4FW3 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE LPXC IN COMPLEX WITH N-[(2S)-3-AMINO-1-(HYDROXYAMINO)-1-OXOPROPAN-2-YL]-4-(4-PHENYLBUTA-1,3-DIYN-1-YL) 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 :   2.35

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

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
	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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
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)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	L52	4	Ligand/Ion	N-[(2S)-3-AMINO-1-(HYDROXYAMINO)-1-OXOPROPAN-2-YL]-4-(4-PHENYLBUTA-1,3-DIYN-1-YL)BENZAMIDE
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	L52	1	Ligand/Ion	N-[(2S)-3-AMINO-1-(HYDROXYAMINO)-1-OXOPROPAN-2-YL]-4-(4-PHENYLBUTA-1,3-DIYN-1-YL)BENZAMIDE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	L52	1	Ligand/Ion	N-[(2S)-3-AMINO-1-(HYDROXYAMINO)-1-OXOPROPAN-2-YL]-4-(4-PHENYLBUTA-1,3-DIYN-1-YL)BENZAMIDE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	L52	1	Ligand/Ion	N-[(2S)-3-AMINO-1-(HYDROXYAMINO)-1-OXOPROPAN-2-YL]-4-(4-PHENYLBUTA-1,3-DIYN-1-YL)BENZAMIDE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	L52	1	Ligand/Ion	N-[(2S)-3-AMINO-1-(HYDROXYAMINO)-1-OXOPROPAN-2-YL]-4-(4-PHENYLBUTA-1,3-DIYN-1-YL)BENZAMIDE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:78 , HIS A:237 , ASP A:241 , L52 A:302	BINDING SITE FOR RESIDUE ZN A 301
02	AC2	SOFTWARE	HIS A:19 , MET A:62 , GLU A:77 , HIS A:78 , THR A:190 , PHE A:191 , GLY A:209 , SER A:210 , HIS A:237 , ASP A:241 , HIS A:264 , ZN A:301 , HOH A:464	BINDING SITE FOR RESIDUE L52 A 302
03	AC3	SOFTWARE	ALA A:84 , PHE A:152 , ILE A:243 , LEU A:246 , TYR A:247 , SER A:252 , LEU A:253 , HOH A:466	BINDING SITE FOR RESIDUE GOL A 303
04	AC4	SOFTWARE	HIS B:78 , HIS B:237 , ASP B:241 , L52 B:301	BINDING SITE FOR RESIDUE ZN B 300
05	AC5	SOFTWARE	GLU B:77 , HIS B:78 , THR B:190 , PHE B:191 , ILE B:197 , ARG B:201 , GLY B:209 , SER B:210 , VAL B:216 , HIS B:237 , ASP B:241 , HIS B:264 , ZN B:300 , HOH B:473	BINDING SITE FOR RESIDUE L52 B 301
06	AC6	SOFTWARE	HIS C:78 , HIS C:237 , ASP C:241 , L52 C:301	BINDING SITE FOR RESIDUE ZN C 300
07	AC7	SOFTWARE	MET 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 , ASP C:241 , HIS C:264 , ZN C:300 , HOH C:469 , HOH C:482	BINDING SITE FOR RESIDUE L52 C 301
08	AC8	SOFTWARE	HIS D:78 , HIS D:237 , ASP D:241 , L52 D:302	BINDING SITE FOR RESIDUE ZN D 301
09	AC9	SOFTWARE	LEU D:18 , HIS D:19 , MET D:62 , GLU D:77 , HIS D:78 , THR D:190 , MET D:194 , ARG D:201 , SER D:210 , HIS D:237 , ASP D:241 , HIS D:264 , ZN D:301	BINDING SITE FOR RESIDUE L52 D 302
10	BC1	SOFTWARE	ALA D:84 , PHE D:152 , ILE D:243 , LEU D:246 , TYR D:247 , SER D:252 , LEU D:253 , HOH D:418	BINDING SITE FOR RESIDUE GOL D 303

(no "SS Bond" information available for 4FW3)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 4FW3)

(no "PROSITE Motif" information available for 4FW3)

(no "Exon" information available for 4FW3)

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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...eeeeee......eeeeeeee......eeeee......eeee.hhhhh........eee..eee..hhhhhhhhhhh....eeeee...........hhhhhhhhhhhheeeeeee..eeee...eeeee..eeeeee....eeeeee....hhhhhh...eeeee....hhhhhh.....eeehhhhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh...eeee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fw3 A  -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 B from PDB  Type:PROTEIN  Length:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...eeeeee......eeeeeeee......eeeee......eeee.hhhhh.......eeee..eeee.hhhhhhhhhhh....eeeee...........hhhhhhhhhhhheeeeeee..eeee...eeeee..eeeeee....eeeeee........hhhh.eeeee....hhhhhh.....eeehhhhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh...eeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fw3 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:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...eeeeee......eeeeeeee......eeeee......eeee.hhhhh.......eeee..eeee.hhhhhhhhhhh....eeeee...........hhhhhhhhhhhheeeeeee..eeee...eeeee..eeeeee....eeeeee.........hhh.eeeee....hhhhhh.....eeehhhhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh...eeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fw3 C  -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 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.hhhhh........eee..eee..hhhhhhhhhhhh...eeeee...........hhhhhhhhhhhheeeeeee..eeee...eeeee..eeeeee....eeeeee....hhhhhh...eeeee....hhhhhh.....eeehhhhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh...eeee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fw3 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)
	-	→ 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 '\|'

(no "SCOP Domain" information available for 4FW3)

(no "CATH Domain" information available for 4FW3)

(no "Pfam Domain" information available for 4FW3)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		L52	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asp A:45 - Pro A:46	[ RasMol ]
		Asp B:45 - Pro B:46	[ RasMol ]
		Asp C:45 - Pro C:46	[ RasMol ]
		Asp D:45 - Pro D:46	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4fw3
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	LPXC_PSEAE \| P47205
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.5.1.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	LPXC_PSEAE \| P47205
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File