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 :  A. FULGIDUS ISCS-ISCU COMPLEX STRUCTURE
 
Authors :  E. N. Marinoni, J. S. De Oliveira, Y. Nicolet, E. C. Raulfs, P. Amara, D. J. C. Fontecilla-Camps
Date :  23 Mar 12  (Deposition) - 02 May 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transferase-Metal Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. N. Marinoni, J. S. De Oliveira, Y. Nicolet, E. C. Raulfs, P. Amara, D. R. Dean, J. C. Fontecilla-Camps
(Iscs-Iscu)2 Complex Structures Provide Insights Into Fe2S2 Biogenesis And Transfer.
Angew. Chem. Int. Ed. Engl. V. 51 5439 2012
PubMed-ID: 22511353  |  Reference-DOI: 10.1002/ANIE.201201708

(-) Compounds

Molecule 1 - PROBABLE CYSTEINE DESULFURASE 2
    Chains: A, B
    EC Number: 2.8.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C41 PRIL
    Expression System Taxid: 562
    Gene: ISCS2, AF_0564
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
 
Molecule 2 - NIFU PROTEIN (NIFU-1)
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: C41 PRIL
    Expression System Taxid: 562
    Gene: AF_0185, AF_0565
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
    Synonym: NIFU PROTEIN (NIFU-2)

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL3Ligand/IonGLYCEROL
4PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:70 , HIS A:98 , ASN A:149 , ASP A:173 , THR A:175 , HOH A:516 , GLY B:233 , SER B:234BINDING SITE FOR RESIDUE PLP A 401
2AC2SOFTWARELEU A:55 , GLY A:179 , ILE A:181 , GLU A:182 , VAL A:183 , TRP A:254 , EPE A:404BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWAREILE A:78 , GLN A:218 , PRO A:219 , VAL A:220 , ILE B:78 , PHE B:107BINDING SITE FOR RESIDUE GOL A 403
4AC4SOFTWARELYS A:54 , ASN A:57 , GLN A:109 , GLY A:112 , PHE A:113 , GLU A:114 , VAL A:115 , ALA A:251 , GOL A:402BINDING SITE FOR RESIDUE EPE A 404
5AC5SOFTWARESER A:234 , ALA B:69 , THR B:70 , HIS B:98 , ASN B:149 , ASP B:173 , THR B:175 , HOH B:504BINDING SITE FOR RESIDUE PLP B 401
6AC6SOFTWARETHR B:66 , SER B:67 , GLY B:205 , ARG B:231 , GLU B:235 , ASN B:236BINDING SITE FOR RESIDUE GOL B 402
7AC7SOFTWARECYS A:321 , CYS C:33 , ASP C:35 , CYS C:58 , HIS C:101 , CYS C:102 , FES C:202BINDING SITE FOR RESIDUE FES C 201
8AC8SOFTWARECYS A:321 , GLY C:34 , ASP C:35 , CYS C:58 , FES C:201BINDING SITE FOR RESIDUE FES C 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EB7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EB7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EB7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EB7)

(-) Exons   (0, 0)

(no "Exon" information available for 4EB7)

(-) 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:378
                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4eb7a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhh....eeeee........hhhhhhhhh...eeeee............hhhhhhhhhh...eeeee..................eeeee.hhhh.....eeeeee.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee..........eeeeee...hhhhhhhhhhhh.......hhhhh....hhhhhhhh.hhhhhhheeeee.....hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4eb7 A   2 AYFDYTSAKPVDERILEAMLPYMTESFGNPSSVHSYGFKAREAVQEAREKVAKLVNGGGGTVVFTSGATEANNLAIIGYAMRNARKGKHILVSAVEHMSVINPAKFLQKQGFEVEYIPVGKYGEVDVSFIDQKLRDDTILVSVQHANNEIGTIQPVEEISEVLAGKAALHIDATASVGQIEVDVEKIGADMLTISSNDIYGPKGVGALWIRKEAKLQPVILGGGQENGLRSGSENVPSIVGFGKAAEITAMEWREEAERLRRLRDRIIDNVLKIEESYLNGHPEKRLPNNVNVRFSYIEGESIVLSLDMAGIQASTGSACSSTLQPSHVLMACGLKHEEAHGTLLLTLGRYNTDEDVDRLLEVLPGVIERLRSMSPLY 380
                                    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 ||    332       342       352       362       372        
                                                                                                                                                                                                                                                                                                                                                           323|                                                       
                                                                                                                                                                                                                                                                                                                                                            325                                                       


Chain B from PDB  Type:PROTEIN  Length:377
                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4eb7b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhh..eeeee........hhhhhhhhh...eeeee............hhhhhhhhhh...eeeee..........hhhhhh..eeeee.hhhh.....eeeeee.............hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee..........eeeeee...hhhhhhhhhhh........hhhhh.....hhhhhhhh...hhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eb7 B   2 AYFDYTSAKPVDERILEAMLPYMTESFGNPSSVHSYGFKAREAVQEAREKVAKLVNGGGGTVVFTSGATEANNLAIIGYAMRNARKGKHILVSAVEHMSVINPAKFLQKQGFEVEYIPVGKYGEVDVSFIDQKLRDDTILVSVQHANNEIGTIQPVEEISEVLAGKAALHIDATASVGQIEVDVEKIGADMLTISSNDIYGPKGVGALWIRKEAKLQPVILGGGQENGLRSGSENVPSIVGFGKAAEITAMEWREEAERLRRLRDRIIDNVLKIEESYLNGHPEKRLPNNVNVRFSYIEGESIVLSLDMAGIQASTGSACSSKTLQPSHVLMACGLKHEEAHGTLLLTLGRYNTDEDVDRLLEVLPGVIERLRSMSP 378
                                    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       


Chain C from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains d4eb7c_ C: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh...........eeeee....eeeeeeee....eeeeeeeee.hhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eb7 C   2 YSDKVFDHFQNPRNVGKIEDADGVGTVVCGDLMTIYIKVKDNRIEDIKFQTFGCAAAIATSSMATEMAKGKTIEEALKITRDAVAEALGGLPKQKMHCSNLAADALRRAIVDYFRKNGKIDKIKELGLEKELEKM 139
                                    11        21      ||34        44        54        64        74        84        94       104       114       124       134     
                                                     28|                                                                                                           
                                                      32
   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  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EB7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EB7)

(-) Gene Ontology  (11, 19)

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
    EPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FES  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PLP  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4eb7)
 

(-) 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
  4eb7
    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
  ISCS2_ARCFU | O29689
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  ISCU1_ARCFU | P0DMG1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  ISCU2_ARCFU | P0DMG2
    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)
  2.8.1.7
    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
  ISCS2_ARCFU | O29689
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  ISCU1_ARCFU | P0DMG1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  ISCU2_ARCFU | P0DMG2
    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
        ISCS2_ARCFU | O29689: 4eb5 4hvk 4r5f
        ISCU1_ARCFU | P0DMG1: 4eb5
        ISCU2_ARCFU | P0DMG2: 4eb5

(-) Related Entries Specified in the PDB File

4eb5