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 :  QUED SOAKED WITH SEPIAPTERIN (SELENOMETHIONINE SUBSTITUTED PROTEIN)
 
Authors :  V. Bandarian, Z. D. Miles, Roberts S. A.
Date :  02 Dec 13  (Deposition) - 16 Jul 14  (Release) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
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, 28)

Asymmetric/Biological Unit (3, 28)
No.NameCountTypeFull Name
12K86Ligand/Ion(6R)-2-AMINO-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDINE-6-CARBOXYLIC ACID
2MSE16Mod. Amino AcidSELENOMETHIONINE
3ZN6Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:16 , HIS A:31 , HIS A:33 , 2K8 A:202BINDING SITE FOR RESIDUE ZN A 201
02AC2SOFTWAREHIS A:16 , HIS A:31 , HIS A:33 , THR A:84 , SER A:85 , GLU A:86 , GLU A:110 , ZN A:201 , HIS C:71 , TRP E:51 , ILE E:53 , ASP E:54 , PHE E:55BINDING SITE FOR RESIDUE 2K8 A 202
03AC3SOFTWAREHIS B:16 , HIS B:31 , HIS B:33 , GLU B:110 , 2K8 B:202BINDING SITE FOR RESIDUE ZN B 201
04AC4SOFTWARELEU A:6 , TRP A:51 , ILE A:53 , ASP A:54 , PHE A:55 , HIS B:16 , CYS B:27 , HIS B:31 , HIS B:33 , THR B:84 , SER B:85 , GLU B:86 , GLU B:110 , ZN B:201 , HOH B:332 , HIS D:71BINDING SITE FOR RESIDUE 2K8 B 202
05AC5SOFTWAREHIS C:16 , HIS C:31 , HIS C:33 , 2K8 C:202BINDING SITE FOR RESIDUE ZN C 201
06AC6SOFTWAREHIS A:71 , HIS C:16 , LEU C:18 , CYS C:27 , HIS C:31 , HIS C:33 , THR C:84 , SER C:85 , GLU C:86 , GLU C:110 , ZN C:201 , LEU D:6 , TRP D:51 , ILE D:53 , ASP D:54 , PHE D:55BINDING SITE FOR RESIDUE 2K8 C 202
07AC7SOFTWAREHIS D:16 , HIS D:31 , HIS D:33 , GLU D:110 , 2K8 D:202BINDING SITE FOR RESIDUE ZN D 201
08AC8SOFTWAREHIS B:71 , HIS D:16 , CYS D:27 , HIS D:31 , THR D:84 , SER D:85 , GLU D:86 , GLU D:110 , ZN D:201 , LEU F:6 , TRP F:51 , ILE F:53 , ASP F:54 , PHE F:55BINDING SITE FOR RESIDUE 2K8 D 202
09AC9SOFTWAREHIS E:16 , HIS E:31 , HIS E:33 , GLU E:110 , 2K8 E:202BINDING SITE FOR RESIDUE ZN E 201
10BC1SOFTWARELEU B:6 , TRP B:51 , ILE B:53 , ASP B:54 , PHE B:55 , HIS E:16 , CYS E:27 , HIS E:31 , HIS E:33 , THR E:84 , SER E:85 , GLU E:86 , GLU E:110 , ZN E:201 , HIS F:71BINDING SITE FOR RESIDUE 2K8 E 202
11BC2SOFTWAREHIS F:16 , HIS F:31 , HIS F:33 , GLU F:110 , 2K8 F:202BINDING SITE FOR RESIDUE ZN F 201
12BC3SOFTWARELEU C:6 , TRP C:51 , ILE C:53 , ASP C:54 , PHE C:55 , HIS E:71 , HIS F:16 , CYS F:27 , HIS F:31 , HIS F:33 , THR F:84 , SER F:85 , GLU F:86 , GLU F:110 , ZN F:201BINDING SITE FOR RESIDUE 2K8 F 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NTM)

(-) 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:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeeeeee........eeeeeeeeeeee...........hhhhhhhhhhhhhhhhh.ee.hhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4ntm A   1 mmSTTLFKDFTFEAAHRLPHCGRLHGHSFmVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVmVKETCTAGCIYRG 120
                            ||      10        20|       36        46        56        66        76        86        96       106|      116    
                            ||                20|       36-MSE                                                                107-MSE         
                            1-MSE              27                                                                                             
                             2-MSE                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               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
                 4ntm B   2 mSTTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFmVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVmVKETCTAGCIYRGE 121
                            |       11        21        31    |   41        51        61        71        81        91       101     | 111       121
                            2-MSE                            36-MSE                                                                107-MSE          


Chain C from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee............eeeeeeeeeeee...........hhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4ntm C   3 STTLFKDFTFEAAHRLPHVPEGCGRLHGHSFmVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVmVKETCTAGCIYR 119
                                    12        22 ||     34 |      44        54        64        74        84        94       104  |    114     
                                                24|       36-MSE                                                                107-MSE        
                                                 27                                                                                            


Chain D from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               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
                 4ntm D   2 mSTTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFmVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVmVKETCTAGCIYRGE 121
                            |       11        21        31    |   41        51        61        71        81        91       101     | 111       121
                            2-MSE                            36-MSE                                                                107-MSE          


Chain E 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
                 4ntm E   3 STTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFmVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVmVKETCTAGCIYRG 120
                                    12        22        32   |    42        52        62        72        82        92       102    |  112        
                                                            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.ee.hhh......hhhhhhhhhhhhhh.....eeeeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 4ntm 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 4NTM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    2K8  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ntm)
 

(-) 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
  4ntm
    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 4ntn

(-) Related Entries Specified in the PDB File

4ntk 4ntn