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 :  IN MESO IN SITU SERIAL X-RAY CRYSTALLOGRAPHY STRUCTURE OF DIACYLGLYCEROL KINASE, DGKA, AT 100 K
 
Authors :  C. -Y. Huang, N. Howe, V. Olieric, R. Warshamanage, K. Diederichs, M. Wa M. Caffrey
Date :  10 Aug 15  (Deposition) - 13 Jan 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Y. Huang, V. Olieric, P. Ma, N. Howe, L. Vogeley, X. Liu, R. Warshamanage, T. Weinert, E. Panepucci, B. Kobilka, K. Diederichs M. Wang, M. Caffrey
In Meso In Situ Serial X-Ray Crystallography Of Soluble And Membrane Proteins At Cryogenic Temperatures.
Acta Crystallogr D Struct V. 72 93 2016 Biol
PubMed-ID: 26894538  |  Reference-DOI: 10.1107/S2059798315021683

(-) Compounds

Molecule 1 - DIACYLGLYCEROL KINASE
    Chains: A, B, C, D, E, F
    EC Number: 2.7.1.107
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DGKA, B4042, JW4002
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Synonym: DAGK,DIGLYCERIDE KINASE,DGK

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
178M11Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
2ACT1Ligand/IonACETATE ION
3FLC1Ligand/IonCITRATE ANION
4ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
178M8Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
2ACT-1Ligand/IonACETATE ION
3FLC-1Ligand/IonCITRATE ANION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
178M3Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
2ACT1Ligand/IonACETATE ION
3FLC1Ligand/IonCITRATE ANION
4ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:22 , TRP A:25 , VAL A:38 , MET A:63 , MET A:66 , 78M A:202binding site for residue 78M A 201
02AC2SOFTWAREALA A:46 , ARG A:55 , 78M A:201 , 78M A:204 , HOH A:303 , 78M B:202binding site for residue 78M A 202
03AC3SOFTWAREARG A:9 , GLU B:34 , VAL B:65 , GLU B:69 , ALA B:108 , TRP B:112 , 78M B:202binding site for residue 78M A 203
04AC4SOFTWAREILE A:10 , ALA A:13 , ALA A:14 , SER A:17 , 78M A:202 , GLU B:69 , SER B:98 , VAL B:101binding site for residue 78M A 204
05AC5SOFTWARETRP B:47 , ASP B:49 , LEU D:102 , ILE D:105binding site for residue 78M B 201
06AC6SOFTWARE78M A:202 , 78M A:203 , ALA B:113 , TRP B:117binding site for residue 78M B 202
07AC7SOFTWARELEU A:116 , ALA B:46 , ARG B:55 , ILE C:114 , TRP C:117 , ALA D:37 , LEU D:40 , 78M D:204binding site for residue 78M B 203
08AC8SOFTWARELEU A:40 , TRP A:47 , GLU C:34 , ILE C:44 , MET C:66 , GLU C:69binding site for residue 78M C 201
09AC9SOFTWAREGLU D:28 , GLU D:76 , FLC D:202 , ACT D:203binding site for residue ZN D 201
10AD1SOFTWAREGLU D:76 , ZN D:201binding site for residue FLC D 202
11AD2SOFTWAREGLU D:28 , GLU D:69 , SER D:73 , GLU D:76 , ZN D:201binding site for residue ACT D 203
12AD3SOFTWAREGLN A:33 , GLU A:34 , CYS A:41 , 78M B:203 , TRP C:117 , ARG D:32 , GLN D:33 , VAL D:36binding site for residue 78M D 204
13AD4SOFTWAREGLY B:35 , VAL B:36 , TRP D:47 , ASP D:49 , PHE D:120binding site for residue 78M D 205
14AD5SOFTWAREALA A:30 , GLU A:34 , GLU A:69 , LEU D:21 , ARG D:22 , TRP D:25 , ILE D:26 , VAL D:42 , ILE E:103 , ILE E:110binding site for residue 78M D 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D56)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D56)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D56)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D56)

(-) Exons   (0, 0)

(no "Exon" information available for 5D56)

(-) 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:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 5d56 A   6 GFTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    15        25        35        45        55        65        75        85        95       105       115      


Chain B from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 5d56 B  24 AWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHF 120
                                    33        43        53        63        73        83        93       103       113       


Chain C from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 5d56 C  32 RQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    41        51        61        71        81        91       101       111       121


Chain D from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5d56 D  14 AGYSWKGLRAAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    23        33        43        53        63        73        83        93       103       113        


Chain E from PDB  Type:PROTEIN  Length:89
                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 5d56 E  33 QEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    42        52        62        72        82        92       102       112         


Chain F from PDB  Type:PROTEIN  Length:85
                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 5d56 F  34 EGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWS 118
                                    43        53        63        73        83        93       103       113
   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 5D56)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D56)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D56)

(-) Gene Ontology  (12, 12)

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
    78M  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FLC  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5d56)
 
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
[ 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 ](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
  5d56
    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 4ck0 4d2e 4up6 4uxw 4uxx 4uxz 4uyo 5d57 5d6i 5dwk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5D56)