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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE INTEGRAL MEMBRANE DIACYLGLYCEROL KINASE - FORM 2
 
Authors :  D. Li, J. A. Lyons, L. Vogeley, D. Aragao, M. Caffrey
Date :  23 Dec 13  (Deposition) - 28 Jan 15  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.92
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transferase, Beta- Gama-Methyleneadenosine 5'-Triphosphate, Dgka, In Meso Crystallisation, Lcp, Lipid Cubic Phase, Lipidic Mesophase, Lipid Metabolism, Membrane Protein, Microcrystal, Monoacylglycerol, Monoolein, 9. 9 Mag, Soaking, Thermostable Mutant (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Li, M. Caffrey
Crystal Structure Of The Integral Membrane Diacylglycerol Kinase With Zn-Amppcp Bound And Its Catalytic Mechanism
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIACYLGLYCEROL KINASE
    Atcc: 29425
    Chains: A, B, C
    EC Number: 2.7.1.107
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCHISB-DGKA-DELTA 4
    Expression System Strain: WH1061
    Expression System Taxid: 562
    Expression System Vector: PTRCHISB
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: DAGK, DIGLYCERIDE KINASE, DGK, DIACYLGLYCEROL KINASE - DELTA 4

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2OLC2Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
3ZN2Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU C:28 , GLU C:76 , ACP C:1122BINDING SITE FOR RESIDUE ZN C1120
2AC2SOFTWAREGLU C:76 , ACP C:1122BINDING SITE FOR RESIDUE ZN C1121
3AC3SOFTWAREARG B:9 , LYS B:12 , TYR B:16 , GLU C:28 , GLU C:76 , GLU C:85 , TYR C:86 , HIS C:87 , SER C:90 , GLY C:91 , LYS C:94 , ASP C:95 , ZN C:1120 , ZN C:1121BINDING SITE FOR RESIDUE ACP C1122
4AC4SOFTWAREALA A:13 , ALA A:14 , SER A:17 , ILE B:44 , GLU B:69 , ASN B:72 , LEU B:102 , ILE B:105BINDING SITE FOR RESIDUE OLC B1121
5AC5SOFTWAREILE A:10 , TRP A:117 , GLN B:33 , GLU B:34 , ALA B:37 , VAL B:62 , ILE B:105 , CYS B:113BINDING SITE FOR RESIDUE OLC B1122

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CK0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CK0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CK0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CK0)

(-) Exons   (0, 0)

(no "Exon" information available for 4CK0)

(-) Sequences/Alignments

Asymmetric/Biological 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:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4ck0 A   7 FTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLAVVIACWLDVDACTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWCILLWSHF 120
                                    16        26        36        46        56        66        76        86        96       106       116    


Chain B from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4ck0 B   7 FTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLAVVIACWLDVDACTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWCILLWSHF 120
                                    16        26        36        46        56        66        76        86        96       106       116    


Chain C from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 4ck0 C  16 YSWKGLRAAWINEAAFRQEGVAVLLAVVIACWLDVDACTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWCILLWSH 119
                                    25        35        45        55        65        75        85        95       105       115
   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 4CK0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CK0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CK0)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    ACP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OLC  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ck0)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4ck0
    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
  KDGL_ECOLI | P0ABN1
    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)
  2.7.1.107
    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
  KDGL_ECOLI | P0ABN1
    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
        KDGL_ECOLI | P0ABN1: 2kdc 3ze3 3ze4 3ze5 4bpd 4brb 4brr 4cjz 4d2e 4up6 4uxw 4uxx 4uxz 4uyo 5d56 5d57 5d6i 5dwk

(-) Related Entries Specified in the PDB File

4cjz CRYSTAL STRUCTURE OF THE INTEGRAL MEMBRANE DIACYLGLYCEROL KINASE DGKA-9.9, DELTA 4