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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PSEUDOMONAS AERUGINOSA LPXC/LPC-040 COMPLEX
 
Authors :  C. -J. Lee, J. Najeeb, P. Zhou
Date :  16 Sep 15  (Deposition) - 09 Mar 16  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym./Biol. Unit :  A
Keywords :  Lpxc, Lipid A, Inhibitor, Gram-Negative Bacteria, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Lee, X. Liang, Q. Wu, J. Najeeb, J. Zhao, R. Gopalaswamy, M. Titecat, F. Sebbane, N. Lemaitre, E. J. Toone, P. Zhou
Drug Design From The Cryptic Inhibitor Envelope.
Nat Commun V. 7 10638 2016
PubMed-ID: 26912110  |  Reference-DOI: 10.1038/NCOMMS10638

(-) 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, ENVA, PA4406
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA (STRAIN ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
    Organism Taxid: 208964
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228
    Synonym: PROTEIN ENVA,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  (3, 32)

Asymmetric/Biological Unit (3, 32)
No.NameCountTypeFull Name
15EM1Ligand/IonN-[(2S)-3-AMINO-1-(HYDROXYAMINO)-3-METHYL-1-OXOBUTAN-2-YL]-4-[4-(4-AMINOPHENYL)BUTA-1,3-DIYN-1-YL]BENZAMIDE
2NO329Ligand/IonNITRATE ION
3ZN2Ligand/IonZINC ION

(-) Sites  (32, 32)

Asymmetric Unit (32, 32)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:78 , HIS A:237 , ASP A:241 , 5EM A:303binding site for residue ZN A 301
02AC2SOFTWAREHIS A:162 , GLU A:219 , ASP A:277 , ASP A:279binding site for residue ZN A 302
03AC3SOFTWAREGLU A:77 , HIS A:78 , PHE A:112 , GLN A:115 , THR A:190 , PHE A:191 , ILE A:197 , ARG A:201 , GLY A:209 , SER A:210 , VAL A:211 , HIS A:237 , ASP A:241 , HIS A:264 , ZN A:301 , NO3 A:304 , NO3 A:307 , HOH A:461 , HOH A:462 , HOH A:476 , HOH A:506 , HOH A:579binding site for residue 5EM A 303
04AC4SOFTWARELYS A:238 , GLY A:263 , HIS A:264 , 5EM A:303 , NO3 A:307 , HOH A:476 , HOH A:478 , HOH A:489 , HOH A:510binding site for residue NO3 A 304
05AC5SOFTWAREVAL A:137 , GLU A:138 , GLN A:269 , HOH A:413 , HOH A:435 , HOH A:566binding site for residue NO3 A 305
06AC6SOFTWAREMET A:194 , ARG A:195 , ASP A:218 , GLU A:219 , HOH A:430 , HOH A:497binding site for residue NO3 A 306
07AC7SOFTWAREPHE A:160 , PHE A:191 , LYS A:238 , 5EM A:303 , NO3 A:304 , HOH A:410 , HOH A:453binding site for residue NO3 A 307
08AC8SOFTWARELYS A:142 , SER A:262 , GLY A:263 , HIS A:264 , ALA A:265 , LEU A:266 , HOH A:429binding site for residue NO3 A 308
09AC9SOFTWAREILE A:158 , ASP A:159 , PHE A:160 , LYS A:261 , HOH A:453 , HOH A:460 , HOH A:495binding site for residue NO3 A 309
10AD1SOFTWAREARG A:189 , SER A:202 , GLN A:203 , ASN A:204 , ARG A:229 , HOH A:458 , HOH A:524 , HOH A:570binding site for residue NO3 A 310
11AD2SOFTWAREGLY A:108 , PRO A:109 , PHE A:112 , ARG A:201 , HOH A:433 , HOH A:456 , HOH A:579binding site for residue NO3 A 311
12AD3SOFTWAREPHE A:176 , SER A:177 , PRO A:293 , ILE A:294 , SER A:295 , HOH A:492binding site for residue NO3 A 312
13AD4SOFTWAREILE A:158 , ARG A:168 , THR A:169 , GLN A:170 , ASP A:232 , GLU A:233 , PHE A:234 , VAL A:235 , HOH A:423binding site for residue NO3 A 313
14AD5SOFTWAREASN A:9 , SER A:116 , ALA A:117 , VAL A:222 , LEU A:223 , NO3 A:315 , HOH A:409binding site for residue NO3 A 314
15AD6SOFTWARELYS A:8 , ASN A:9 , SER A:116 , ALA A:117 , GLY A:118 , LEU A:223 , GLU A:225 , NO3 A:314 , HOH A:409binding site for residue NO3 A 315
16AD7SOFTWARETHR A:14 , TYR A:25 , ARG A:133 , GLU A:134 , PRO A:148 , ARG A:195 , HOH A:457 , HOH A:513binding site for residue NO3 A 316
17AD8SOFTWARETYR A:25 , SER A:96 , PRO A:148 , PHE A:149 , ASP A:150 , HOH A:414 , HOH A:464binding site for residue NO3 A 317
18AD9SOFTWAREILE A:10 , ARG A:12 , LYS A:29 , ARG A:143 , ARG A:258 , PHE A:260binding site for residue NO3 A 318
19AE1SOFTWARETYR A:230 , GLU A:231 , ASP A:232 , LYS A:236binding site for residue NO3 A 319
20AE2SOFTWAREHIS A:19 , MET A:62 , LEU A:205 , ALA A:206binding site for residue NO3 A 320
21AE3SOFTWAREGLU A:59 , THR A:60 , THR A:61 , MET A:62 , SER A:63 , HOH A:406 , HOH A:434binding site for residue NO3 A 321
22AE4SOFTWAREARG A:166 , GLN A:269 , ARG A:272 , THR A:273binding site for residue NO3 A 322
23AE5SOFTWARETHR A:285 , PHE A:286 , GLU A:287 , ASP A:288 , THR A:291 , HOH A:438binding site for residue NO3 A 323
24AE6SOFTWARELYS A:23 , LYS A:132 , ARG A:133binding site for residue NO3 A 324
25AE7SOFTWAREMET A:1 , ALA A:125 , THR A:285 , PHE A:286 , GLU A:287binding site for residue NO3 A 325
26AE8SOFTWAREVAL A:284 , THR A:285binding site for residue NO3 A 326
27AE9SOFTWAREARG A:41 , ASP A:70 , VAL A:71 , LYS A:72binding site for residue NO3 A 327
28AF1SOFTWAREARG A:53 , ALA A:54 , GLU A:55 , LEU A:248 , LEU A:249 , ILE A:275 , HOH A:571binding site for residue NO3 A 328
29AF2SOFTWAREGLU A:59 , THR A:60 , THR A:61 , HOH A:428 , HOH A:535binding site for residue NO3 A 329
30AF3SOFTWAREARG A:168 , VAL A:222 , GLY A:227 , LEU A:228 , HOH A:402binding site for residue NO3 A 330
31AF4SOFTWARELEU A:44 , ASP A:45 , HOH A:559binding site for residue NO3 A 331
32AF5SOFTWAREASP A:159 , PHE A:160 , ASP A:161 , HIS A:162 , HOH A:436 , HOH A:460binding site for residue NO3 A 332

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DRQ)

(-) 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:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeee......eeeeeee.......eeeee......eeee.hhhhh........eee..eee..hhhhhhhhhhhh...eeeee...........hhhhhhhhhhhheeeeeee..eeee...eeeee..eeeeee....eeeeee....hhhhh....eeeee....hhhhhh.....eeehhhhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh...eeee...hhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5drq A   1 MIKQRTLKNIIRATGVGLHSGEKVYLTLKPAPVDTGIVFSRTDLDPVVEIPARAENVGETTMSTTLVKGDVKVDTVEHLLSAMAGLGIDNAYVELSASEVPIMDGSAGPFVFLIQSAGLQEQEAAKKFIRIKREVSVEEGDKRAVFVPFDGFKVSFEIDFDHPVFRGRTQQASVDFSSTSFVKEVSRARTFGFMRDIEYLRSQNLALGGSVENAIVVDENRVLNEDGLRYEDEFVKHKILDAIGDLYLLGNSLIGEFRGFKSGHALNNQLLRTLIADKDAWEVVTFEDARTAPISY 296
                                    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)
  - → 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 5DRQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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        LPXC_PSEAE | P47205: 2ves 3p3e 3u1y 3uhm 4fw3 4fw4 4fw5 4fw6 4fw7 4j3d 4lcf 4lcg 4lch 4okg 5drr 5n8c 5u39 5u3b 5upg 5vwm

(-) Related Entries Specified in the PDB File

5dro 5drp 5drr