Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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 :  X-RAY CRYSTAL STRUCTURE OF PROTEIN AGR_C_984 FROM AGROBACTERIUM TUMEFACIENS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ATR120.
 
Authors :  J. Seetharaman, F. Forouhar, M. Su, L. Zhao, K. Cunningham, L. -C. Ma, H. R. Xiao, J. Liu, M. C. Baran, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Northeast Structural Genomics Consortium (Nesg)
Date :  12 Dec 06  (Deposition) - 30 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  All Alpha-Helical Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Seetharaman, F. Forouhar, M. Su, L. Zhao, K. Cunningham, L. -C. Ma, H. Janjua, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of The Hypothetical Protein Agr_c_984 Fro Agrobacterium Tumefaciens, Northeast Structural Genomics Target Atr120.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AGR_C_984P
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BL21
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PET21
    Gene: LOCUS_TAG="AGR_C_984"
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 176299
    Strain: STR. C58

 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  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:125 , SER B:136 , ASP B:137BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREALA A:160 , GLY A:161 , HOH A:415 , TYR B:122 , ALA B:123 , LYS B:124 , ALA B:125BINDING SITE FOR RESIDUE SO4 B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O8S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O8S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O8S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O8S)

(-) Exons   (0, 0)

(no "Exon" information available for 2O8S)

(-) 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:230
 aligned with Q7D182_AGRFC | Q7D182 from UniProtKB/TrEMBL  Length:211

    Alignment length:235
                                                                                      1                                                                                                                                                                                
                                     -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172     
         Q7D182_AGRFC     - ----------------------------------------------------------MADTRLYNYALKAHGLEDMAYAKAFIRKVLTEGASDKNAFANKLSDNRYAELAKSLDFAGLGAAATATEAAKSGVIGNYARQTLEQEAGDDNNGVRLALYFERKAPTIKSGLDFLADDALAQVFRTTFNLPDAFAAADVDKQAALIEKSINIKDLQDPEKVGKLLERFTIMWEMQNP 177
               SCOP domains ----------d2o8sa1 A:54-278 Uncharacterized protein AGR_C_984p                                                                                                                                                                               SCOP domains
               CATH domains ---------2o8sA01 A:29-278 AGR_C_984p-like                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....-----.....hhhhhhhhh.........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o8s A  20 PPSPQPVSHKVTSTYTSYRLISQDIGKSLERVSKQPDVARETEYYREKIGSVKSIDDFmADTRLYNYALKAHGLEDmAYAKAFIRKVLTEGASDKNAFANKLSDNRYAELAKSLDFAGLGAAATATEAAKSGVIGNYARQTLEQEAGDDNNGVRLALYFERKAPTIKSGLDFLADDALAQVFRTTFNL-----AADVDKQAALIEKSINIKDLQDPEKVGKLLERFTImWEmQNP 278
                                    29|       63        73        83        93       103       113      |123       133       143       153       163       173       183       193       203       213       223       | -   |   243       253       263       273 |   
                                    29|                                             102-MSE           120-MSE                                                                                                        231   237                                272-MSE  
                                     54                                                                                                                                                                                                                          275-MSE


Chain B from PDB  Type:PROTEIN  Length:230
 aligned with Q7D182_AGRFC | Q7D182 from UniProtKB/TrEMBL  Length:211

    Alignment length:235
                                                                                      1                                                                                                                                                                                
                                     -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172     
         Q7D182_AGRFC     - ----------------------------------------------------------MADTRLYNYALKAHGLEDMAYAKAFIRKVLTEGASDKNAFANKLSDNRYAELAKSLDFAGLGAAATATEAAKSGVIGNYARQTLEQEAGDDNNGVRLALYFERKAPTIKSGLDFLADDALAQVFRTTFNLPDAFAAADVDKQAALIEKSINIKDLQDPEKVGKLLERFTIMWEMQNP 177
               SCOP domains ----------d2o8sb1 B:54-278 Uncharacterized protein AGR_C_984p                                                                                                                                                                               SCOP domains
               CATH domains ---------2o8sB01 B:29-278 AGR_C_984p-like                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....-----.....hhhhhhhhh.........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o8s B  20 PPSPQPVSHKVTSTYTSYRLISQDIGKSLERVSKQPDVARETEYYREKIGSVKSIDDFmADTRLYNYALKAHGLEDmAYAKAFIRKVLTEGASDKNAFANKLSDNRYAELAKSLDFAGLGAAATATEAAKSGVIGNYARQTLEQEAGDDNNGVRLALYFERKAPTIKSGLDFLADDALAQVFRTTFNL-----AADVDKQAALIEKSINIKDLQDPEKVGKLLERFTImWEmQNP 278
                                    29|       63        73        83        93       103       113      |123       133       143       153       163       173       183       193       203       213       223       | -   |   243       253       263       273 |   
                                    29|                                             102-MSE           120-MSE                                                                                                        231   237                                272-MSE  
                                     54                                                                                                                                                                                                                          275-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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2O8S)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2O8S)

 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 ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2o8s)
 
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
  2o8s
    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
  Q7D182_AGRFC | Q7D182
    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
  Q7D182_AGRFC | Q7D182
    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 2O8S)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2O8S)