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 :  CRYSTAL STRUCTURE OF AN ANCESTOR OF ALL FAVIINA PROTEINS
 
Authors :  H. Kim, R. M. Wachter
Date :  27 Feb 12  (Deposition) - 27 Feb 13  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta Barrel, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Kim, T. Zou, C. Modi, K. Dorner, T. J. Grunkemeyer, L. Chen, R. Fromme M. V. Matz, S. B. Ozkan, R. M. Wachter
A Hinge Migration Mechanism Unlocks The Evolution Of Green-To-Red Photoconversion In Gfp-Like Proteins.
Structure V. 23 34 2015
PubMed-ID: 25565105  |  Reference-DOI: 10.1016/J.STR.2014.11.011

(-) Compounds

Molecule 1 - GREEN FLUORESCENT PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: ARTIFICIAL
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CRQ4Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETICACID
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:149 , ASP A:150 , HOH A:598BINDING SITE FOR RESIDUE MG A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DXI)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ala A:48 -Pro A:49
2Phe A:83 -Pro A:84
3Ala B:48 -Pro B:49
4Phe B:83 -Pro B:84
5Ala C:48 -Pro C:49
6Phe C:83 -Pro C:84
7Ala D:48 -Pro D:49
8Phe D:83 -Pro D:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DXI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DXI)

(-) Exons   (0, 0)

(no "Exon" information available for 4DXI)

(-) 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:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhh.................hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.hhh.eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dxi A   2 SVIKSDMKIKLRMEGTVNGHKFVIEGEGEGKPYEGTQTMNLKVKEGAPLPFAYDILTTAFqNRVFTKYPKDIPDYFKQSFPEGYSWERSMTFEDGGICTATSDITLEGDCFFYEIRFDGVNFPPNGPVMQKKTLKWEPSTEKMYVRDGVLMGDVNMALLLEGGGHYRCDFKTTYKAKKGVQLPDYHFVDHRIEILSHDKDYNNVKLYEHAVARSSLLP 221
                                    11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213        
                                                                                       62-CRQ                                                                                                                                                         
                                                                                        65                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeee.....eeeeeeeeee......hhhhhhhhh.............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dxi B   2 SVIKSDMKIKLRMEGTVNGHKFVIEGEGEGKPYEGTQTMNLKVKEGAPLPFAYDILTTAFqNRVFTKYPKDIPDYFKQSFPEGYSWERSMTFEDGGICTATSDITLEGDCFFYEIRFDGVNFPPNGPVMQKKTLKWEPSTEKMYVRDGVLMGDVNMALLLEGGGHYRCDFKTTYKAKKGVQLPDYHFVDHRIEILSHDKDYNNVKLYEHAVARSSLLPMTAA 225
                                    11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  
                                                                                       62-CRQ                                                                                                                                                             
                                                                                        65                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dxi C   2 SVIKSDMKIKLRMEGTVNGHKFVIEGEGEGKPYEGTQTMNLKVKEGAPLPFAYDILTTAFqNRVFTKYPKDIPDYFKQSFPEGYSWERSMTFEDGGICTATSDITLEGDCFFYEIRFDGVNFPPNGPVMQKKTLKWEPSTEKMYVRDGVLMGDVNMALLLEGGGHYRCDFKTTYKAKKGVQLPDYHFVDHRIEILSHDKDYNNVKLYEHAVARSSLLPMT 223
                                    11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
                                                                                       62-CRQ                                                                                                                                                           
                                                                                        65                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh...............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.hhh.eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dxi D   2 SVIKSDMKIKLRMEGTVNGHKFVIEGEGEGKPYEGTQTMNLKVKEGAPLPFAYDILTTAFqNRVFTKYPKDIPDYFKQSFPEGYSWERSMTFEDGGICTATSDITLEGDCFFYEIRFDGVNFPPNGPVMQKKTLKWEPSTEKMYVRDGVLMGDVNMALLLEGGGHYRCDFKTTYKAKKGVQLPDYHFVDHRIEILSHDKDYNNVKLYEHAVARSSLLP 221
                                    11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213        
                                                                                       62-CRQ                                                                                                                                                         
                                                                                        65
   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 4DXI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DXI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DXI)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4DXI)

 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
    CRQ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:48 - Pro A:49   [ RasMol ]  
    Ala B:48 - Pro B:49   [ RasMol ]  
    Ala C:48 - Pro C:49   [ RasMol ]  
    Ala D:48 - Pro D:49   [ RasMol ]  
    Phe A:83 - Pro A:84   [ RasMol ]  
    Phe B:83 - Pro B:84   [ RasMol ]  
    Phe C:83 - Pro C:84   [ RasMol ]  
    Phe D:83 - Pro D:84   [ 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
  4dxi
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4DXI)

(-) Related Entries Specified in the PDB File

4dxm 4dxn 4dxo 4dxp 4dxq