Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)

(-) Description

Title :  X-RAY STRUCTURE OF THE PROTEIN Q7CQI7. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET STR87A
 
Authors :  A. P. Kuzin, M. Su, J. Seetharaman, S. M. Vorobiev, D. Wang, Y. Fang, L. Owens, L-C. Mao, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  20 Sep 07  (Deposition) - 09 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  A (1x),C (1x)
Biol. Unit 5:  B  (2x)
Keywords :  X-Ray, Nesg, Q7Cqi7, Str87A, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Lipoprotein, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. P. Kuzin, M. Su, J. Seetharaman, S. M. Vorobiev, D. Wan, Y. Fang, L. Owens, L-C. Ma, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong
X-Ray Structure Of The Protein Q7Cqi7.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE OUTER MEMBRANE LIPOPROTEIN
    Atcc700720
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 20-73
    GeneSTM1585
    Organism ScientificSALMONELLA TYPHIMURIUM LT2
    Organism Taxid99287
    StrainLT2, SGSC1412

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C
Biological Unit 4 (1x)A (1x) C (1x)
Biological Unit 5 (2x) B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 5 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2RD1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RD1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RD1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RD1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RD1)

(-) Exons   (0, 0)

(no "Exon" information available for 2RD1)

(-) 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:57
 aligned with Q7CQI7_SALTY | Q7CQI7 from UniProtKB/TrEMBL  Length:73

    Alignment length:57
                                                                              73     
                                    31        41        51        61        71 |     
          Q7CQI7_SALTY   22 TNYVMTTKNGQTIVTQGKPQLDKETGMTSYTDQEGNQREINSNDVAQLIKAD-----  -
               SCOP domains d2rd1a1 A:22-73                                     ----- SCOP domains
               CATH domains 2rd1A00 A:22-78  [code=2.30.30.100, no name defined]      CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee...ee.....eeeee.....eeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                  2rd1 A 22 TNYVmTTKNGQTIVTQGKPQLDKETGmTSYTDQEGNQREINSNDVAQLIKADLEHHH 78
                                |   31        41      | 51        61        71       
                                |                    48-MSE                          
                               26-MSE                                                

Chain B from PDB  Type:PROTEIN  Length:58
 aligned with Q7CQI7_SALTY | Q7CQI7 from UniProtKB/TrEMBL  Length:73

    Alignment length:58
                                                                               73     
                                    30        40        50        60        70  |     
          Q7CQI7_SALTY   21 TTNYVMTTKNGQTIVTQGKPQLDKETGMTSYTDQEGNQREINSNDVAQLIKAD-----  -
               SCOP domains d2rd1b_ B: Putative outer membrane lipoprotein STM1585     SCOP domains
               CATH domains 2rd1B00 B:21-78  [code=2.30.30.100, no name defined]       CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeee...ee.....eeeee.....eeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  2rd1 B 21 TTNYVmTTKNGQTIVTQGKPQLDKETGmTSYTDQEGNQREINSNDVAQLIKADLEHHH 78
                                 |  30        40       |50        60        70        
                                26-MSE                48-MSE                          

Chain C from PDB  Type:PROTEIN  Length:58
 aligned with Q7CQI7_SALTY | Q7CQI7 from UniProtKB/TrEMBL  Length:73

    Alignment length:58
                                                                               73     
                                    30        40        50        60        70  |     
          Q7CQI7_SALTY   21 TTNYVMTTKNGQTIVTQGKPQLDKETGMTSYTDQEGNQREINSNDVAQLIKAD-----  -
               SCOP domains d2rd1c_ C: Putative outer membrane lipoprotein STM1585     SCOP domains
               CATH domains 2rd1C00 C:21-78  [code=2.30.30.100, no name defined]       CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeee...ee.....eeeee.....eeeee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  2rd1 C 21 TTNYVmTTKNGQTIVTQGKPQLDKETGmTSYTDQEGNQREINSNDVAQLIKADLEHHH 78
                                 |  30        40       |50        60        70        
                                26-MSE                48-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  (1, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2RD1)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2RD1)

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2rd1)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2rd1)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2rd1
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q7CQI7_SALTY | Q7CQI7
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q7CQI7_SALTY | Q7CQI7
    Protein Disorder PredictionDisEMBL | 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 2RD1)

(-) Related Entries Specified in the PDB File

2jn0 SOLUTION NMR STRUCTURE OF E.COLI YGDR PROTEIN (STRUCTURAL HOMOLOG)