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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  X-RAY CRYSTAL STRUCTURE PROTEIN Q88CH6 FROM PSEUDOMONAS PUTIDA. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET PPR72.
 
Authors :  A. P. Kuzin, Y. Chen, M. Abashidze, T. Acton, K. Conover, H. Janjua, L. -C C. K. Ho, K. Cunningham, G. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  16 Feb 06  (Deposition) - 14 Mar 06  (Release) - 13 Jul 11  (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)
Keywords :  Ppr72, Nesg, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bertonati, M. Punta, M. Fischer, G. Yachdav, F. Forouhar, W. Zhou, A. P. Kuzin, J. Seetharaman, M. Abashidze, T. A. Ramelot, M. A. Kennedy J. R. Cort, A. Belachew, J. F. Hunt, L. Tong, G. T. Montelione, B. Rost
Structural Genomics Reveals Eve As A New Asch/Pua-Related Domain.
Proteins V. 75 760 2009
PubMed-ID: 19191354  |  Reference-DOI: 10.1002/PROT.22287

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN PP5205
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) + MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PET21
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 160488
    Strain: KT2440

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 3 (2, 5)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:8 , TRP A:26 , ASP A:27 , TYR A:82BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARESER B:8 , TRP B:26 , ASP B:27 , TYR B:82BINDING SITE FOR RESIDUE SO4 B 302
3AC3SOFTWARESER C:8 , TRP C:26 , ASP C:27 , TYR C:82 , HOH C:334BINDING SITE FOR RESIDUE SO4 C 303
4AC4SOFTWAREPRO C:71 , THR C:89 , ASP C:90 , LYS C:91 , ASN C:92 , HOH C:312BINDING SITE FOR RESIDUE SO4 C 304
5AC5SOFTWAREPRO A:71 , THR A:89 , ASP A:90 , LYS A:91 , ASN A:92 , HOH A:317BINDING SITE FOR RESIDUE SO4 A 305
6AC6SOFTWAREPRO B:71 , THR B:89 , ASP B:90 , LYS B:91 , ASN B:92BINDING SITE FOR RESIDUE SO4 B 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2G2X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2G2X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G2X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2G2X)

(-) Exons   (0, 0)

(no "Exon" information available for 2G2X)

(-) 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:149
 aligned with Q88CH6_PSEPK | Q88CH6 from UniProtKB/TrEMBL  Length:149

    Alignment length:149
                                                                                                                                                                             149 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       | 
         Q88CH6_PSEPK     2 AYWLMKSEPDELSIEALARLGEARWDGVRNYQARNFLRAMSVGDEFFFYHSSCPQPGIAGIARITRAAYPDPTALDPESHYHDAKATTDKNPWSAVDVAHVQTFPRVLELGRLKQQAGLVELPLVQKGSRLSVMPVTPEQWAVIVALR-   -
               SCOP domains d2g2xa1 A:2-149 Hypothetical protein PP5205                                                                                                         - SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhheeee....hhhhhhhhh......eeeeee......eeeeeeeeeeeeee.hhhh..................eeeeeeeeeeeeeeeehhhhhhhhhhh.hhhhh......eee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g2x A   2 AYWLmKSEPDELSIEALARLGEARWDGVRNYQARNFLRAmSVGDEFFFYHSSCPQPGIAGIARITRAAYPDPTALDPESHYHDAKATTDKNPWSAVDVAHVQTFPRVLELGRLKQQAGLVELPLVQKGSRLSVmPVTPEQWAVIVALRL 150
                                |   11        21        31        41        51        61        71        81        91       101       111       121       131   |   141         
                                |                                 41-MSE                                                                                       135-MSE           
                                6-MSE                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:149
 aligned with Q88CH6_PSEPK | Q88CH6 from UniProtKB/TrEMBL  Length:149

    Alignment length:149
                                                                                                                                                                             149 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       | 
         Q88CH6_PSEPK     2 AYWLMKSEPDELSIEALARLGEARWDGVRNYQARNFLRAMSVGDEFFFYHSSCPQPGIAGIARITRAAYPDPTALDPESHYHDAKATTDKNPWSAVDVAHVQTFPRVLELGRLKQQAGLVELPLVQKGSRLSVMPVTPEQWAVIVALR-   -
               SCOP domains d2g2xb_ B: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhheeee....hhhhhhhhh......eeeeee......eeeeeeeeeeeeee.hhhh..................eeeeeeeeeeeeeeeehhhhhhhhhhh.hhhhh......eee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g2x B   2 AYWLmKSEPDELSIEALARLGEARWDGVRNYQARNFLRAmSVGDEFFFYHSSCPQPGIAGIARITRAAYPDPTALDPESHYHDAKATTDKNPWSAVDVAHVQTFPRVLELGRLKQQAGLVELPLVQKGSRLSVmPVTPEQWAVIVALRL 150
                                |   11        21        31        41        51        61        71        81        91       101       111       121       131   |   141         
                                6-MSE                             41-MSE                                                                                       135-MSE           


Chain C from PDB  Type:PROTEIN  Length:149
 aligned with Q88CH6_PSEPK | Q88CH6 from UniProtKB/TrEMBL  Length:149

    Alignment length:149
                                                                                                                                                                             149 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       | 
         Q88CH6_PSEPK     2 AYWLMKSEPDELSIEALARLGEARWDGVRNYQARNFLRAMSVGDEFFFYHSSCPQPGIAGIARITRAAYPDPTALDPESHYHDAKATTDKNPWSAVDVAHVQTFPRVLELGRLKQQAGLVELPLVQKGSRLSVMPVTPEQWAVIVALR-   -
               SCOP domains d2g2xc_ C: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhheeee....hhhhhhhhh......eeeeee......eeeeeeeeeeeeee.hhhh..................eeeeeeeeeeeeeeeehhhhhhhhhhh.hhhhh......eee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g2x C   2 AYWLmKSEPDELSIEALARLGEARWDGVRNYQARNFLRAmSVGDEFFFYHSSCPQPGIAGIARITRAAYPDPTALDPESHYHDAKATTDKNPWSAVDVAHVQTFPRVLELGRLKQQAGLVELPLVQKGSRLSVmPVTPEQWAVIVALRL 150
                                |   11        21        31        41        51        61        71        81        91       101       111       121       131   |   141         
                                6-MSE                             41-MSE                                                                                       135-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  (2, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2G2X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G2X)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2G2X)

 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 ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2g2x)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  2g2x
    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
  Q88CH6_PSEPK | Q88CH6
    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
  Q88CH6_PSEPK | Q88CH6
    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 2G2X)

(-) Related Entries Specified in the PDB File

1zce RELATED ID: PPR72 RELATED DB: TARGETDB
2ar1
2eve