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

(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE DNA DAMAGE-INDUCIBLE PROTEIN (CHU_0679) FROM CYTOPHAGA HUTCHINSONII ATCC 33406 AT 1.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  18 Jul 07  (Deposition) - 31 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Putative Dna Damage-Inducible Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Uncharacterized Protein Chu_0679 (Yp_677306. 1) From Cytophaga Hutchinsonii Atcc 33406 At 1. 5 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_677306.1, CHU_0679
    Organism Scientific: CYTOPHAGA HUTCHINSONII ATCC 33406
    Organism Taxid: 269798
    Strain: NCIMB 9469

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL5Ligand/IonGLYCEROL
3MSE3Mod. Amino AcidSELENOMETHIONINE
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL10Ligand/IonGLYCEROL
3MSE6Mod. Amino AcidSELENOMETHIONINE
4SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:19 , ARG A:22 , LEU A:153 , GOL A:169 , HOH A:386BINDING SITE FOR RESIDUE CL A 162
2AC2SOFTWAREALA A:34 , LEU A:159 , LYS A:161 , HOH A:224BINDING SITE FOR RESIDUE CL A 163
3AC3SOFTWAREARG A:22 , ASN A:144 , GOL A:169 , HOH A:231 , HOH A:356 , HOH A:383BINDING SITE FOR RESIDUE SO4 A 164
4AC4SOFTWAREHIS A:122 , VAL A:141 , ARG A:145 , GOL A:167 , HOH A:348BINDING SITE FOR RESIDUE GOL A 165
5AC5SOFTWAREGLY A:0 , MSE A:1 , HIS A:2 , THR A:3 , GLN A:28 , GLU A:104 , HOH A:351BINDING SITE FOR RESIDUE GOL A 166
6AC6SOFTWAREHIS A:122 , ARG A:136 , GOL A:165 , HOH A:347BINDING SITE FOR RESIDUE GOL A 167
7AC7SOFTWAREARG A:43 , ASN A:44 , TYR A:158 , HOH A:197 , HOH A:269 , HOH A:412BINDING SITE FOR RESIDUE GOL A 168
8AC8SOFTWAREGLN A:19 , ASN A:147 , HIS A:148 , TYR A:151 , CL A:162 , SO4 A:164 , HOH A:231 , HOH A:241BINDING SITE FOR RESIDUE GOL A 169

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QNL)

(-) 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:162
 aligned with Q11XA0_CYTH3 | Q11XA0 from UniProtKB/TrEMBL  Length:161

    Alignment length:162
                             1                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159  
         Q11XA0_CYTH3     - -MHTQEALFVRLALDAWNTQSSRTDKLIQSLSNEALAVETAPGRNSGTYLLGHLTAVHDAMLPLLELGDTLYPQLAPVFIQNPDKSGLEKPEINDLRLYWSLVQERLANQFNQLQPADWFNKHAAISREDFLKEPHRNKLSVLINRTNHMAYHLGQLAYLKK 161
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2qnlA00 A:0-161 dinb family like domain                                                                                                                            CATH domains
               Pfam domains ---------------DinB_2-2qnlA01 A:15-156                                                                                                                       ----- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh........hhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qnl A   0 GmHTQEALFVRLALDAWNTQSSRTDKLIQSLSNEALAVETAPGRNSGTYLLGHLTAVHDAmLPLLELGDTLYPQLAPVFIQNPDKSGLEKPEINDLRLYWSLVQERLANQFNQLQPADWFNKHAAISREDFLKEPHRNKLSVLINRTNHmAYHLGQLAYLKK 161
                             |       9        19        29        39        49        59|       69        79        89        99       109       119       129       139       149       159  
                             |                                                         60-MSE                                                                                  149-MSE        
                             1-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 2QNL)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: DinB (11)

(-) Gene Ontology  (0, 0)

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

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2qnl)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  2qnl
    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
  Q11XA0_CYTH3 | Q11XA0
    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
  Q11XA0_CYTH3 | Q11XA0
    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 2QNL)

(-) Related Entries Specified in the PDB File

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