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

(-) Description

Title :  MROUGE
 
Authors :  S. L. Mayo, R. A. Chica, M. M. Moore
Date :  08 Jun 10  (Deposition) - 24 Nov 10  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Rfp, Mcherry, Beta Barrel, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. A. Chica, M. M. Moore, B. D. Allen, S. L. Mayo
Generation Of Longer Emission Wavelength Red Fluorescent Proteins Using Computationally Designed Libraries.
Proc. Natl. Acad. Sci. Usa V. 107 20257 2010
PubMed-ID: 21059931  |  Reference-DOI: 10.1073/PNAS.1013910107
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PAMCHERRY1 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21 GOLD (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PAMCHERRY, PAMCHERRY1
    Mutation: YES
    Organism Common: SEA ANEMONE
    Organism Scientific: DISCOSOMA SP.
    Organism Taxid: 86600

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CH61Mod. Residue{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3EYG1Mod. Residue{(2R,4Z)-2-[(1R)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-2-HYDROXY-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXOIMIDAZOLIDIN-1-YL}ACETIC ACID
4NA3Ligand/IonSODIUM ION
5NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:127 , ASN A:128 , HOH A:600BINDING SITE FOR RESIDUE NA A 232
2AC2SOFTWAREGLY A:191 , ALA A:192 , HOH A:533 , HOH A:599 , HOH A:602 , HOH A:613BINDING SITE FOR RESIDUE ACT A 233
3AC3SOFTWAREGLU A:10 , ARG A:36 , PRO A:37 , TYR A:38 , GLU A:39 , HOH A:489BINDING SITE FOR RESIDUE NA A 234
4AC4SOFTWAREGLY A:35 , ARG A:36 , THR A:41 , GLN A:42 , HOH A:631BINDING SITE FOR RESIDUE NA A 235

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NED)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:52 -Pro A:53
2Phe A:87 -Pro A:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NED)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NED)

(-) Exons   (0, 0)

(no "Exon" information available for 3NED)

(-) Sequences/Alignments

Asymmetric/Biological 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:229
 aligned with D1MPT3_DISSP | D1MPT3 from UniProtKB/TrEMBL  Length:236

    Alignment length:231
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235 
         D1MPT3_DISSP     6 EEDNMAIIKEFMRFKVHMEGSVNGHVFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFTWDILSPQFMYGSNAYVKHPADIPDYFKLSFPEGFKWERVMKFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEALSERMYPEDGALKGEVKPRVKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNRKLDITSHNEDYTIVEQYERAEGRHSTGGMDELYK 236
               SCOP domains d3neda_ A: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----GFP-3nedA01 A:5-222                                                                                                                                                                                                       --------- Pfam domains
         Sec.struct. author hhhhhhhh...eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh-.-hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeeee..hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ned A   1 EEDNMAIIKEFMRFKTHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQF-m-SKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEACSERMYPEDGALKGEMKMRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNTNTKLDITSHNEDYTIVEQYERNEGRHSTGGMDELYK 231
                                    10        20        30        40        50        60    | | 70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
                                                                                           65 | |                                                                                                                                                                  
                                                                                             67-NRQ                                                                                                                                                                
                                                                                               69
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NED)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: GFP (101)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (D1MPT3_DISSP | D1MPT3)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    GO:0006091    generation of precursor metabolites and energy    The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CH6  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EYG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NRQ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:52 - Pro A:53   [ RasMol ]  
    Phe A:87 - Pro A:88   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  3ned
    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
  D1MPT3_DISSP | D1MPT3
    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
  D1MPT3_DISSP | D1MPT3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        D1MPT3_DISSP | D1MPT3: 3kcs 3kct 3lf3 3lf4 3nez 5h87 5h89

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3NED)