Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF 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
 
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 :  1.50
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, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
11P91Ligand/Ion(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
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:25 , GLU A:78 , GLU A:84 , LYS A:109 , HOH A:627BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREHIS A:101 , HIS A:233 , HOH A:593BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREASN A:72 , THR A:74 , GLU A:75 , THR A:154 , HOH A:587BINDING SITE FOR RESIDUE NAG A 303
4AC4SOFTWARECYS A:42 , HIS A:57 , ALA A:190 , PHE A:191 , LYS A:192 , GLY A:193 , SER A:195 , VAL A:213 , SER A:214 , GLY A:216 , ALA A:226 , HOH A:575 , HOH A:578 , HOH A:579 , HOH A:585BINDING SITE FOR RESIDUE 1P9 A 304

(-) 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 4K69)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K69)

(-) Exons   (0, 0)

(no "Exon" information available for 4K69)

(-) 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:215
                                                                                                                                                                                                                                                        
               SCOP domains d4k69a_ A: Chymase (mast cell protease I)                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.........eeeeeee..eeeeee..eeee..eeeehhhhh..eeeeee............eeeeeeeeee.............eeeee...............eeeeee..............eeeeeeeehhhhhh.........eeee................eeee..eeeeeeee........eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k69 A   16 IIGGTECKPHSRPYMAYLEIVTSNGPSKFCGGFLIRRNFVLTAAHCAGRSITVTLGAHNITEEEDTWQKLEVIKQFRHPKYNTSTLHHDIMLLKLKEKASLTLAVGTLGRMCRVAGWGRTGVLKPGSDTLQEVKLRLMDPQACSHFRDFDHNLQLCVGNPRKTKSAFKGDSGGPLLCAGAAQGIVSYGRSDAKPPAVFTRISHYQPWINQILQAN  245
                                    25        35 |||    42        52        63        73 ||  |  83        93       103       113       134       144   ||  155       165   ||  177|     185A|      194       208       218  ||   230       240     
                                               36A||                       61|          75|  |                                       121|            148|                169|  177A     185A|              202|           221|                     
                                                36B|                        63           77  |                                        133             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 4K69)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K69)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    1P9  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:224 - Pro A:225   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4k69
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CMA1_HUMAN | P23946
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.39
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CMA1_HUMAN | P23946
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 4k5z 4k60 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
4k5z HUMAN CHYMASE IN COMPLEX WITH FRAGMENT INHIBITOR 6-CHLORO- 2,3-DIHYDRO-1H-ISOINDOL-1-ONE
4k60 HUMAN CHYMASE IN COMPLEX WITH FRAGMENT 6-BROMO-1,3-DIHYDRO- 2H-INDOL-2-ONE