Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC COMPLEXED WITH IMIDAZOLE.
 
Authors :  H. A. Gennadios, D. A. Whittington, X. Li, C. A. Fierke, D. W. Christians
Date :  12 Apr 06  (Deposition) - 04 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Lpxc-Imidazole Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. A. Gennadios, D. A. Whittington, X. Li, C. A. Fierke, D. W. Christianson
Mechanistic Inferences From The Binding Of Ligands To Lpxc, A Metal-Dependent Deacetylase
Biochemistry V. 45 7940 2006
PubMed-ID: 16800620  |  Reference-DOI: 10.1021/BI060823M

(-) Compounds

Molecule 1 - UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE DEACETYLASE
    Chains: A, B
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DELTA 11 C-TERMINAL DELETION
    Gene: LPXC, ENVA
    Mutation: YES
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: UDP-3-O-ACYL-GLCNAC DEACETYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric Unit (6, 18)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3IMD4Ligand/IonIMIDAZOLE
4MYR2Ligand/IonMYRISTIC ACID
5PLM1Ligand/IonPALMITIC ACID
6ZN5Ligand/IonZINC ION
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3IMD2Ligand/IonIMIDAZOLE
4MYR1Ligand/IonMYRISTIC ACID
5PLM1Ligand/IonPALMITIC ACID
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3IMD2Ligand/IonIMIDAZOLE
4MYR1Ligand/IonMYRISTIC ACID
5PLM-1Ligand/IonPALMITIC ACID
6ZN-1Ligand/IonZINC ION
Biological Unit 3 (4, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3IMD2Ligand/IonIMIDAZOLE
4MYR1Ligand/IonMYRISTIC ACID
5PLM1Ligand/IonPALMITIC ACID
6ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS B:79 , HIS B:238 , ASP B:242 , IMD B:804 , HOH B:1117 , HOH B:1118BINDING SITE FOR RESIDUE ZN B 601
02AC2SOFTWAREHIS A:79 , HIS A:238 , ASP A:242 , IMD A:803 , HOH A:1094 , HOH A:1095BINDING SITE FOR RESIDUE ZN A 602
03AC3SOFTWAREHIS A:29 , GLU A:95 , GLY B:2 , GLU B:126BINDING SITE FOR RESIDUE ZN B 603
04AC4SOFTWAREHIS A:58 , HIS A:200 , CL A:607 , IMD A:801BINDING SITE FOR RESIDUE ZN A 604
05AC5SOFTWAREHIS B:58 , HIS B:200 , CL B:606 , IMD B:802BINDING SITE FOR RESIDUE ZN B 605
06AC6SOFTWAREPHE B:167 , ZN B:605 , IMD B:802BINDING SITE FOR RESIDUE CL B 606
07AC7SOFTWAREPHE A:167 , ZN A:604 , IMD A:801 , HOH A:1049BINDING SITE FOR RESIDUE CL A 607
08AC8SOFTWAREHIS A:58 , ILE A:198 , TYR A:224 , ILE B:198 , MYR B:702BINDING SITE FOR RESIDUE PLM A 701
09AC9SOFTWAREPLM A:701 , ILE B:18 , HIS B:58 , PHE B:192 , GLY B:210 , HOH B:905 , HOH B:972 , HOH B:1049BINDING SITE FOR RESIDUE MYR B 702
10BC1SOFTWARELYS A:202 , GLY A:210 , SER A:211 , LEU A:212 , LYS A:213 , HOH A:962 , HOH A:1044 , HOH A:1096 , LYS B:202 , GLY B:210 , SER B:211 , LEU B:212 , LYS B:213 , HOH B:919BINDING SITE FOR RESIDUE MYR A 703
11BC2SOFTWAREHIS A:58 , PHE A:167 , HIS A:200 , ZN A:604 , CL A:607BINDING SITE FOR RESIDUE IMD A 801
12BC3SOFTWAREHIS B:58 , PHE B:167 , HIS B:200 , ZN B:605 , CL B:606BINDING SITE FOR RESIDUE IMD B 802
13BC4SOFTWAREHIS A:58 , GLU A:78 , HIS A:79 , THR A:191 , HIS A:238 , ASP A:242 , HIS A:265 , ZN A:602 , HOH A:1094 , HOH A:1095BINDING SITE FOR RESIDUE IMD A 803
14BC5SOFTWAREHIS B:58 , GLU B:78 , HIS B:79 , THR B:191 , HIS B:238 , ASP B:242 , HIS B:265 , ZN B:601 , HOH B:1117 , HOH B:1118BINDING SITE FOR RESIDUE IMD B 804
15BC6SOFTWAREHIS B:85 , LEU B:86 , GLU B:88 , TYR B:129 , LEU B:153 , VAL B:254 , LYS B:255 , HOH B:941 , HOH B:1119BINDING SITE FOR RESIDUE GOL B 901
16BC7SOFTWAREHIS A:85 , LEU A:86 , GLU A:88 , LEU A:153 , VAL A:254 , LYS A:255 , HOH A:992BINDING SITE FOR RESIDUE GOL A 902
17BC8SOFTWAREVAL B:53 , VAL B:54 , HIS B:55 , GLU B:158 , ARG B:170 , LYS B:172 , LYS B:273 , HOH B:976 , HOH B:1097BINDING SITE FOR RESIDUE GOL B 903
18BC9SOFTWARELYS A:10 , HIS A:29 , TYR B:129 , ASP B:151 , HOH B:984 , HOH B:1084BINDING SITE FOR RESIDUE GOL B 904

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GO3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GO3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GO3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GO3)

(-) Exons   (0, 0)

(no "Exon" information available for 2GO3)

(-) 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:266
 aligned with LPXC_AQUAE | O67648 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:266
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261      
           LPXC_AQUAE     2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFCFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQ 267
               SCOP domains d2go3a1 A:2-127 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                       d2go3a2 A:128-279 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                                                SCOP domains
               CATH domains 2go3A01 A:2-128 lpxc deacetylase, domain 1                                                                               2go3A02 A:129-279 lpxc deacetylase, domain 2                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeee......eeeeeeee......eeeee..eeee.hhh.eee.....eeee..eee..hhhhhhhhhhh....eeeeee..........hhhhhhhhhh.eeeeeee...ee....eeeee..eeeeee.....eeeeeee......eeeeeee..hhhhh.....eee..hhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh..ee.eeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2go3 A   2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFAFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQ 279
                                    11        21        31        41        51        61 ||     76        86        96       106       116 ||    127       137       147       157     ||170    || 183       193       203       213       223       233       243       253       263       273      
                                                                                        63|                                              118|                                        163|     175|                                                                                                    
                                                                                         69                                               120                                         167      179                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:266
 aligned with LPXC_AQUAE | O67648 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:266
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261      
           LPXC_AQUAE     2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFCFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQ 267
               SCOP domains d2go3b1 B:2-127 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                       d2go3b2 B:128-279 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                                                SCOP domains
               CATH domains 2go3B01 B:2-128 lpxc deacetylase, domain 1                                                                               2go3B02 B:129-279 lpxc deacetylase, domain 2                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeee......eeeeeeee......eeeee..eeee.hhh.eee.....eeee..eee..hhhhhhhhhhh....eeeeee..........hhhhhhhhhh.eeeeeee...ee....eeeee..eeeeee....eeeeeeee......eeeeeee..hhhhh.....eee..hhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2go3 B   2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFAFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQ 279
                                    11        21        31        41        51        61 ||     76        86        96       106       116 ||    127       137       147       157     ||170    || 183       193       203       213       223       233       243       253       263       273      
                                                                                        63|                                              118|                                        163|     175|                                                                                                    
                                                                                         69                                               120                                         167      179
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GO3)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LPXC_AQUAE | O67648)
molecular function
    GO:0008759    UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity    Catalysis of the removal of an acetyl group from the 2-N position of glucosamine in the lipid A precursor UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine.
    GO:0103117    UDP-3-O-acyl-N-acetylglucosamine deacetylase activity    Catalysis of the reaction: UDP-3-O-[(3R)-3-hydroxytetradecanoyl]-N-acetylglucosamine(2-) + H2O <=> UDP-3-O-[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosamine(1-) + acetate
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009245    lipid A biosynthetic process    The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.

 Visualization

(-) Interactive Views

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IMD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MYR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PLM  [ 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 ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2go3)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

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 ](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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2go3
    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_AQUAE | O67648
    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

(-) Analysis Tools

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_AQUAE | O67648
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LPXC_AQUAE | O67648: 1p42 1xxe 1yh8 1yhc 2go4 2ier 2ies 2j65 2jt2 2o3z 3p3c 3p76 4oze 4u3b 4u3d 5dro 5drp

(-) Related Entries Specified in the PDB File

1p42 ZINC-INHIBITED FORM
1yh8 LPXC-PALMITATE COMPLEX
1yhc LPXC-CACODYLATE COMPLEX