIMIDAZOLONE INHIBITOR: (3S)-3-{3-[(6-BROMO-2-OXO-2,3- DIHYDRO-1H-INDOL-4-YL)METHYL]-2-OXO-2,3-DIHYDRO-1H- BENZIMIDAZOL-1-YL}HEXANOIC ACID