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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI LPXC/BB-78485 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 :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Lipid A Synthesis, Lpxc, Baab Sandwich, Deacetylation, Antibiotic, Acyl Udp-Glcnac, Hydroxamate, Bb-78485, 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
    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

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 21)

Asymmetric/Biological Unit (4, 21)
No.NameCountTypeFull Name
1D1D1Ligand/Ion(4S,5S)-1,2-DITHIANE-4,5-DIOL
2FMT17Ligand/IonFORMIC ACID
3GVR2Ligand/Ion(2R)-N-HYDROXY-3-NAPHTHALEN-2-YL-2-[(NAPHTHALEN-2-YLSULFONYL)AMINO]PROPANAMIDE
4ZN1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:79 , HIS A:238 , ASP A:242 , GVR A:402BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWARELEU A:18 , LEU A:62 , CYS A:63 , THR A:76 , GLU A:78 , HIS A:79 , ILE A:103 , THR A:191 , PHE A:192 , GLY A:193 , ILE A:198 , CYS A:214 , ALA A:215 , HIS A:238 , ASP A:242 , HIS A:265 , ZN A:401BINDING SITE FOR RESIDUE GVR A 402
03AC3SOFTWAREMET A:61 , LEU A:116 , ASP A:180 , MET A:183 , ARG A:184 , ASP A:197 , TYR A:200 , LEU A:201 , PRO A:300 , FMT A:404 , FMT A:412 , D1D A:421BINDING SITE FOR RESIDUE GVR A 403
04AC4SOFTWAREGVR A:403 , HOH A:1229 , HOH A:1277BINDING SITE FOR RESIDUE FMT A 404
05AC5SOFTWAREMET A:195 , ILE A:198 , HOH A:1230 , HOH A:1260 , HOH A:1262BINDING SITE FOR RESIDUE FMT A 405
06AC6SOFTWARELYS A:143 , ALA A:181 , ARG A:184 , GLN A:185BINDING SITE FOR RESIDUE FMT A 406
07AC7SOFTWARETYR A:221 , ARG A:222 , ASP A:227 , HOH A:1094 , HOH A:1280BINDING SITE FOR RESIDUE FMT A 407
08AC8SOFTWAREASP A:160 , PHE A:161 , ASN A:162 , ARG A:184 , GLN A:185BINDING SITE FOR RESIDUE FMT A 408
09AC9SOFTWARETHR A:60 , LEU A:62 , CYS A:63 , HOH A:1256BINDING SITE FOR RESIDUE FMT A 409
10BC1SOFTWAREMET A:104 , ASP A:105 , PRO A:110 , HOH A:1119 , HOH A:1148BINDING SITE FOR RESIDUE FMT A 410
11BC2SOFTWAREPHE A:161 , ARG A:184 , PHE A:192 , GVR A:403BINDING SITE FOR RESIDUE FMT A 412
12BC3SOFTWARELYS A:55 , HOH A:1307BINDING SITE FOR RESIDUE FMT A 413
13BC4SOFTWAREARG A:196 , HOH A:1296BINDING SITE FOR RESIDUE FMT A 414
14BC5SOFTWARETRP A:144 , TYR A:261 , HOH A:1159BINDING SITE FOR RESIDUE FMT A 415
15BC6SOFTWAREGLU A:134 , THR A:135BINDING SITE FOR RESIDUE FMT A 416
16BC7SOFTWARESER A:154 , LEU A:155 , MET A:175 , ASN A:176BINDING SITE FOR RESIDUE FMT A 417
17BC8SOFTWAREARG A:29BINDING SITE FOR RESIDUE FMT A 418
18BC9SOFTWAREASP A:71 , TYR A:284BINDING SITE FOR RESIDUE FMT A 419
19CC1SOFTWAREPHE A:153 , ASN A:253 , ILE A:254 , PHE A:297 , HOH A:1002 , HOH A:1050BINDING SITE FOR RESIDUE FMT A 420
20CC2SOFTWARETYR A:113 , MET A:183 , SER A:187 , ARG A:188 , ASP A:197 , GVR A:403 , HOH A:1043BINDING SITE FOR RESIDUE D1D A 421

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:45 -Pro A:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ISA)

(-) 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:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...eeeeee......eeeeeeee......eeeee......eeee.hhh.eee....eeee.....eee.hhhhhhhhhhhh...eeeee...........hhhhhhhhhhhheeeeeee..eeee...eeeee..eeeeee....eeeeee........hhhh.eeeee.hhhhhhhhh.....eeehhhhhhhhhh......hhhhheee..............hhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhh...eeee...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4isa 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
   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 4ISA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:45 - Pro A:46   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        LPXC_ECOLI | P0A725: 4is9 4mdt 4mqy

(-) Related Entries Specified in the PDB File

4is9