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(-) Description

Title :  FIRST CONDENSATION DOMAIN OF THE CALCIUM-DEPENDENT ANTIBIOTIC SYNTHETASE IN COMPLEX WITH SUBSTRATE ANALOGUE 2A
 
Authors :  K. Bloudoff, D. A. Alonzo, T. M. Schmeing
Date :  18 Sep 15  (Deposition) - 30 Mar 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nonribosomal Peptide Synthetase, Condensation Domain, Chemical Probe, Substrate Analogue, Phosphopantetheine Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Bloudoff, D. A. Alonzo, T. M. Schmeing
Chemical Probes Allow Structural Insight Into The Condensation Reaction Of Nonribosomal Peptide Synthetases.
Cell Chem Biol V. 23 331 2016
PubMed-ID: 26991102  |  Reference-DOI: 10.1016/J.CHEMBIOL.2016.02.012

(-) Compounds

Molecule 1 - CDA PEPTIDE SYNTHETASE I
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES1-449
    Gene: SCO3230
    Mutation: YES
    Organism Scientific: STREPTOMYCES COELICOLOR (STRAIN ATCC BAA-471 / A3(2) / M145)
    Organism Taxid: 100226
    Strain: ATCC BAA-471 / A3(2) / M145

 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, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2SO41Ligand/IonSULFATE ION
3UM22Ligand/Ion(2S)-2-AMINO-N-BUTYL-PROPANAMIDE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO41Ligand/IonSULFATE ION
3UM21Ligand/Ion(2S)-2-AMINO-N-BUTYL-PROPANAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO4-1Ligand/IonSULFATE ION
3UM21Ligand/Ion(2S)-2-AMINO-N-BUTYL-PROPANAMIDE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:280 , ALA A:299 , ASN A:300 , HOH A:629 , HOH A:630 , HOH A:635 , HOH A:788 , HOH A:927 , HOH A:1024binding site for residue SO4 A 501
2AC2SOFTWAREHIS A:157 , ASP A:161 , GLY A:162 , SER A:309 , UM2 A:503 , HOH A:1144binding site for residue CL A 502
3AC3SOFTWARECYS A:17 , HIS A:157 , ARG A:311 , GLU A:347 , SER A:386 , CL A:502 , HOH A:677 , HOH A:851 , HOH A:928 , HOH A:967binding site for residue UM2 A 503
4AC4SOFTWAREHIS B:157 , ASP B:161 , GLY B:162 , SER B:309 , UM2 B:502 , HOH B:1011binding site for residue CL B 501
5AC5SOFTWARESER B:13 , ALA B:14 , GLN B:15 , HIS B:16 , VAL B:18 , TRP B:19 , LEU B:20 , ALA B:21 , HIS B:157 , ARG B:311 , GLU B:347 , SER B:386 , CL B:501 , HOH B:682 , HOH B:746 , HOH B:801 , HOH B:854binding site for Di-peptide UM2 B 502 and CYS B 17

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DU9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:234 -Gly B:235

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DU9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DU9)

(-) Exons   (0, 0)

(no "Exon" information available for 5DU9)

(-) 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:427
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh.......eeeeeeee....hhhhhhhhhhhhhhhhhhh.eeeee.....eeeee............eeeee.....hhhhhhhhhhhhhhh..........eeeeeeeee..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeeehhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeeee....hhhhhh......eeeeeeee.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.......eeee......ee....eeeeeeee......eeeeeeee...eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh...hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5du9 A   6 SVRHGLTSAQHCVWLAQQLDPRGAHYRTGSCLEIDGPLDHAVLSRALRLTVAGTETLCSRFLTDEEGRPYRAYCPPAPVPYTPVLLRHIDLSGHEDPEGEAQRWMDRDRATPLPLDRPGLSSHALFTLGGGRHLYYLGVHHIVIDGTSMALFYERLAEVYRALRDGRAVPAAAFGDTDRMVAGEEAYRASARYERDRAYWTGLFTDRPEPVSLRALAPTVRSLGLPPERTEVLGRAAEATGAHWARVVIAGVAAFLHRTTGARDVVVSVPVTGRYGANARITPGMVSNRLPLRLAVRPGESFARVVETVSEAMSGLLAHSRFRGEDLDRELGGAGVSGPTVNVMPYIRPVDFGGPVGLMRSISSGPTTDLNIVLTGTPESGLRVDFEGNPQVYGGQDLTVLQERFVRFLAELAADPAATVDEVALLT 449
                                    15        25        35        45        55        65        75       |96       106       116       126       136       146       156       166       176       186       196       206       216       226  ||   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       
                                                                                                        83|                                                                                                                                   229|                                                                                                                                                                                                                     
                                                                                                         95                                                                                                                                    236                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh......eeeeeeee....hhhhhhhhhhhhhhhhhhh.eeeee.....eeeee............eeeee.....hhhhhhhhhhhhhhh..........eeeeeeeee..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................eeeeeeehhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeeee....hhhhhh......eeeeeeee.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.......eeee...........eeeeeee......eeeeeeee...eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh...hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5du9 B   6 SVRHGLTSAQHCVWLAQQLDPRGAHYRTGSCLEIDGPLDHAVLSRALRLTVAGTETLCSRFLTDEEGRPYRAYCPPAPVPYTPVLLRHIDLSGHEDPEGEAQRWMDRDRATPLPLDRPGLSSHALFTLGGGRHLYYLGVHHIVIDGTSMALFYERLAEVYRALRDGRAVPAAAFGDTDRMVAGEEAYRASARYERDRAYWTGLFTDRPEPVSLTGRGGGRALAPTVRSLGLPPERTEVLGRAAEATGAHWARVVIAGVAAFLHRTTGARDVVVSVPVTGRYGANARITPGMVSNRLPLRLAVRPGESFARVVETVSEAMSGLLAHSRFRGEDLDRELGGAGVSGPTVNVMPYIRPVDFGVGLMRSISSGPTTDLNIVLTGTPESGLRVDFEGNPQVYGGQDLTVLQERFVRFLAELAADPAATVDEVAL 447
                                    15        25        35        45        55        65        75       |96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       378       388       398       408       418       428       438         
                                                                                                        83|                                                                                                                                                                                                                                                                                     375|                                                                     
                                                                                                         95                                                                                                                                                                                                                                                                                      378
   Legend:   → Mismatch (orange background)
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  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 5DU9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DU9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DU9)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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        Q9Z4X6_STRCO | Q9Z4X6: 4jn3 4jn5 5dua

(-) Related Entries Specified in the PDB File

5dua