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 PUTATIVE MEMBRANE PROTEIN FROM CLOSTRIDIUM DIFFICILE 630
 
Authors :  C. Chang, E. Rakowski, J. Bearden, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  10 Nov 09  (Deposition) - 17 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, E. Rakowski, J. Bearden, A. Joachimiak
Crystal Structure Of Putative Membrane Protein From Clostridium Difficile 630
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE MEMBRANE PROTEIN COG4129
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3) MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 144-317
    Gene: CD3042
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    Organism Taxid: 272563
    Strain: 630

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2FMT2Ligand/IonFORMIC ACID
3MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN B:158 , ILE B:221 , GLN B:224 , ARG B:311 , ALA B:314BINDING SITE FOR RESIDUE EDO B 401
2AC2SOFTWAREHIS A:253 , TYR A:257 , HOH B:4 , HIS B:246BINDING SITE FOR RESIDUE FMT B 402
3AC3SOFTWAREGLN B:158 , ARG B:311 , GLN B:315BINDING SITE FOR RESIDUE FMT B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KMI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KMI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KMI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KMI)

(-) Exons   (0, 0)

(no "Exon" information available for 3KMI)

(-) 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:172
 aligned with Q184N1_PEPD6 | Q184N1 from UniProtKB/TrEMBL  Length:324

    Alignment length:172
                                   155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315  
         Q184N1_PEPD6   146 NIHKIHEVQKKLQEEVSIVLIDIADIIVNPKKENGYSRDLYTLNSLIDSSISETYDNINNTLLSDTRFFLEHMDIIKSQRDILENLYSYVSQLNSTPPQAHILSAFIHKIGYTEFEAETGNLLLEELKRLMISMKNQPLPVDRTEFENRAILFLCLTELKQFLVNRKHAQML 317
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kmi A 146 NIHKIHEVQKKLQEEVSIVLIDIADIIVNPKKENGYSRDLYTLNSLIDSSISETYDNINNTLLSDTRFFLEHmDIIKSQRDILENLYSYVSQLNSTPPQAHILSAFIHKIGYTEFEAETGNLLLEELKRLmISmKNQPLPVDRTEFENRAILFLCLTELKQFLVNRKHAQmL 317
                                   155       165       175       185       195       205       215  |    225       235       245       255       265       275|  |   285       295       305       315| 
                                                                                                  218-MSE                                                   276-MSE                                 316-MSE
                                                                                                                                                               279-MSE                                  


Chain B from PDB  Type:PROTEIN  Length:168
 aligned with Q184N1_PEPD6 | Q184N1 from UniProtKB/TrEMBL  Length:324

    Alignment length:169
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308         
         Q184N1_PEPD6   149 KIHEVQKKLQEEVSIVLIDIADIIVNPKKENGYSRDLYTLNSLIDSSISETYDNINNTLLSDTRFFLEHMDIIKSQRDILENLYSYVSQLNSTPPQAHILSAFIHKIGYTEFEAETGNLLLEELKRLMISMKNQPLPVDRTEFENRAILFLCLTELKQFLVNRKHAQML 317
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...-hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kmi B 149 KIHEVQKKLQEEVSIVLIDIADIIVNPKKENGYSRDLYTLNSLIDSSISETYDNINNTLLSDTRFFLEHmDIIKSQRDILENLYSYVSQLNSTPPQAHILSAFIHKIGYTEFE-ETGNLLLEELKRLmISmKNQPLPVDRTEFENRAILFLCLTELKQFLVNRKHAQmL 317
                                   158       168       178       188       198       208       218       228       238       248       258  | |  268       278|      288       298       308       | 
                                                                                               218-MSE                                    261 |          276-MSE                                 316-MSE
                                                                                                                                            263             279-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3KMI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q184N1_PEPD6 | Q184N1)
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 3kmi)
 

(-) 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
  3kmi
    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
  Q184N1_PEPD6 | Q184N1
    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
  Q184N1_PEPD6 | Q184N1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3KMI)

(-) Related Entries Specified in the PDB File

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