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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]BIPHENYL-4-CARBOXAMIDE INHIBITOR
 
Authors :  Y. N. Kang, J. A. Stuckey
Date :  30 Jun 12  (Deposition) - 15 May 13  (Release) - 15 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
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  (4, 32)

Asymmetric Unit (4, 32)
No.NameCountTypeFull Name
1ACT7Ligand/IonACETATE ION
2GOL17Ligand/IonGLYCEROL
3L634Ligand/IonN-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOBUTAN-2-YL]BIPHENYL-4-CARBOXAMIDE
4ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL4Ligand/IonGLYCEROL
3L631Ligand/IonN-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOBUTAN-2-YL]BIPHENYL-4-CARBOXAMIDE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2GOL6Ligand/IonGLYCEROL
3L631Ligand/IonN-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOBUTAN-2-YL]BIPHENYL-4-CARBOXAMIDE
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (3, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL5Ligand/IonGLYCEROL
3L631Ligand/IonN-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOBUTAN-2-YL]BIPHENYL-4-CARBOXAMIDE
4ZN-1Ligand/IonZINC ION
Biological Unit 4 (3, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3L631Ligand/IonN-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOBUTAN-2-YL]BIPHENYL-4-CARBOXAMIDE
4ZN-1Ligand/IonZINC ION

(-) Sites  (32, 32)

Asymmetric Unit (32, 32)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:78 , HIS A:237 , ASP A:241 , L63 A:302BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREMET A:62 , GLU A:77 , HIS A:78 , THR A:190 , PHE A:191 , ILE A:197 , ARG A:201 , ALA A:206 , GLY A:209 , SER A:210 , HIS A:237 , LYS A:238 , ASP A:241 , HIS A:264 , ZN A:301 , GOL A:304BINDING SITE FOR RESIDUE L63 A 302
03AC3SOFTWAREPHE A:152 , ILE A:243 , LEU A:246 , TYR A:247 , SER A:252 , LEU A:253 , HOH A:442 , HOH A:443 , HOH A:551BINDING SITE FOR RESIDUE GOL A 303
04AC4SOFTWAREPHE A:191 , GLY A:192 , PHE A:193 , ASP A:196 , L63 A:302 , HOH A:560BINDING SITE FOR RESIDUE GOL A 304
05AC5SOFTWARESER A:40 , VAL A:47 , GLU A:49 , TYR A:92 , GLU A:94BINDING SITE FOR RESIDUE GOL A 305
06AC6SOFTWAREGLU A:138 , GLY A:140 , LEU A:228 , ARG A:229 , TYR A:230 , GLU A:231 , HOH A:423 , ASP D:288 , ARG D:290BINDING SITE FOR RESIDUE GOL A 306
07AC7SOFTWAREARG A:201 , HOH A:571BINDING SITE FOR RESIDUE ACT A 307
08AC8SOFTWAREASP A:218 , ARG A:221 , ASP D:34 , HOH D:432BINDING SITE FOR RESIDUE ACT A 308
09AC9SOFTWAREASP B:218 , ARG B:221 , ASP C:34 , GLU C:123 , HOH C:429BINDING SITE FOR RESIDUE ACT B 401
10BC1SOFTWAREHIS B:78 , HIS B:237 , ASP B:241 , L63 B:403BINDING SITE FOR RESIDUE ZN B 402
11BC2SOFTWAREMET B:62 , GLU B:77 , HIS B:78 , THR B:190 , PHE B:191 , ILE B:197 , ARG B:201 , ALA B:206 , GLY B:209 , SER B:210 , HIS B:237 , LYS B:238 , ASP B:241 , HIS B:264 , ZN B:402BINDING SITE FOR RESIDUE L63 B 403
12BC3SOFTWAREPHE B:152 , ILE B:243 , LEU B:246 , TYR B:247 , SER B:252 , LEU B:253 , GOL B:407 , HOH B:517 , HOH B:583 , HOH B:631BINDING SITE FOR RESIDUE GOL B 404
13BC4SOFTWAREMET B:194 , ARG B:201 , SER B:210 , VAL B:211BINDING SITE FOR RESIDUE GOL B 405
14BC5SOFTWAREGLY B:108 , PRO B:109 , VAL B:111 , PHE B:112 , SER B:186 , GLN B:269 , ARG B:272 , THR B:273 , HOH B:616 , HOH B:629BINDING SITE FOR RESIDUE GOL B 406
15BC6SOFTWAREGLY B:85 , PHE B:152 , PHE B:176 , PHE B:181 , SER B:295 , TYR B:296 , GOL B:404 , HOH B:676BINDING SITE FOR RESIDUE GOL B 407
16BC7SOFTWAREARG B:53 , LEU B:249 , TRP B:281 , HOH B:543 , HOH B:554 , HOH B:680BINDING SITE FOR RESIDUE GOL B 408
17BC8SOFTWARESER B:155 , GLU B:157 , GLN B:171 , GLY B:259 , ACT B:410BINDING SITE FOR RESIDUE ACT B 409
18BC9SOFTWAREARG B:143 , ARG B:258 , GLY B:259 , PHE B:260 , ACT B:409BINDING SITE FOR RESIDUE ACT B 410
19CC1SOFTWARESER B:40 , THR B:42 , VAL B:47 , GLU B:49 , TYR B:92 , GLU B:94 , HOH B:654 , HOH B:677BINDING SITE FOR RESIDUE GOL B 411
20CC2SOFTWAREHIS C:78 , HIS C:237 , ASP C:241 , L63 C:302BINDING SITE FOR RESIDUE ZN C 301
21CC3SOFTWAREMET C:62 , GLU C:77 , HIS C:78 , THR C:190 , PHE C:191 , GLY C:192 , GLY C:209 , VAL C:216 , HIS C:237 , ASP C:241 , HIS C:264 , ZN C:301 , HOH C:414 , HOH C:563BINDING SITE FOR RESIDUE L63 C 302
22CC4SOFTWAREPHE C:152 , ILE C:243 , LEU C:246 , TYR C:247 , SER C:252 , LEU C:253 , HOH C:435 , HOH C:441 , HOH C:446BINDING SITE FOR RESIDUE GOL C 303
23CC5SOFTWAREALA C:31 , PRO C:32 , GLN C:122 , HOH C:425 , HOH C:439BINDING SITE FOR RESIDUE GOL C 304
24CC6SOFTWAREARG C:53 , ILE C:129 , LEU C:249 , ASN C:251 , TRP C:281 , HOH C:535BINDING SITE FOR RESIDUE GOL C 305
25CC7SOFTWAREASP C:104 , SER C:106 , GLY C:108 , PRO C:109 , ARG C:187 , ARG C:229 , GLN C:269 , ARG C:272 , THR C:273 , HOH C:450 , HOH C:518BINDING SITE FOR RESIDUE GOL C 306
26CC8SOFTWAREGLU C:55 , VAL C:57 , ARG C:272BINDING SITE FOR RESIDUE GOL C 307
27CC9SOFTWARELYS A:23 , LYS C:29 , SER C:40 , GLU C:49 , TYR C:92 , GLU C:94BINDING SITE FOR RESIDUE ACT C 308
28DC1SOFTWAREHIS D:78 , HIS D:237 , ASP D:241 , L63 D:302BINDING SITE FOR RESIDUE ZN D 301
29DC2SOFTWAREMET D:62 , GLU D:77 , HIS D:78 , THR D:190 , PHE D:191 , GLY D:192 , ILE D:197 , GLY D:209 , VAL D:216 , HIS D:237 , ASP D:241 , HIS D:264 , ZN D:301BINDING SITE FOR RESIDUE L63 D 302
30DC3SOFTWAREPHE D:152 , ILE D:243 , LEU D:246 , TYR D:247 , SER D:252 , LEU D:253 , TYR D:296 , HOH D:435 , HOH D:446 , HOH D:535BINDING SITE FOR RESIDUE GOL D 303
31DC4SOFTWAREARG D:53 , ILE D:129 , LEU D:249 , ASN D:251 , TRP D:281 , HOH D:422 , HOH D:577BINDING SITE FOR RESIDUE GOL D 304
32DC5SOFTWARELYS B:23 , LYS D:29 , SER D:40 , GLU D:49 , TYR D:92 , GLU D:94BINDING SITE FOR RESIDUE ACT D 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FW7)

(-) 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 4FW7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FW7)

(-) Exons   (0, 0)

(no "Exon" information available for 4FW7)

(-) 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:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...eeeeee......eeeeeee.......eeeee......eeee.hhh.eee.....eeee..eeee.hhhhhhhhhhhh...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
                 4fw7 A  -1 NAMIKQRTLKNIIRATGVGLHSGEKVYLTLKPAPVDTGIVFSRTDLDPVVEIPARAENVGETTMSTTLVKGDVKVDTVEHLLSAMAGLGIDNAYVELSASEVPIMDGSAGPFVFLIQSAGLQEQEAAKKFIRIKREVSVEEGDKRAVFVPFDGFKVSFEIDFDHPVFRGRTQQASVDFSSTSFVKEVSRARTFGFMRDIEYLRSQNLALGGSVENAIVVDENRVLNEDGLRYEDEFVKHKILDAIGDLYLLGNSLIGEFRGFKSGHALNNQLLRTLIADKDAWEVVTFEDARTAPISYMRP 299
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298 


Chain B from PDB  Type:PROTEIN  Length:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...eeeeee......eeeeeee.......eeeee......eeee.hhh.eee.....eeee..eeee.hhhhhhhhhhhh...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
                 4fw7 B  -1 NAMIKQRTLKNIIRATGVGLHSGEKVYLTLKPAPVDTGIVFSRTDLDPVVEIPARAENVGETTMSTTLVKGDVKVDTVEHLLSAMAGLGIDNAYVELSASEVPIMDGSAGPFVFLIQSAGLQEQEAAKKFIRIKREVSVEEGDKRAVFVPFDGFKVSFEIDFDHPVFRGRTQQASVDFSSTSFVKEVSRARTFGFMRDIEYLRSQNLALGGSVENAIVVDENRVLNEDGLRYEDEFVKHKILDAIGDLYLLGNSLIGEFRGFKSGHALNNQLLRTLIADKDAWEVVTFEDARTAPISYMRP 299
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298 


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.....eee..hhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh...eeee...hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fw7 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.....eee..hhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh...eeee...hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fw7 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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  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 4FW7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FW7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FW7)

(-) 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 4fw6 4j3d 4lcf 4lcg 4lch 4okg 5drq 5drr 5n8c 5u39 5u3b 5upg 5vwm

(-) Related Entries Specified in the PDB File

4fw3 4fw4 4fw5 4fw6