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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LPXC IN COMPLEX WITH N-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOBUTAN-2-YL]-4-(PHENYLETHYNYL)BENZAMIDE INHIBITOR
 
Authors :  Y. N. Kang, J. A. Stuckey
Date :  29 Jun 12  (Deposition) - 15 May 13  (Release) - 15 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. N. Kang, J. A. Stuckey
Crystal Structure Of The Lpxc
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE DEACETYLASE
    Chains: A, B, C, D
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMOCR
    Expression System Strain: BL21 AI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ENVA, LPXC, PA4406
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 32)

Asymmetric Unit (6, 32)
No.NameCountTypeFull Name
1ACT9Ligand/IonACETATE ION
2GOL9Ligand/IonGLYCEROL
3L594Ligand/IonN-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOBUTAN-2-YL]-4-(PHENYLETHYNYL)BENZAMIDE
4NA1Ligand/IonSODIUM ION
5PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
6ZN4Ligand/IonZINC ION
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3L591Ligand/IonN-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOBUTAN-2-YL]-4-(PHENYLETHYNYL)BENZAMIDE
4NA-1Ligand/IonSODIUM ION
5PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3L591Ligand/IonN-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOBUTAN-2-YL]-4-(PHENYLETHYNYL)BENZAMIDE
4NA-1Ligand/IonSODIUM ION
5PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
6ZN-1Ligand/IonZINC ION
Biological Unit 3 (3, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL3Ligand/IonGLYCEROL
3L591Ligand/IonN-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOBUTAN-2-YL]-4-(PHENYLETHYNYL)BENZAMIDE
4NA-1Ligand/IonSODIUM ION
5PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
6ZN-1Ligand/IonZINC ION
Biological Unit 4 (3, 5)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3L591Ligand/IonN-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOBUTAN-2-YL]-4-(PHENYLETHYNYL)BENZAMIDE
4NA-1Ligand/IonSODIUM ION
5PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
6ZN-1Ligand/IonZINC ION

(-) Sites  (32, 32)

Asymmetric Unit (32, 32)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:78 , HIS A:237 , ASP A:241 , L59 A:302BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREGLU A:77 , HIS A:78 , THR A:190 , PHE A:191 , ILE A:197 , LEU A:200 , ARG A:201 , GLY A:209 , SER A:210 , VAL A:216 , HIS A:237 , ASP A:241 , HIS A:264 , ZN A:301 , PEG A:308 , HOH A:449BINDING SITE FOR RESIDUE L59 A 302
03AC3SOFTWAREILE A:243 , LEU A:246 , TYR A:247 , ASN A:251 , SER A:252 , LEU A:253 , HOH A:440BINDING SITE FOR RESIDUE GOL A 303
04AC4SOFTWAREPHE A:149 , HOH A:430 , HOH A:436BINDING SITE FOR RESIDUE GOL A 304
05AC5SOFTWAREARG A:143 , ARG A:258 , GLY A:259 , PHE A:260 , HOH A:498BINDING SITE FOR RESIDUE ACT A 305
06AC6SOFTWAREGLU A:139 , GLY A:140 , ASP A:141 , ASP A:226 , ASN C:-1 , ALA C:0BINDING SITE FOR RESIDUE ACT A 306
07AC7SOFTWAREGLU A:139 , ARG A:189 , ARG A:229 , GLN A:269 , HOH A:475 , HOH A:551BINDING SITE FOR RESIDUE ACT A 307
08AC8SOFTWAREMET A:194 , SER A:210 , VAL A:211 , L59 A:302BINDING SITE FOR RESIDUE PEG A 308
09AC9SOFTWAREARG A:53 , GLU A:55 , SER A:116 , LEU A:249 , ILE A:275 , HOH A:443BINDING SITE FOR RESIDUE PEG A 309
10BC1SOFTWAREHIS B:78 , HIS B:237 , ASP B:241 , L59 B:302BINDING SITE FOR RESIDUE ZN B 301
11BC2SOFTWAREMET B:62 , GLU B:77 , HIS B:78 , THR B:190 , PHE B:191 , ILE B:197 , LEU B:200 , ARG B:201 , GLY B:209 , SER B:210 , VAL B:216 , HIS B:237 , ASP B:241 , HIS B:264 , ZN B:301 , HOH B:533BINDING SITE FOR RESIDUE L59 B 302
12BC3SOFTWAREPHE B:152 , ILE B:243 , LEU B:246 , TYR B:247 , SER B:252 , LEU B:253 , HOH B:556 , HOH B:576BINDING SITE FOR RESIDUE GOL B 303
13BC4SOFTWAREHOH B:443 , HOH B:461BINDING SITE FOR RESIDUE GOL B 304
14BC5SOFTWAREGLU B:139 , GLY B:140 , ASP B:141 , ASP B:226BINDING SITE FOR RESIDUE ACT B 305
15BC6SOFTWAREARG B:143 , VAL B:145 , ARG B:258 , GLY B:259 , PHE B:260BINDING SITE FOR RESIDUE ACT B 306
16BC7SOFTWARETHR B:285 , LEU D:207BINDING SITE FOR RESIDUE PEG B 307
17BC8SOFTWAREVAL B:211 , HOH B:425 , HOH B:594BINDING SITE FOR RESIDUE PEG B 308
18BC9SOFTWAREGLY B:108 , PRO B:109 , VAL B:111 , SER B:186 , ARG B:272 , THR B:273 , HOH B:473BINDING SITE FOR RESIDUE PEG B 309
19CC1SOFTWAREHIS C:78 , HIS C:237 , ASP C:241 , L59 C:302BINDING SITE FOR RESIDUE ZN C 301
20CC2SOFTWAREMET C:62 , GLU C:77 , HIS C:78 , THR C:190 , PHE C:191 , ILE C:197 , GLY C:209 , SER C:210 , VAL C:216 , HIS C:237 , LYS C:238 , ASP C:241 , HIS C:264 , ZN C:301BINDING SITE FOR RESIDUE L59 C 302
21CC3SOFTWAREILE C:243 , LEU C:246 , TYR C:247 , ASN C:251 , SER C:252 , LEU C:253 , HOH C:502BINDING SITE FOR RESIDUE GOL C 303
22CC4SOFTWAREASP C:104 , GLY C:108 , PRO C:109 , VAL C:111 , PHE C:112 , ARG C:187 , ARG C:272 , THR C:273 , HOH C:445BINDING SITE FOR RESIDUE GOL C 304
23CC5SOFTWAREARG C:53 , ILE C:129 , LEU C:249 , ASN C:251BINDING SITE FOR RESIDUE GOL C 305
24CC6SOFTWAREGLU C:59 , SER C:63 , ASP C:74 , HOH C:523BINDING SITE FOR RESIDUE ACT C 306
25CC7SOFTWAREGLY C:140 , LEU C:228 , GLU C:231 , HOH C:535BINDING SITE FOR RESIDUE ACT C 307
26CC8SOFTWAREHIS D:78 , HIS D:237 , ASP D:241 , L59 D:302BINDING SITE FOR RESIDUE ZN D 301
27CC9SOFTWAREMET D:62 , GLU D:77 , HIS D:78 , THR D:190 , PHE D:191 , ILE D:197 , ARG D:201 , GLY D:209 , SER D:210 , VAL D:216 , HIS D:237 , LYS D:238 , ASP D:241 , HIS D:264 , ZN D:301BINDING SITE FOR RESIDUE L59 D 302
28DC1SOFTWAREPHE D:152 , ILE D:243 , LEU D:246 , TYR D:247 , SER D:252 , LEU D:253 , HOH D:517BINDING SITE FOR RESIDUE GOL D 303
29DC2SOFTWAREASP D:104 , GLY D:108 , PRO D:109 , VAL D:111 , PHE D:112 , ARG D:187 , ARG D:272 , THR D:273 , HOH D:440BINDING SITE FOR RESIDUE GOL D 304
30DC3SOFTWAREALA D:31 , GLN D:122 , HOH D:439BINDING SITE FOR RESIDUE ACT D 305
31DC4SOFTWARESER D:40 , GLU D:49 , GLU D:94BINDING SITE FOR RESIDUE ACT D 306
32DC5SOFTWAREPRO B:32 , VAL B:33 , ASP D:70BINDING SITE FOR RESIDUE NA D 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FW6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:45 -Pro A:46
2Asp B:45 -Pro B:46
3Asp C:45 -Pro C:46
4Asp D:45 -Pro D:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FW6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FW6)

(-) Exons   (0, 0)

(no "Exon" information available for 4FW6)

(-) 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.hhhhh.......eeee..eeee.hhhhhhhhhhh....eeeee...........hhhhhhhhhhhheeeeeee..eeee...eeeee..eeeeee....eeeeee........hhhh.eeeee....hhhhhh.....eeehhhhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh...eeee...hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4fw6 A   0 AMIKQRTLKNIIRATGVGLHSGEKVYLTLKPAPVDTGIVFSRTDLDPVVEIPARAENVGETTMSTTLVKGDVKVDTVEHLLSAMAGLGIDNAYVELSASEVPIMDGSAGPFVFLIQSAGLQEQEAAKKFIRIKREVSVEEGDKRAVFVPFDGFKVSFEIDFDHPVFRGRTQQASVDFSSTSFVKEVSRARTFGFMRDIEYLRSQNLALGGSVENAIVVDENRVLNEDGLRYEDEFVKHKILDAIGDLYLLGNSLIGEFRGFKSGHALNNQLLRTLIADKDAWEVVTFEDARTAPISYMRP 299
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299


Chain B 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.hhhhh.......eeee..eeee.hhhhhhhhhhh....eeeee...........hhhhhhhhhhhheeeeeee..eeee...eeeee..eeeeee....eeeeee........hhhh.eeeee....hhhhhh.....eeehhhhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh...eeee...hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4fw6 B   0 AMIKQRTLKNIIRATGVGLHSGEKVYLTLKPAPVDTGIVFSRTDLDPVVEIPARAENVGETTMSTTLVKGDVKVDTVEHLLSAMAGLGIDNAYVELSASEVPIMDGSAGPFVFLIQSAGLQEQEAAKKFIRIKREVSVEEGDKRAVFVPFDGFKVSFEIDFDHPVFRGRTQQASVDFSSTSFVKEVSRARTFGFMRDIEYLRSQNLALGGSVENAIVVDENRVLNEDGLRYEDEFVKHKILDAIGDLYLLGNSLIGEFRGFKSGHALNNQLLRTLIADKDAWEVVTFEDARTAPISYMRP 299
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299


Chain C from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...eeeeee......eeeeeeee......eeeee......eeee.hhh.eee.....eeee..eee..hhhhhhhhhhh....eeeee...........hhhhhhhhhhhheeeeeee..eeee...eeeee..eeeeee....eeeeee....hhhhhh...eeeee....hhhhhh.....eeehhhhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh...eeee...hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fw6 C  -2 SNAMIKQRTLKNIIRATGVGLHSGEKVYLTLKPAPVDTGIVFSRTDLDPVVEIPARAENVGETTMSTTLVKGDVKVDTVEHLLSAMAGLGIDNAYVELSASEVPIMDGSAGPFVFLIQSAGLQEQEAAKKFIRIKREVSVEEGDKRAVFVPFDGFKVSFEIDFDHPVFRGRTQQASVDFSSTSFVKEVSRARTFGFMRDIEYLRSQNLALGGSVENAIVVDENRVLNEDGLRYEDEFVKHKILDAIGDLYLLGNSLIGEFRGFKSGHALNNQLLRTLIADKDAWEVVTFEDARTAPISYMRP 299
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297  


Chain D from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...eeeeee......eeeeeeee......eeeee......eeee.hhh.eee.....eeee..eee..hhhhhhhhhhh....eeeee...........hhhhhhhhhhhheeeeeee..eeee...eeeee..eeeeee....eeeeee....hhhhhh...eeeee....hhhhhh.....eeehhhhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh...eeee...hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fw6 D  -2 SNAMIKQRTLKNIIRATGVGLHSGEKVYLTLKPAPVDTGIVFSRTDLDPVVEIPARAENVGETTMSTTLVKGDVKVDTVEHLLSAMAGLGIDNAYVELSASEVPIMDGSAGPFVFLIQSAGLQEQEAAKKFIRIKREVSVEEGDKRAVFVPFDGFKVSFEIDFDHPVFRGRTQQASVDFSSTSFVKEVSRARTFGFMRDIEYLRSQNLALGGSVENAIVVDENRVLNEDGLRYEDEFVKHKILDAIGDLYLLGNSLIGEFRGFKSGHALNNQLLRTLIADKDAWEVVTFEDARTAPISYMRP 299
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297
   Legend:   → Mismatch (orange background)
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    → 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 4FW6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FW6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FW6)

(-) Gene Ontology  (6, 6)

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

UniProtKB/Swiss-Prot
        LPXC_PSEAE | P47205: 2ves 3p3e 3u1y 3uhm 4fw3 4fw4 4fw5 4fw7 4j3d 4lcf 4lcg 4lch 4okg 5drq 5drr 5n8c 5u39 5u3b 5upg 5vwm

(-) Related Entries Specified in the PDB File

4fw3 4fw4 4fw5 4fw7