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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI LPXC/L-161,240 COMPLEX
 
Authors :  C. -J. Lee, P. Zhou
Date :  16 Jan 13  (Deposition) - 30 Oct 13  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.13
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lpxc, Deacetylation, Antibiotic, Acyl Udp-Glcnac, Hydroxamate, L-161, 240, Baab Sandwich, Lipid A Biosynthesis, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Lee, X. Liang, R. Gopalaswamy, J. Najeeb, E. D. Ark, E. J. Toone, P. Zhou
Structural Basis Of The Promiscuous Inhibitor Susceptibilit Of Escherichia Coli Lpxc.
Acs Chem. Biol. V. 9 237 2014
PubMed-ID: 24117400  |  Reference-DOI: 10.1021/CB400067G

(-) Compounds

Molecule 1 - UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE DEACETYLASE
    Chains: A, B
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LPXC, ECOK1_0097
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 714962
    Strain: IHE3034 / EXPEC
    Synonym: UDP-3-O-ACYL-GLCNAC DEACETYLASE

 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  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1IPA2Ligand/IonISOPROPYL ALCOHOL
2LTF2Ligand/Ion(4R)-2-(3,4-DIMETHOXY-5-PROPYLPHENYL)-N-HYDROXY-4,5-DIHYDRO-1,3-OXAZOLE-4-CARBOXAMIDE
3NA1Ligand/IonSODIUM ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1IPA1Ligand/IonISOPROPYL ALCOHOL
2LTF1Ligand/Ion(4R)-2-(3,4-DIMETHOXY-5-PROPYLPHENYL)-N-HYDROXY-4,5-DIHYDRO-1,3-OXAZOLE-4-CARBOXAMIDE
3NA-1Ligand/IonSODIUM ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1IPA1Ligand/IonISOPROPYL ALCOHOL
2LTF1Ligand/Ion(4R)-2-(3,4-DIMETHOXY-5-PROPYLPHENYL)-N-HYDROXY-4,5-DIHYDRO-1,3-OXAZOLE-4-CARBOXAMIDE
3NA-1Ligand/IonSODIUM ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:250 , TYR A:284BINDING SITE FOR RESIDUE IPA A 501
2AC2SOFTWAREHIS A:79 , HIS A:238 , ASP A:242 , LTF A:503BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWARELEU A:18 , LEU A:62 , GLU A:78 , HIS A:79 , THR A:191 , GLY A:193 , ILE A:198 , LEU A:201 , GLY A:210 , SER A:211 , ALA A:215 , HIS A:238 , ASP A:242 , HIS A:265 , ZN A:502 , HOH A:616 , HOH A:721BINDING SITE FOR RESIDUE LTF A 503
4AC4SOFTWAREHIS B:79 , HIS B:238 , ASP B:242 , LTF B:402BINDING SITE FOR RESIDUE ZN B 401
5AC5SOFTWARELEU B:62 , GLU B:78 , HIS B:79 , THR B:191 , PHE B:192 , GLY B:193 , ILE B:198 , GLY B:210 , ALA B:215 , HIS B:238 , ASP B:242 , HIS B:265 , ZN B:401BINDING SITE FOR RESIDUE LTF B 402
6AC6SOFTWAREILE A:254BINDING SITE FOR RESIDUE NA B 403
7AC7SOFTWARETRP B:144 , TYR B:150 , SER B:154BINDING SITE FOR RESIDUE IPA B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IS9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:45 -Pro A:46
2Asn B:45 -Pro B:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IS9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IS9)

(-) Exons   (0, 0)

(no "Exon" information available for 4IS9)

(-) 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:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...eeeeee......eeeeeee.......eeeee......eeee.hhh.eee....eeee.....eee.hhhhhhhhhhh....eeeee...........hhhhhhhhhhhheeeeeee..eeee...eeeee..eeeeee....eeeeee........hhhh.eeeee.hhhhhhhhh.....eeehhhhhhhhh............eee..............hhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhh...eeee...hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4is9 A   1 MIKQRTLKRIVQATGVGLHTGKKVTLTLRPAPANTGVIYRRTDLNPPVDFPADAKSVRDTMLCTCLVNEHDVRISTVEHLNAALAGLGIDNIVIEVNAPEIPIMDGSAAPFVYLLLDAGIDELNCAKKFVRIKETVRVEDGDKWAEFKPYNGFSLDFTIDFNHPAIDSSNQRYAMNFSADAFMRQISRARTFGFMRDIEYLQSRGLCLGGSFDCAIVVDDYRVLNEDGLRFEDEFVRHKMLDAIGDLFMCGHNIIGAFTAYKSGHALNNKLLQAVLAKQEAWEYVTFQDDAELPLAFKAP 300
                                    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:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeee......eeeeeee.......eeeee......eeee.hhh.eee....eeee.....eee.hhhhhhhhhhh....eeeee...........hhhhhhhhhhhheeeeeee.eeeee...eeeee..eeeeee....eeeeee.............eeeee.hhhhhhhhh.....eeehhhhhhhhhhh..........eee..............hhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhh...eeeee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4is9 B   1 MIKQRTLKRIVQATGVGLHTGKKVTLTLRPAPANTGVIYRRTDLNPPVDFPADAKSVRDTMLCTCLVNEHDVRISTVEHLNAALAGLGIDNIVIEVNAPEIPIMDGSAAPFVYLLLDAGIDELNCAKKFVRIKETVRVEDGDKWAEFKPYNGFSLDFTIDFNHPAIDSSNQRYAMNFSADAFMRQISRARTFGFMRDIEYLQSRGLCLGGSFDCAIVVDDYRVLNEDGLRFEDEFVRHKMLDAIGDLFMCGHNIIGAFTAYKSGHALNNKLLQAVLAKQEAWEYVTFQDDAELPLAFKA 299
                                    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
   Legend:   → Mismatch (orange background)
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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 4IS9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IS9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IS9)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LPXC_ECOLI | P0A725: 4isa 4mdt 4mqy

(-) Related Entries Specified in the PDB File

4isa