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(-) Description

Title :  IN MESO X-RAY CRYSTALLOGRAPHY STRUCTURE OF DIACYLGLYCEROL KINASE, DGKA, AT 100 K
 
Authors :  C. -Y. Huang, N. Howe, V. Olieric, M. Wang, 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  (1, 16)

Asymmetric Unit (1, 16)
No.NameCountTypeFull Name
178M16Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
178M12Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
178M4Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:46 , TRP A:47 , ASP A:49 , 78M A:205binding site for residue 78M A 201
02AC2SOFTWAREILE A:44 , PHE A:120 , 78M B:203 , ILE C:105 , VAL C:109 , 78M C:201 , LEU D:39 , 78M D:204binding site for residue 78M A 202
03AC3SOFTWAREARG A:92 , ASP A:95 , ILE A:103 , TRP D:18binding site for residue 78M A 203
04AC4SOFTWARETRP A:18 , ARG A:22 , TRP A:25 , VAL A:38 , LEU A:39 , VAL A:42 , MET A:63 , 78M A:205 , ILE B:103 , ILE B:110binding site for residue 78M A 204
05AC5SOFTWAREALA A:46 , ARG A:55 , 78M A:201 , 78M A:204 , 78M A:206 , HOH A:303 , ILE B:106 , 78M B:201binding site for residue 78M A 205
06AC6SOFTWAREILE A:10 , ALA A:13 , ALA A:14 , SER A:17 , 78M A:205 , GLU B:69 , SER B:98 , VAL B:101 , 78M B:201 , 78M B:202binding site for residue 78M A 206
07AC7SOFTWARE78M A:205 , 78M A:206 , TRP B:117 , 78M B:202binding site for residue 78M B 201
08AC8SOFTWAREARG A:9 , 78M A:206 , GLU B:34 , VAL B:62 , VAL B:65 , GLU B:69 , ILE B:105 , ALA B:108 , TRP B:112 , ALA B:113 , 78M B:201binding site for residue 78M B 202
09AC9SOFTWARELEU A:116 , 78M A:202 , ALA B:46 , ARG B:55 , HOH B:303 , ILE C:114 , VAL D:36 , ALA D:37 , 78M D:204binding site for residue 78M B 203
10AD1SOFTWARETRP B:47 , LEU B:48 , ASP B:49 , HOH B:301 , HOH B:302 , LEU D:102 , ILE D:105binding site for residue 78M B 204
11AD2SOFTWARETRP A:47 , 78M A:202 , ALA C:37 , CYS C:41 , ILE C:105 , 78M C:202binding site for residue 78M C 201
12AD3SOFTWARELEU A:40 , TRP A:47 , GLU C:34 , GLU C:69 , TRP C:112 , 78M C:201binding site for residue 78M C 202
13AD4SOFTWARETRP A:117 , ALA D:46 , ARG D:55 , ILE D:59 , 78M D:202 , ILE E:110 , TRP E:117binding site for residue 78M D 201
14AD5SOFTWAREALA A:30 , PHE A:31 , GLU A:34 , GLU A:69 , LEU A:102 , ILE A:105 , LEU D:21 , ARG D:22 , TRP D:25 , ILE D:26 , MET D:63 , 78M D:201 , HOH D:301 , ILE E:103 , ILE E:110binding site for residue 78M D 202
15AD6SOFTWAREILE B:26 , ARG B:32 , GLY B:35 , VAL B:36 , MET B:63 , TRP D:47 , LEU D:48 , ASP D:49 , PHE D:120binding site for residue 78M D 203
16AD7SOFTWAREGLN A:33 , GLU A:34 , ALA A:37 , CYS A:41 , 78M A:202 , 78M B:203 , TRP C:117 , ARG D:32 , GLN D:33 , VAL D:36 , HOH D:301 , HOH D:304binding site for residue 78M D 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D57)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D57)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D57)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D57)

(-) Exons   (0, 0)

(no "Exon" information available for 5D57)

(-) 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..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 5d57 A   6 GFTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    15        25        35        45        55        65        75        85        95       105       115      


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 5d57 B  23 AAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    32        42        52        62        72        82        92       102       112         


Chain C from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 5d57 C  30 AFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    39        49        59        69        79        89        99       109       119  


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
                 5d57 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 .hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 5d57 E  33 QEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    42        52        62        72        82        92       102       112         


Chain F from PDB  Type:PROTEIN  Length:88
                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 5d57 F  34 EGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    43        53        63        73        83        93       103       113
   Legend:   → Mismatch (orange background)
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    → 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 5D57)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D57)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D57)

(-) Gene Ontology  (12, 12)

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 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 5d56 5d6i 5dwk

(-) Related Entries Specified in the PDB File

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