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
(-)Biological Unit 4
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)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  REFINED STRUCTURE OF CRO REPRESSOR PROTEIN FROM BACTERIOPHAGE LAMBDA
 
Authors :  D. H. Ohlendorf, D. E. Tronrud, B. W. Matthews
Date :  17 Apr 98  (Deposition) - 17 Jun 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,O
Biol. Unit 1:  B,O  (1x)
Biol. Unit 2:  A,C  (1x)
Biol. Unit 3:  A,B,C,O  (6x)
Biol. Unit 4:  A,B,C,O  (1x)
Keywords :  Gene Regulating Protein, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. H. Ohlendorf, D. E. Tronrud, B. W. Matthews
Refined Structure Of Cro Repressor Protein From Bacteriophage Lambda Suggests Both Flexibility And Plasticity.
J. Mol. Biol. V. 280 129 1998
PubMed-ID: 9653036  |  Reference-DOI: 10.1006/JMBI.1998.1849
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CRO REPRESSOR PROTEIN
    ChainsO, A, B, C
    Organism ScientificENTEROBACTERIA PHAGE LAMBDA
    Organism Taxid10710
    Other DetailsWATER MOLECULES AND TWO PHOSPHATE RADICALS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCO
Biological Unit 1 (1x) B O
Biological Unit 2 (1x)A C 
Biological Unit 3 (6x)ABCO
Biological Unit 4 (1x)ABCO

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 3 (1, 12)
No.NameCountTypeFull Name
1PO412Ligand/IonPHOSPHATE ION
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER O:28 , LYS O:32 , PO4 O:101 , HOH O:549BINDING SITE FOR RESIDUE PO4 O 100
2AC2SOFTWARELYS O:32 , PO4 O:100BINDING SITE FOR RESIDUE PO4 O 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CRO)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe O:58 -Pro O:59
2Phe A:58 -Pro A:59
3Phe B:58 -Pro B:59
4Phe C:58 -Pro C:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CRO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CRO)

(-) Exons   (0, 0)

(no "Exon" information available for 5CRO)

(-) 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:61
                                                                                            
               SCOP domains d5croa_ A: cro lambda repressor                               SCOP domains
               CATH domains 5croA00 A:1-61 CRO Repressor                                  CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhhhh...hhhhhhhhh....eeeee.....eeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  5cro A  1 MEQRITLKDYAMRFGQTKTAKDLGVYQSAINKAIHAGRKIFLTINADGSVYAEEVKPFPSN 61
                                    10        20        30        40        50        60 

Chain B from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains d5crob_ B: cro lambda repressor                               SCOP domains
               CATH domains 5croB00 B:1-61 CRO Repressor                                  CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhhh....hhhhhhhhh....eeeee.....eeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  5cro B  1 MEQRITLKDYAMRFGQTKTAKDLGVYQSAINKAIHAGRKIFLTINADGSVYAEEVKPFPSN 61
                                    10        20        30        40        50        60 

Chain C from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains d5croc_ C: cro lambda repressor                               SCOP domains
               CATH domains 5croC00 C:1-61 CRO Repressor                                  CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhh.hhhhhhh....hhhhhhhhhh...eeeee.....eeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  5cro C  1 MEQRITLKDYAMRFGQTKTAKDLGVYQSAINKAIHAGRKIFLTINADGSVYAEEVKPFPSN 61
                                    10        20        30        40        50        60 

Chain O from PDB  Type:PROTEIN  Length:60
                                                                                           
               SCOP domains d5croo_ O: cro lambda repressor                              SCOP domains
               CATH domains 5croO00 O:1-60 CRO Repressor                                 CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhhhh...hhhhhhhhh....eeeee.....eeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  5cro O  1 MEQRITLKDYAMRFGQTKTAKDLGVYQSAINKAIHAGRKIFLTINADGSVYAEEVKPFPS 60
                                    10        20        30        40        50        60

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CRO)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

 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
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:58 - Pro A:59   [ RasMol ]  
    Phe B:58 - Pro B:59   [ RasMol ]  
    Phe C:58 - Pro C:59   [ RasMol ]  
    Phe O:58 - Pro O:59   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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
  5cro
    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
  RCRO_LAMBD | P03040
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  RCRO_LAMBD | P03040
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RCRO_LAMBD | P030401cop 1d1l 1d1m 1orc 2a63 2ecs 2orc 2ovg 3orc 4cro 6cro

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5CRO)