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(-) Description

Title :  DIACYLGLYCEROL KINASE SOLVED BY MULTI CRYSTAL MULTI ORIENTATION NATIVE SAD
 
Authors :  T. Weinert, V. Olieric, A. D. Finke, D. Li, M. Caffrey, M. Wang
Date :  22 Sep 15  (Deposition) - 23 Mar 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,D  (1x)
Biol. Unit 2:  C,E,F  (1x)
Keywords :  Native Sad, Dagk, Multi Crystal, Multi Orientation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Olieric, T. Weinert, A. D. Finke, C. Anders, D. Li, N. Olieric, C. N. Borca, M. O. Steinmetz, M. Caffrey, M. Jinek, M. Wang
Data-Collection Strategy For Challenging Native Sad Phasing
Acta Crystallogr D Struct V. 72 421 2016 Biol
PubMed-ID: 26960129  |  Reference-DOI: 10.1107/S2059798315024110

(-) 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 Plasmid: PTRCHISB_DGKA_DELTA7
    Expression System Strain: WH1061
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2-122
    Gene: DGKA, B4042, JW4002
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: DAGK,DIGLYCERIDE KINASE,DGK

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB D  
Biological Unit 2 (1x):   C EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 17)

Asymmetric Unit (6, 17)
No.NameCountTypeFull Name
178M6Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
278N7Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
3ACT1Ligand/IonACETATE ION
4CIT1Ligand/IonCITRIC ACID
5NA1Ligand/IonSODIUM ION
6ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
178M2Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
278N7Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
3ACT-1Ligand/IonACETATE ION
4CIT-1Ligand/IonCITRIC ACID
5NA-1Ligand/IonSODIUM ION
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
178M4Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
278N-1Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
3ACT1Ligand/IonACETATE ION
4CIT1Ligand/IonCITRIC ACID
5NA-1Ligand/IonSODIUM ION
6ZN-1Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:72 , SER A:98 , VAL A:101 , LEU A:102 , ILE A:110 , 78N A:202 , ALA B:13 , ALA B:14 , SER B:17binding site for residue 78N A 201
02AC2SOFTWAREGLU A:34 , GLU A:69 , ALA A:108 , TRP A:112 , ALA A:113 , 78N A:201 , ILE B:10 , 78N B:203binding site for residue 78N A 202
03AC3SOFTWAREALA A:46 , ARG A:55 , 78M B:204 , GLN C:33 , VAL C:36 , LEU C:40 , 78M C:202 , ILE D:114 , TRP D:117 , SER D:118binding site for residue 78N A 203
04AC4SOFTWARETRP A:47 , LEU A:48 , LEU C:102 , VAL C:109 , ALA C:113binding site for residue 78M A 204
05AC5SOFTWARETRP B:18 , ARG B:22 , TRP B:25 , ILE B:26 , LEU B:39 , MET B:63 , 78N B:202binding site for residue 78N B 201
06AC6SOFTWAREARG B:55 , 78N B:201 , 78N B:203binding site for residue 78N B 202
07AC7SOFTWAREALA A:113 , ILE A:114 , TRP A:117 , 78N A:202 , VAL B:50 , ALA B:52 , ARG B:55 , 78N B:202binding site for residue 78N B 203
08AC8SOFTWARE78N A:203 , CYS B:41 , LEU B:48 , PHE B:123 , 78M C:202 , LEU D:102 , ILE D:105 , 78N D:201binding site for residue 78M B 204
09AC9SOFTWARELEU A:64 , ASP A:107 , SER B:60 , LEU B:64binding site for residue NA B 205
10AD1SOFTWAREILE B:113 , TRP B:120 , ALA C:46 , TRP C:47 , LEU C:48 , ARG C:55binding site for residue 78M C 201
11AD2SOFTWARE78N A:203 , GLN B:33 , GLU B:34 , 78M B:204 , TRP C:25 , ALA C:29 , ARG C:32 , GLN C:33 , VAL C:36 , HOH C:301 , TRP D:117binding site for residue 78M C 202
12AD3SOFTWAREALA B:30 , PHE B:31 , GLU B:34 , GLU B:72 , LEU B:105 , ILE B:108 , LEU C:21 , ARG C:22 , TRP C:25 , ILE C:26 , GLY C:35binding site for residue 78M C 203
13AD4SOFTWAREGLY A:35 , VAL A:36 , TRP C:47 , LEU C:48 , ASP C:49 , PHE C:120binding site for residue 78M C 204
14AD5SOFTWAREGLU C:28 , GLU C:76 , CIT C:206 , ACT C:207binding site for residue ZN C 205
15AD6SOFTWAREGLU C:76 , ZN C:205binding site for residue CIT C 206
16AD7SOFTWAREGLU C:28 , ALA C:30 , GLU C:69 , ZN C:205binding site for residue ACT C 207
17AD8SOFTWARELEU B:40 , TRP B:47 , 78M B:204 , GLU D:69 , ALA D:108binding site for residue 78N D 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DWK)

(-) 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:95
                                                                                                                               
               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
                 5dwk A  25 WINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSH 119
                                    34        44        54        64        74        84        94       104       114     


Chain B from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5dwk B   7 FTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHF 123
                                    16        26        36        46        56        66 ||     79      ||92       102       112       122 
                                                                                        68|            86|                                 
                                                                                         72             90                                 


Chain C from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 5dwk C  15 GYSWKGLRAAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHF 120
                                    24        34        44        54        64        74        84        94       104       114      


Chain D from PDB  Type:PROTEIN  Length:87
                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 5dwk D  34 EGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHF 120
                                    43        53        63        73        83        93       103       113       


Chain E from PDB  Type:PROTEIN  Length:84
                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 5dwk E  36 VAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSH 119
                                    45        55        65        75        85        95       105       115    


Chain F from PDB  Type:PROTEIN  Length:83
                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 5dwk F  35 GVAVLLCVVIAAWLDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSH 119
                                    44   ||   56        66        76        86        96       106       116   
                                        48|                                                                    
                                         51
   Legend:   → Mismatch (orange background)
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  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 5DWK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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        KDGL_ECOLI | P0ABN1: 2kdc 3ze3 3ze4 3ze5 4bpd 4brb 4brr 4cjz 4ck0 4d2e 4up6 4uxw 4uxx 4uxz 4uyo 5d56 5d57 5d6i

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