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(-) Description

Title :  ISPH IN COMPLEX WITH (E)-4-AMINO-3-METHYLBUT-2-ENYL DIPHOSPHATE
 
Authors :  I. Span, W. Eisenreich, J. Jauch, A. Bacher, M. Groll
Date :  17 Sep 12  (Deposition) - 23 Jan 13  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Iron-Sulfur Protein, Reductase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Span, K. Wang, W. Wang, J. Jauch, W. Eisenreich, A. Bacher, E. Oldfield, M. Groll
Structures Of Fluoro, Amino, And Thiol Inhibitors Bound To The [Fe(4) S(4) ] Protein Isph.
Angew. Chem. Int. Ed. Engl. V. 52 2118 2013
PubMed-ID: 23307751  |  Reference-DOI: 10.1002/ANIE.201208469

(-) Compounds

Molecule 1 - 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE
    Chains: A, B
    EC Number: 1.17.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B0029, ISPH, JW0027, LYTB, YAAE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: ISPH

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
110E2Ligand/Ion(2E)-4-AMINO-3-METHYLBUT-2-EN-1-YL TRIHYDROGENDIPHOSPHATE
2SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
110E1Ligand/Ion(2E)-4-AMINO-3-METHYLBUT-2-EN-1-YL TRIHYDROGENDIPHOSPHATE
2SF41Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
110E1Ligand/Ion(2E)-4-AMINO-3-METHYLBUT-2-EN-1-YL TRIHYDROGENDIPHOSPHATE
2SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:12 , GLY A:14 , CYS A:96 , THR A:167 , CYS A:197 , 10E A:402BINDING SITE FOR RESIDUE SF4 A 401
2AC2SOFTWAREVAL A:15 , VAL A:40 , HIS A:41 , ALA A:73 , HIS A:74 , VAL A:99 , HIS A:124 , GLU A:126 , THR A:167 , THR A:168 , ASN A:224 , SER A:225 , SER A:226 , ASN A:227 , SER A:269 , SF4 A:401 , HOH A:743BINDING SITE FOR RESIDUE 10E A 402
3AC3SOFTWARECYS B:12 , GLY B:14 , CYS B:96 , THR B:167 , CYS B:197 , 10E B:402BINDING SITE FOR RESIDUE SF4 B 401
4AC4SOFTWAREVAL B:15 , VAL B:40 , HIS B:41 , ALA B:73 , HIS B:74 , VAL B:99 , HIS B:124 , GLU B:126 , THR B:167 , THR B:168 , ASN B:224 , SER B:225 , SER B:226 , ASN B:227 , SER B:269 , SF4 B:401 , HOH B:760BINDING SITE FOR RESIDUE 10E B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H4D)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:7 -Pro A:8
2Ala A:31 -Pro A:32
3Asn B:7 -Pro B:8
4Ala B:31 -Pro B:32

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H4D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H4D)

(-) Exons   (0, 0)

(no "Exon" information available for 4H4D)

(-) 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:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh.eeee.hhhhh....eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhh........eeee.hhhhhhhh.......eeeee....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh....eee.......eee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h4d A   1 MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFEVPKELR 309
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300         


Chain B from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh.eeee.hhhhh....eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhh........eeee.hhhhhhhh.......eeeee....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh....eee.......eee..hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h4d B   1 MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVARLQQLGGGEAIPLEGREENIVFEVPKELRV 310
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
   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 4H4D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H4D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H4D)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  4h4d
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  ISPH_ECOLI | P62623
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  1.17.1.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        ISPH_ECOLI | P62623: 3f7t 3ke8 3ke9 3kef 3kel 3kem 3szl 3szo 3szu 3t0f 3t0g 3urk 3utc 3utd 3uv3 3uv6 3uv7 3uwm 3zgl 3zgn 4eb3 4h4c 4h4e

(-) Related Entries Specified in the PDB File

3dnf STRUCTURE OF (E)-4-HYDROXY-3-METHYL-BUT-2-ENYL DIPHOSPHATE REDUCTASE, THE TERMINAL ENZYME OF THE NON-MEVALONATE PATHWAY
3f7t STRUCTURE OF ACTIVE ISPH SHOWS A NOVEL FOLD WITH A [3FE-4S] CLUSTER IN THE CATALYTIC CENTER
3ke8 CRYSTAL STRUCTURE OF ISPH:HMBPP-COMPLEX
4h4c
4h4e