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(-) Description

Title :  CA. KORARCHAEUM CRYPTOFILUM DINUCLEOTIDE FORMING ACETYL-COENZYME A SYNTHETASE 1 IN COMPLEX WITH ADP AND ADDITIONAL ADP BOUND TO PHOSPHATE BINDING SITE
 
Authors :  R. H. -J. Weisse, A. J. Scheidig
Date :  16 Feb 15  (Deposition) - 27 Jan 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dinucleotide Forming Acetyl-Coa Synthetase, Complex, Acd, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. H. Weie, A. Faust, M. Schmidt, P. Schonheit, A. J. Scheidig
Structure Of Ndp-Forming Acetyl-Coa Synthetase Acd1 Reveals A Large Rearrangement For Phosphoryl Transfer.
Proc. Natl. Acad. Sci. Usa V. 113 E519 2016
PubMed-ID: 26787904  |  Reference-DOI: 10.1073/PNAS.1518614113

(-) Compounds

Molecule 1 - ALPHA SUBUNIT OF ACETYL-COA SYNTHETASE (NDP FORMING)
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET17B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: KCR_0198
    Organism Scientific: KORARCHAEUM CRYPTOFILUM (STRAIN OPF8)
    Organism Taxid: 374847
    Synonym: ACYL-COA SYNTHETASE (NDP FORMING)
 
Molecule 2 - BETA SUBUNIT OF ACETYL-COA SYNTHETASE (NDP FORMING)
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET17B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: KCR_0115
    Organism Scientific: KORARCHAEUM CRYPTOFILUM (STRAIN OPF8)
    Organism Taxid: 374847

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG4Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:104 , ASN A:129 , GLN A:159 , SER A:160 , GLY A:161 , ALA A:162 , ASN A:186 , ALA A:251 , HIS A:254 , HOH A:746 , HOH A:747 , HOH A:835 , HOH A:868 , HOH A:877 , HOH A:902 , HOH A:904 , GLY C:308 , GLY C:309 , VAL C:312 , MG C:601 , HOH C:727 , HOH C:728 , HOH C:748binding site for residue ADP A 600
2AC2SOFTWAREASP A:351 , HOH A:911 , ADP C:602binding site for residue MG A 601
3AC3SOFTWAREVAL B:58 , LYS B:60 , VAL B:67 , LYS B:69 , SER B:70 , GLN B:111 , GLU B:112 , ALA B:114 , PRO B:212 , VAL B:223 , ASP B:224 , ARG B:226 , MG B:301 , HOH B:444binding site for residue ADP B 300
4AC4SOFTWAREASP B:224 , ADP B:300binding site for residue MG B 301
5AC5SOFTWAREADP A:600 , HOH A:746 , ASP C:351 , HOH C:727 , HOH C:728 , HOH C:729 , HOH C:730binding site for residue MG C 601
6AC6SOFTWAREGLY A:308 , GLY A:309 , VAL A:312 , MG A:601 , ASN C:129 , GLN C:159 , SER C:160 , GLY C:161 , ALA C:162 , ALA C:251 , HIS C:254 , HOH C:815 , HOH C:829binding site for residue ADP C 602
7AC7SOFTWARELYS D:60 , LYS D:69 , SER D:70 , GLN D:111 , GLU D:112 , PHE D:113 , ALA D:114 , PRO D:212 , VAL D:223 , ASP D:224 , ARG D:226 , MG D:301 , HOH D:439binding site for residue ADP D 300
8AC8SOFTWAREASN D:211 , ASP D:224 , ADP D:300binding site for residue MG D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y8V)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Gly A:127 -Pro A:128
2Asn A:348 -Pro A:349
3Phe B:55 -Pro B:56
4Ala B:154 -Pro B:155
5Asn B:211 -Pro B:212
6Gly C:127 -Pro C:128
7Asn C:348 -Pro C:349
8Phe D:55 -Pro D:56
9Ala D:154 -Pro D:155
10Asn D:211 -Pro D:212

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y8V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y8V)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y8V)

(-) 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:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..eeeee.......hhhhhhhhhhhhhh...eeeee.....ee..ee...hhhhh.....eeee..hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhhh..eee.....eeee.hhheeee.......eeeeeeee.hhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh....hhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhh.......hhhhhhhhhh...........ee.....hhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y8v A   1 MNDLERLFNPSAIAVVGASKDPSKIGSQILRNLLSYGFKGKVYPINPTADELMGLKCYPKVSDVPDKVDVAVISVPSDKVLGVIDDCGKAGVKFAVVITSGFKEVGNEELEEELVRRAHSYGMRVLGPNIFGYLYAPARLNATFGPKDVLSGNVAFISQSGALGIALMGYTVVENIGISSIVSVGNKADLDDVDLLDFFDKDPNTGVIMIYLEGIAPGRGRMFIDVASRVSLRKPIIVIKAGRTEVGARAAASHTGSIAGSVAIYESAFKQSGILMAKSVEDAFDWTKALSWNPIPEGERLIVLTNGGGAGVQSTDTFADNGIYLSKPPESLIQEIKKFVPPFASFANPIDITGMAPDDWYYMGTLAALKNPDVDALTVLYCQTAVTTPIGVAKGIVDAIKEAGNSKPVTVGMVGGPEVAEAVSFLNKQRIAAYPTPERASSAMSALYAYARARSYVMKSLAVR 464
                                    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       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460    


Chain B from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhhhhhhhhh.......eeee.hhhhhhhhhhhhh..eeeeee......hhhhh.eeeee.hhhhhhhhhhhhhhhhhhhh......eeeeee.....eeeeeeeeee...eeeeeeee.hhhhhh...eeeee...hhhhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y8v B   2 SSRDLLLKAKENGRKSLLEHEAKYFISSYGIPVTNIRLAKSEEEAVNFSREIGFPVVLKIVSPQVVHKSDVGGVKVNLRSEEEVRKAYREIIENVKRNVPNAEIEGILVQEFAPPGVELIIGLLRDPQFGPTVMFGLGGVFVELFRDVSFRVAPLSEQDAESMIKEVKAYKLLTGFRGMEPVDIEAIKDALIRAGRIGVENEEIAEMDLNPVIAYPKGIKVVDARIILR 230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221         


Chain C from PDB  Type:PROTEIN  Length:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..eeeee.......hhhhhhhhhhhhhh...eeeee.....ee..ee...hhhhh.....eeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhh..eee.....eeee.hhheeee.......eeeeeeee..hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh....hhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhhh.......hhhhhhhhhh...........ee.....hhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y8v C   1 MNDLERLFNPSAIAVVGASKDPSKIGSQILRNLLSYGFKGKVYPINPTADELMGLKCYPKVSDVPDKVDVAVISVPSDKVLGVIDDCGKAGVKFAVVITSGFKEVGNEELEEELVRRAHSYGMRVLGPNIFGYLYAPARLNATFGPKDVLSGNVAFISQSGALGIALMGYTVVENIGISSIVSVGNKADLDDVDLLDFFDKDPNTGVIMIYLEGIAPGRGRMFIDVASRVSLRKPIIVIKAGRTEVGARAAASHTGSIAGSVAIYESAFKQSGILMAKSVEDAFDWTKALSWNPIPEGERLIVLTNGGGAGVQSTDTFADNGIYLSKPPESLIQEIKKFVPPFASFANPIDITGMAPDDWYYMGTLAALKNPDVDALTVLYCQTAVTTPIGVAKGIVDAIKEAGNSKPVTVGMVGGPEVAEAVSFLNKQRIAAYPTPERASSAMSALYAYARARSYVMKSLAVR 464
                                    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       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460    


Chain D from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhhhhhhhhh........eee.hhhhhhhhhhhhh..eeeeee......hhhhh.eeeee.hhhhhhhhhhhhhhhhhhhh......eeeeee.....eeeeeeeeee...eeeeeeee.hhhhhh...eeeee...hhhhhhhhhhhh.hhhhhh........hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eee..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y8v D   2 SSRDLLLKAKENGRKSLLEHEAKYFISSYGIPVTNIRLAKSEEEAVNFSREIGFPVVLKIVSPQVVHKSDVGGVKVNLRSEEEVRKAYREIIENVKRNVPNAEIEGILVQEFAPPGVELIIGLLRDPQFGPTVMFGLGGVFVELFRDVSFRVAPLSEQDAESMIKEVKAYKLLTGFRGMEPVDIEAIKDALIRAGRIGVENEEIAEMDLNPVIAYPKGIKVVDARIILR 230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4Y8V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y8V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y8V)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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    Gly A:127 - Pro A:128   [ RasMol ]  
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  4y8v
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 Related Entries

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

UniProtKB/TrEMBL
        B1L3C9_KORCO | B1L3C9: 4xyl 4xym 4xz3 4yaj 4yak 4yb8 4ybz 5hbr
        B1L7P8_KORCO | B1L7P8: 4xyl 4xym 4xz3 4yaj 4yak 4yb8 4ybz 5hbr

(-) Related Entries Specified in the PDB File

4xym 4xz3 4y8v 4yaj 4yak 4yb8 4ybz 5hbr