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

(-) Description

Title :  HUMAN LTC4 SYNTHASE IN COMPLEX WITH PRODUCT ANALOGS - IMPLICATIONS FOR ENZYME CATALYSIS
 
Authors :  D. Niegowski, A. Rinaldo-Matthis, J. Z. Haeggstrom
Date :  14 Feb 13  (Deposition) - 01 Jan 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  A  (12x)
Keywords :  Leukotriene C4 Synthase, Product Analogs, Lipid Biosynthesis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Niegowski, T. Kleinschmidt, U. Olsson, S. Ahmad, A. Rinaldo-Matthis, J. Z. Haeggstrom
Crystal Structures Of Leukotriene C4 Synthase In Complex With Product Analogs: Implications For The Enzyme Mechanism
J. Biol. Chem. V. 289 5199 2014
PubMed-ID: 24366866  |  Reference-DOI: 10.1074/JBC.M113.534628

(-) Compounds

Molecule 1 - LEUKOTRIENE C4 SYNTHASE
    ChainsA
    EC Number4.4.1.20
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System Taxid4922
    GeneLTC4S
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLTC4 SYNTHASE, LEUKOTRIENE-C(4) SYNTHASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A
Biological Unit 2 (12x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
11JP1Ligand/IonD-GAMMA-GLUTAMYL-(Z)-N-(CARBOXYMETHYLIDENE)-S-[(2R)-2-HYDROXY-4-PHENYLBUTYL]-L-CYSTEINAMIDE
2NI1Ligand/IonNICKEL (II) ION
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
11JP3Ligand/IonD-GAMMA-GLUTAMYL-(Z)-N-(CARBOXYMETHYLIDENE)-S-[(2R)-2-HYDROXY-4-PHENYLBUTYL]-L-CYSTEINAMIDE
2NI-1Ligand/IonNICKEL (II) ION
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 24)
No.NameCountTypeFull Name
11JP12Ligand/IonD-GAMMA-GLUTAMYL-(Z)-N-(CARBOXYMETHYLIDENE)-S-[(2R)-2-HYDROXY-4-PHENYLBUTYL]-L-CYSTEINAMIDE
2NI-1Ligand/IonNICKEL (II) ION
3SO412Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:1BINDING SITE FOR RESIDUE NI A 201
2AC2SOFTWAREARG A:48 , SER A:100 , ALA A:101 , GLN A:102BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWAREALA A:20 , SER A:23 , LEU A:24 , VAL A:26 , ILE A:27 , ARG A:30 , TYR A:50 , GLN A:53 , ASN A:55 , GLU A:58 , TYR A:59 , TYR A:93 , ARG A:104 , LEU A:108 , LEU A:115 , TRP A:116 , VAL A:119BINDING SITE FOR RESIDUE 1JP A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J7Y)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Pro A:37 -Pro A:38
2Leu A:143 -Arg A:144
3Arg A:144 -Thr A:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J7Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J7Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4J7Y)

(-) 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:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j7y A  -1 HHHKDEVALLAAVTLLGVLLQAYFSLQVISARRAFRVSPPLTTGPPEFERVYRAQVNCSEYFPLFLATLWVAGIFFHEGAAALCGLVYLFARLRYFQGYARSAQLRLAPLYASARALWLLVALAALGLLAHFLPAALRAALLGRLRTA 150
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138      ||
                                                                                                                                                                            145|
                                                                                                                                                                             150

   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 4J7Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J7Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J7Y)

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)

 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
    1JP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:144 - Thr A:145   [ RasMol ]  
    Leu A:143 - Arg A:144   [ RasMol ]  
    Pro A:37 - Pro A:38   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4j7y
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LTC4S_HUMAN | Q16873
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.4.1.20
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  LTC4S_HUMAN | Q16873
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LTC4S_HUMAN | Q168732pno 2uuh 2uui 3b29 3hkk 3leo 3pcv 4bpm 4j7t 4jc7 4jcz 4jrz 4wab 5hv9

(-) Related Entries Specified in the PDB File

2uuh 2uui 4j7t