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 :  E.COLI QUED, SEMET PROTEIN, 2A RESOLUTION
 
Authors :  V. Bandarian, S. A. Roberts, Z. D. Miles
Date :  02 Dec 13  (Deposition) - 16 Jul 14  (Release) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  T-Fold, 6-Ptps, Queuosine Biosynthesis Enzyme, Sepiapterin, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. D. Miles, S. A. Roberts, R. M. Mccarty, V. Bandarian
Biochemical And Structural Studies Of 6-Carboxy-5, 6, 7, 8-Tetrahydropterin Synthase Reveal The Molecular Basis Of Catalytic Promiscuity Within The Tunnel-Fold Superfamily.
J. Biol. Chem. V. 289 23641 2014
PubMed-ID: 24990950  |  Reference-DOI: 10.1074/JBC.M114.555680

(-) Compounds

Molecule 1 - 6-CARBOXY-5,6,7,8-TETRAHYDROPTERIN SYNTHASE
    Chains: A, B, C, D, E, F
    EC Number: 4.1.2.50
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET29A
    Gene: B2765, JW2735, QUED, YGCM
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: CPH4 SYNTHASE, QUEUOSINE BIOSYNTHESIS PROTEIN QUED

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric/Biological Unit (3, 20)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2MSE13Mod. Amino AcidSELENOMETHIONINE
3ZN6Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:16 , HIS A:31 , HIS A:33 , HOH A:302BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREHIS B:16 , HIS B:31 , HIS B:33 , HOH B:303BINDING SITE FOR RESIDUE ZN B 201
3AC3SOFTWAREHIS C:16 , HIS C:31 , HIS C:33 , GLU C:110 , HOH C:302BINDING SITE FOR RESIDUE ZN C 201
4AC4SOFTWAREHIS D:16 , HIS D:31 , HIS D:33 , HOH D:302BINDING SITE FOR RESIDUE ZN D 201
5AC5SOFTWAREHIS E:16 , HIS E:31 , HIS E:33 , HOH E:302BINDING SITE FOR RESIDUE ZN E 201
6AC6SOFTWAREHIS F:16 , HIS F:31 , HIS F:33 , HOH F:302BINDING SITE FOR RESIDUE ZN F 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NTN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NTN)

(-) 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:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhh.eeeeeeeeeeee...........hhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 4ntn A   3 STTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFmVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVmVKETCTAGCIYRG 120
                                    12        22        32   |    42        52        62        72        82        92       102    |  112        
                                                            36-MSE                                                                107-MSE         


Chain B from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhh.eeeeeeeeeeee...........hhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4ntn B   3 STTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFmVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVmVKETCTAGCIYRGE 121
                                    12        22        32   |    42        52        62        72        82        92       102    |  112         
                                                            36-MSE                                                                107-MSE          


Chain C from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee........hhhhh.eeeeeeeeeeee...........hhhhhhhhhhhhhhhhh.ee.hhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 4ntn C   4 TTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFmVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVmVKETCTAGCIYRG 120
                                    13        23        33  |     43        53        63        73        83        93       103   |   113       
                                                           36-MSE                                                                107-MSE         


Chain D from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhh.eeeeeeeeeeee...........hhhhhhhhhhhhhhhhh.ee.hhh......hhhhhhhhhhhhhhhhh..eeeeeeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4ntn D   3 STTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFmVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVmVKETCTAGCIYRGE 121
                                    12        22        32   |    42        52        62        72        82        92       102    |  112         
                                                            36-MSE                                                                107-MSE          


Chain E from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee........hhhhh.eeeeeeeeeeee...........hhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4ntn E   2 mSTTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFmVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVmVKETCTAGCIYRG 120
                            |       11        21        31    |   41        51        61        71        81        91       101     | 111         
                            2-MSE                            36-MSE                                                                107-MSE         


Chain F from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee........hhhhh.eeeeeeeeeeee...........hhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhh.....eeeeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 4ntn F   4 TTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFmVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVmVKETCTAGCIYRGE 121
                                    13        23        33  |     43        53        63        73        83        93       103   |   113        
                                                           36-MSE                                                                107-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 4NTN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 4ntn)
 

(-) 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
  4ntn
    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
  QUED_ECOLI | P65870
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.1.2.50
    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
  QUED_ECOLI | P65870
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        QUED_ECOLI | P65870: 3qn0 3qn9 3qna 4ntk 4ntm

(-) Related Entries Specified in the PDB File

4ntk 4ntm