Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HOLO-PHUS, A HEME-BINDING PROTEIN FROM PSEUDOMONAS AERUGINOSA
 
Authors :  M. J. Y. Lee, Z. Jia, Montreal-Kingston Bacterial Structural Genom Initiative (Bsgi)
Date :  27 Aug 13  (Deposition) - 05 Mar 14  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Host-Pathogen Interactions, Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Heme-Trafficking Protein, Heme-Degrading Enzyme, Heme, Hemo, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Lee, D. Schep, B. Mclaughlin, M. Kaufmann, Z. Jia
Structural Analysis And Identification Of Phus As A Heme-Degrading Enzyme From Pseudomonas Aeruginosa.
J. Mol. Biol. V. 426 1936 2014
PubMed-ID: 24560694  |  Reference-DOI: 10.1016/J.JMB.2014.02.013

(-) Compounds

Molecule 1 - HEMIN DEGRADING FACTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PHUS
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:103 , ARG A:112 , PHE A:114 , THR A:208 , HIS A:209 , ARG A:222 , PHE A:259 , LYS A:307 , GLN A:329 , PHE A:331 , ARG A:334 , PRO A:336 , HOH A:602 , HOH A:689BINDING SITE FOR RESIDUE HEM A 400
2AC2SOFTWARELEU B:103 , ARG B:112 , THR B:208 , HIS B:209 , ARG B:222 , MET B:257 , PHE B:259 , LYS B:307 , GLN B:329 , PHE B:331 , ARG B:334 , HOH B:534 , HOH B:558 , HOH B:690BINDING SITE FOR RESIDUE HEM B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MF9)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Arg A:91 -Glu A:92
2Arg B:91 -Glu B:92
3Ala B:129 -Arg B:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MF9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MF9)

(-) Exons   (0, 0)

(no "Exon" information available for 4MF9)

(-) 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:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4mf9a_ A: automated matches                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhh.....eeee..hhhhhhhhhhhh.eeeeeee...eeeeeeee...eee.....eeee......eeee...eeeeeeeeee....eeeeeeeee....eeeeeee....hhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhh...eeee..hhhhhhhhhhhhhh..eeeeeee..eeeeeee....eeee..eeeeee..eeeeee.hhh.eeeeeee......eeeeeee.....eeeeeee........hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mf9 A   9 HSPAELYRAWQDLRAERPQLRARDAAALLQVSEGELVASRVGIDAVRLRPDWAALLPALGELGPIMALTRNEHCVHERKGPYREVTVSANGQMGLVVSPDIDLRLFLGGWNAVFAIAEETARGTQRSIQVFDQQGVAVHKVFLAEASDVRAWEPLVERLRAAEQDAVLALHEPRAPAAALVDAQIDAAALREGWAALKDTHHFHALLKKHGAQRTQALRLAGGEWAERLDNGDLAKLFEAAAESGLPIMVFVGNAHCIQIHTGPVCNLKWLDDWFNVLDPEFNLHLKTTGIAELWRVRKPSTDGIVTSWEAFDPDGELIVQLFGARKPGEPERDDWRELAESFKAL 354
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348      


Chain B from PDB  Type:PROTEIN  Length:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4mf9b_ B: automated matches                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...hhhhhhhhh..hhhhhhhh.....eeee..hhhhhhhhhhhh.eeeeeee...eeeeeeee...eee.....eeee......eeee...eeeeeeeee......eeeeeeee....eeeeeee....hhhhhhhhhhhhh....................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhh...eeee..hhhhhhhhhhhhhh..eeeeeee..eeeeeee....eeee..eeeeee..eeeeee.hhh.eeeeeee......eeeeeee.....eeeeeee........hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mf9 B  14 LYRAWQDLRAERPQLRARDAAALLQVSEGELVASRVGIDAVRLRPDWAALLPALGELGPIMALTRNEHCVHERKGPYREVTVSANGQMGLVVSPDIDLRLFLGGWNAVFAIAEETARGTQRSIQVFDQQGVAVHKVFLAEASDVRAWEPLVERLRAAEQDAVLALHEPRAPAAALVDAQIDAAALREGWAALKDTHHFHALLKKHGAQRTQALRLAGGEWAERLDNGDLAKLFEAAAESGLPIMVFVGNAHCIQIHTGPVCNLKWLDDWFNVLDPEFNLHLKTTGIAELWRVRKPSTDGIVTSWEAFDPDGELIVQLFGARKPGEPERDDWRELAESFKAL 354
                                    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       293       303       313       323       333       343       353
   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, 2)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MF9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MF9)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala B:129 - Arg B:130   [ RasMol ]  
    Arg A:91 - Glu A:92   [ RasMol ]  
    Arg B:91 - Glu B:92   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4mf9
    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
  O68880_PSEAI | O68880
    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)
  (no 'Enzyme Classificator' available)
    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
  O68880_PSEAI | O68880
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O68880_PSEAI | O68880: 4imh 4mgf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4MF9)