Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
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)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF 5-FORMYL-TETRAHYDROFOLATE CYCLOLIGASE FROM BACILLUS ANTHRACIS (BA4489)
 
Authors :  C. Meier, L. G. Carter, G. Winter, R. J. Owens, D. I. Stuart, R. M. Esnouf, Oxford Protein Production Facility (Oppf), Structural Proteo Europe (Spine)
Date :  21 Dec 06  (Deposition) - 20 Feb 07  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ligase, Folate Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Meier, L. G. Carter, G. Winter, R. J. Owens, D. I. Stuart, R. M. Esnouf
Structure Of 5-Formyltetrahydrofolate Cyclo-Ligase From Bacillus Anthracis (Ba4489).
Acta Crystallogr. , Sect. F V. 63 168 2007
PubMed-ID: 17329806  |  Reference-DOI: 10.1107/S1744309107007221

(-) Compounds

Molecule 1 - 5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE FAMILY PROTEIN
    Chains: A, B
    EC Number: 6.3.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: GATEWAY
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PLYSS
    Expression System Vector: PDEST14
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 198094
    Strain: AMES
    Synonym: 5-FORMYL-TETRAHYDROFOLATE CYCLOLIGASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:135 , GLY A:137 , TYR A:138 , GLY A:140 , GLY A:141 , TYR A:142 , TYR A:143 , ADP A:1190 , HOH A:2200 , HOH A:2201 , HOH A:2202BINDING SITE FOR RESIDUE PO4 A1191
2AC2SOFTWARELYS A:5 , ASP A:144 , ASP A:173 , ADP A:1190 , HOH A:2157 , HOH A:2198BINDING SITE FOR RESIDUE MG A1192
3AC3SOFTWAREARG B:135 , GLY B:137 , TYR B:138 , GLY B:141 , TYR B:142 , TYR B:143 , ADP B:1189 , HOH B:2121 , HOH B:2122BINDING SITE FOR RESIDUE PO4 B1190
4AC4SOFTWAREASP B:144 , ASP B:173 , ADP B:1189 , HOH B:2092 , HOH B:2120BINDING SITE FOR RESIDUE MG B1191
5AC5SOFTWAREARG A:2 , LYS A:5 , ARG A:9 , GLY A:137 , TYR A:138 , GLY A:139 , GLY A:140 , GLY A:141 , ASP A:144 , ARG A:145 , PHE A:172 , ASP A:173 , PO4 A:1191 , MG A:1192 , HOH A:2024 , HOH A:2178 , HOH A:2197 , HOH A:2198 , HOH A:2199 , HOH A:2200BINDING SITE FOR RESIDUE ADP A1190
6AC6SOFTWAREARG B:2 , LYS B:5 , ARG B:9 , ILE B:136 , GLY B:137 , TYR B:138 , GLY B:139 , GLY B:140 , GLY B:141 , ASP B:144 , ARG B:145 , PHE B:172 , ASP B:173 , PO4 B:1190 , MG B:1191 , HOH B:2093 , HOH B:2120 , HOH B:2121BINDING SITE FOR RESIDUE ADP B1189

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JCB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JCB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JCB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JCB)

(-) Exons   (0, 0)

(no "Exon" information available for 2JCB)

(-) 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:194
 aligned with Q81LX0_BACAN | Q81LX0 from UniProtKB/TrEMBL  Length:192

    Alignment length:194
                                 1                                                                                                                                                                                            
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185    
         Q81LX0_BACAN     - -----MREEKLRLRKQIIEHMNSLSKERYTTLSEQIVFSLYEQKEWAEAKTIGITLSMENEVNTYPIIEKAWKEGKRVVVPKCNKETRTMSFRQISNFDQLETVYMNLREPIPALTEEVNADEIDLQIVPGVAYTERGERIGYGGGYYDRYLVHYKGKTLSLAYSFQMVEHIPVEPFDKNVEKIITEKGTMVKN 189
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee..........hhhhhhhhhhh..eeeeeeee....eeeeeee.hhh.eeeee..eeee.hhhhee.hhhhh.eee....ee.....ee....hhhhhhh.....eeeee.hhhh...............eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jcb A  -4 HHHHHVREEKLRLRKQIIEHMNSLSKERYTTLSEQIVFSLYEQKEWAEAKTIGITLSMENEVNTYPIIEKAWKEGKRVVVPKCNKETRTMSFRQISNFDQLETVYMNLREPIPALTEEVNADEIDLQIVPGVAYTERGERIGYGGGYYDRYLVHYKGKTLSLAYSFQMVEHIPVEPFDKNVEKIITEKGTMVKN 189
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185    


Chain B from PDB  Type:PROTEIN  Length:190
 aligned with Q81LX0_BACAN | Q81LX0 from UniProtKB/TrEMBL  Length:192

    Alignment length:190
                              1                                                                                                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
         Q81LX0_BACAN     - --MREEKLRLRKQIIEHMNSLSKERYTTLSEQIVFSLYEQKEWAEAKTIGITLSMENEVNTYPIIEKAWKEGKRVVVPKCNKETRTMSFRQISNFDQLETVYMNLREPIPALTEEVNADEIDLQIVPGVAYTERGERIGYGGGYYDRYLVHYKGKTLSLAYSFQMVEHIPVEPFDKNVEKIITEKGTMVK 188
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------5-FTHF_cyc-lig-2jcbB01 B:5-182                                                                                                                                                    ------ Pfam domains (1)
           Pfam domains (2) ------5-FTHF_cyc-lig-2jcbB02 B:5-182                                                                                                                                                    ------ Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee..........hhhhhhhhhhh..eeeeee........eeeee.hhh.eeeee..eeee.hhhh...hhhhh.eee....ee.....ee....hhhhhhh.....eeeee.hhhh...............eee....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jcb B  -1 HHVREEKLRLRKQIIEHMNSLSKERYTTLSEQIVFSLYEQKEWAEAKTIGITLSMENEVNTYPIIEKAWKEGKRVVVPKCNKETRTMSFRQISNFDQLETVYMNLREPIPALTEEVNADEIDLQIVPGVAYTERGERIGYGGGYYDRYLVHYKGKTLSLAYSFQMVEHIPVEPFDKNVEKIITEKGTMVK 188
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
   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 2JCB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JCB)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: ISOCOT_Fold (53)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q81LX0_BACAN | Q81LX0)
molecular function
    GO:0030272    5-formyltetrahydrofolate cyclo-ligase activity    Catalysis of the reaction: 5-formyltetrahydrofolate + ATP = 5,10-methenyltetrahydrofolate + ADP + H(+) + phosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.

 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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 2jcb)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  2jcb
    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
  Q81LX0_BACAN | Q81LX0
    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)
  6.3.3.2
    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
  Q81LX0_BACAN | Q81LX0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2JCB)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2JCB)