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

(-) Description

Title :  2.0 ANGSTROM CRYSTAL STRUCTURE OF GLUTAMATE--CYSTEINE LIGASE (GSHA) FTOM FRANCISELLA TULARENSIS IN COMPLEX WITH AMP
 
Authors :  G. Minasov, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papa W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date :  16 Jul 10  (Deposition) - 28 Jul 10  (Release) - 28 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha And Beta Proteins, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, A. Halavaty, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papazisi, W. F. Anderson
2. 0 Angstrom Crystal Structure Of Glutamate--Cysteine Ligas (Gsha) Ftom Francisella Tularensis In Complex With Amp.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUTAMATE--CYSTEINE LIGASE
    Chains: A
    EC Number: 6.3.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMSCG7
    Expression System Strain: BL21-DE3 (MAGIC)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: FTT_0367C, GSHA
    Organism Scientific: FRANCISELLA TULARENSIS SUBSP. TULARENSIS
    Organism Taxid: 119856
    Strain: SCHU S4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2SO411Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:10 , GLY A:12 , ILE A:13 , ILE A:56 , THR A:57 , LYS A:58 , PRO A:59 , ASN A:139 , SER A:141 , ILE A:289 , GLU A:306 , TYR A:307 , HOH A:741 , HOH A:782 , HOH A:795 , HOH A:805 , HOH A:831BINDING SITE FOR RESIDUE AMP A 502
02AC2SOFTWARESER A:62 , ILE A:63 , ASP A:64 , LYS A:325 , GLU A:404 , HOH A:636 , HOH A:833 , HOH A:835BINDING SITE FOR RESIDUE SO4 A 503
03AC3SOFTWARETHR A:250 , LYS A:255 , SER A:379 , GLU A:380 , HOH A:669BINDING SITE FOR RESIDUE SO4 A 504
04AC4SOFTWARELYS A:115 , ARG A:119 , HOH A:702 , HOH A:785BINDING SITE FOR RESIDUE SO4 A 505
05AC5SOFTWAREHIS A:137 , ASN A:278 , ARG A:285 , ARG A:311 , HOH A:532 , HOH A:655 , HOH A:725 , HOH A:792 , HOH A:809BINDING SITE FOR RESIDUE SO4 A 506
06AC6SOFTWAREGLU A:16 , ILE A:133 , SER A:134 , GLY A:135 , HIS A:137 , ARG A:215 , HOH A:541 , HOH A:576 , HOH A:810BINDING SITE FOR RESIDUE SO4 A 507
07AC7SOFTWAREASN A:278 , LYS A:287 , PRO A:296 , HOH A:613 , HOH A:690 , HOH A:798BINDING SITE FOR RESIDUE SO4 A 508
08AC8SOFTWARETHR A:21 , CYS A:23 , ASN A:25BINDING SITE FOR RESIDUE SO4 A 509
09AC9SOFTWAREHIS A:60 , ASP A:61 , LYS A:65BINDING SITE FOR RESIDUE SO4 A 510
10BC1SOFTWAREHIS A:82 , SER A:83BINDING SITE FOR RESIDUE SO4 A 511
11BC2SOFTWAREARG A:113 , GLN A:265 , ARG A:266 , HOH A:580 , HOH A:819BINDING SITE FOR RESIDUE SO4 A 512
12BC3SOFTWAREPRO A:402 , LYS A:403 , HOH A:730BINDING SITE FOR RESIDUE SO4 A 513

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:298 -A:500

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NZT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NZT)

(-) 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:498
 aligned with Q5NHS8_FRATT | Q5NHS8 from UniProtKB/TrEMBL  Length:501

    Alignment length:500
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501
         Q5NHS8_FRATT     2 YDFKKINNLRGIERETLRVTDCGNLATSNHPDGLGHKLTNNSITVDFSENLLELITKPHDSIDKAIGELYQLSAFTLDNMHSDEIILNTSMPLSANDNDIQEADFGSSNSGRMKRVYRKGLSARYGKIMQIISGIHYNFSFDKDLISNIATNKQVSISDIYFDVLNNYFEFMWLLPYLFGASPICAKTSVKNKPDYLSVLDDKFYVGEYATSLRMSDLGYTSPAQKDLAISYDNVKAYVKDLIQATDDTFADYKRIGLYNSQGQRIQLNDGILQIENEYYSAIRPKQIAKRGERPACALYNRGVEYVEVRVLDVDPFEPVGISKDTALFVEVMLMTCLDKDAKKYHKDIIKQAKQNLTAVAIQGRNPQLKLKKLDDDSEILLKDYALELFDEIEAVAKKMPKEYLDAVEIQKRKVLDISQTPSAKIIELARQHGYKKFILDISRRVSQQFRSYELPAAIVAKLKDQAGQSVAAEKELVANDKISLDEYINRYYKSSKGCC 501
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Glu_cys_ligase-3nztA01 A:4-362                                                                                                                                                                                                                                                                                                                                         ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeeee..........hhhhh.......eee.....eeeee.....hhhhhhhhhhhhhhhhhhhh...eee.........hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhh.......ee....eee.....hhhhh...--hhhhhh......hhhhhhhhhhhhhhh.hhhhhhhh.................hhhhh...eeee.......hhhhhhhhhh..eeee.............hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....eee......eeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nzt A   2 YDFKKINNLRGIERETLRVTDCGNLATSNHPDGLGHKLTNNSITVDFSENLLELITKPHDSIDKAIGELYQLSAFTLDNMHSDEIILNTSMPLSANDNDIQEADFGSSNSGRMKRVYRKGLSARYGKIMQIISGIHYNFSFDKDLISNIATNKQVSISDIYFDVLNNYFEFMWLLPYLFGASPICAKTSVKNKPDYLSVLDDKFYVGEYATSLRMSDLG--SPAQKDLAISYDNVKAYVKDLIQATDDTFADYKRIGLYNSQGQRIQLNDGILQIENEYYSAIRPKQIAKRGERPACALYNRGVEYVEVRVLDVDPFEPVGISKDTALFVEVMLMTCLDKDAKKYHKDIIKQAKQNLTAVAIQGRNPQLKLKKLDDDSEILLKDYALELFDEIEAVAKKMPKEYLDAVEIQKRKVLDISQTPSAKIIELARQHGYKKFILDISRRVSQQFRSYELPAAIVAKLKDQAGQSVAAEKELVANDKISLDEYINRYYKSSKGCC 501
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        |- |     231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501
                                                                                                                                                                                                                                                    220  |                                                                                                                                                                                                                                                                                      
                                                                                                                                                                                                                                                       223
   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 3NZT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: GCS (23)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5NHS8_FRATT | Q5NHS8)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004357    glutamate-cysteine ligase activity    Catalysis of the reaction: L-cysteine + L-glutamate + ATP = L-gamma-glutamyl-L-cysteine + ADP + 2 H(+) + phosphate.
    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: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:0006750    glutathione biosynthetic process    The chemical reactions and pathways resulting in the formation of glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins.

 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
    AMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 3nzt)
 

(-) 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
  3nzt
    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
  Q5NHS8_FRATT | Q5NHS8
    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)
  6.3.2.2
    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
  Q5NHS8_FRATT | Q5NHS8
    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 3NZT)

(-) Related Entries Specified in the PDB File

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