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 CYTOCHROME C PEROXIDASE W191G-GATELESS IN COMPLEX WITH 4-AZAINDOLE
 
Authors :  S. E. Boyce, M. Fischer, I. Fish
Date :  19 Mar 13  (Deposition) - 31 Jul 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.41
Chains :  Asym./Biol. Unit :  A
Keywords :  Model System, Ligand Binding, Free Energy Calculation, Molecular Dynamics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. J. Rocklin, S. E. Boyce, M. Fischer, I. Fish, D. L. Mobley, B. K. Shoichet, K. A. Dill
Blind Prediction Of Charged Ligand Binding Affinities In A Model Binding Site.
J. Mol. Biol. V. 425 4569 2013
PubMed-ID: 23896298  |  Reference-DOI: 10.1016/J.JMB.2013.07.030

(-) Compounds

Molecule 1 - CYTOCHROME C PEROXIDASE
    Chains: A
    EC Number: 1.11.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 72-362, DELETIONS G192-A193
    Gene: CCP1 CCP CPO YKR066C, SCRG_04081
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 285006
    Strain: RM11-1A

 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
14JP1Ligand/Ion1H-PYRROLO[3,2-B]PYRIDINE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:44 , ARG A:48 , TRP A:51 , PRO A:145 , ASP A:146 , ALA A:147 , LEU A:171 , MET A:172 , ALA A:174 , HIS A:175 , LEU A:177 , GLY A:178 , LYS A:179 , THR A:180 , HIS A:181 , ASN A:184 , SER A:185 , LEU A:230 , THR A:232 , 4JP A:302 , HOH A:419 , HOH A:458 , HOH A:500 , HOH A:507BINDING SITE FOR RESIDUE HEM A 301
2AC2SOFTWAREHIS A:175 , LEU A:177 , GLY A:178 , LYS A:179 , MET A:228 , MET A:229 , ASP A:233 , HEM A:301 , HOH A:635 , HOH A:770BINDING SITE FOR RESIDUE 4JP A 302
3AC3SOFTWARELEU A:30 , ASN A:194 , HOH A:437 , HOH A:481 , HOH A:753BINDING SITE FOR RESIDUE PO4 A 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JPL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JPL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JPL)

(-) 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:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4jpla_ A: Cytochrome c peroxidase, CCP                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.......hhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..............hhhhh...........hhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhh...........hhhhhhhhhh..eeee.....eeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee............hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jpl A   4 LVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGGGANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL 292
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283
   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 alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

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
    4JP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4jpl)
 

(-) 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
  4jpl
    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
  B3LRE1_YEAS1 | B3LRE1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.11.1.5
    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
  B3LRE1_YEAS1 | B3LRE1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B3LRE1_YEAS1 | B3LRE1: 4jm5 4jm6 4jm8 4jm9 4jma 4jmb 4jms 4jmt 4jmv 4jmw 4jmz 4jn0 4jpt 4jpu 4jqj 4jqk 4jqm 4jqn 4nva 4nvb 4nvc 4nvd 4nve 4nvf 4nvg 4nvh 4nvi 4nvj 4nvk 4nvl 4nvm 4nvn 4nvo 4oq7 5u5u 5u5v 5u5w 5u5x 5u5y 5u5z 5u60 5u61 5ug2

(-) Related Entries Specified in the PDB File

1kxm 1kxn 4jm5 4jm6 4jm8 4jm9 4jma 4jmw 4jpl 4jpt 4jpu 4jqj 4jqk 4jqm 4jqn