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(-) Description

Title :  STRUCTURE OF DELTA4-DGKA WITH AMPPCP IN 9.9 MAG
 
Authors :  D. Li, L. Vogeley, M. Caffrey
Date :  27 Aug 14  (Deposition) - 30 Sep 15  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transferase, Atp Analogue, Dgka, Diacylglyerol Kinase, In Meso Crystallization, Lipid Cubic Phase, Lipidic Cubic Phase, Lipid Mesophase, Lipidic Mesophase, Membrane Protein, 9. 9 Mag, Monoacylglycerol, Non- Hydrolyzable Atp Analogue, Nucleotide Analogue (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Li, P. J. Stansfeld, M. S. P. Sansom, A. Keogh, L. Vogeley, N. Howe, J. A. Lyons, D. Aragao, P. Fromme, R. Fromme, S. Basu, I. Grotjohann, C. Kupitz, K. Rendek, U. Weierstall, N. A. Zatsepin, V. Cherezov, W. Liu, S. Bandaru, N. J. English, C. Gati, A. Barty, O. Yefanov, H. N. Chapman, K. Diederichs, M. Messerschmidt, S. Boutet, G. J. Williams, M. Marvin Seibert, M. Caffrey
Ternary Structure Reveals Mechanism Of A Membrane Diacylglycerol Kinase.
Nat. Commun. V. 6 10140 2015
PubMed-ID: 26673816  |  Reference-DOI: 10.1038/NCOMMS10140

(-) 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-DELTA4
    Expression System Strain: WH1061
    Expression System Taxid: 562
    Expression System Vector: PTRCHISB
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Synonym: DAGK, DIGLYCERIDE KINASE, DGK

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 17)

Asymmetric/Biological Unit (7, 17)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2ACT3Ligand/IonACETATE ION
3CL1Ligand/IonCHLORIDE ION
4MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NA3Ligand/IonSODIUM ION
6OLC6Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
7ZN2Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU C:28 , GLU C:76 , ACP C:1123BINDING SITE FOR RESIDUE ZN C1121
02AC2SOFTWAREGLU C:76 , ACP C:1123BINDING SITE FOR RESIDUE ZN C1122
03AC3SOFTWAREASN A:27 , ALA A:29 , ARG A:32BINDING SITE FOR RESIDUE CL A1121
04AC4SOFTWAREARG B:9 , TYR B:16 , HOH B:2001 , GLU C:28 , ASN C:72 , 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:1121 , ZN C:1122 , OLC C:1125 , HOH C:2004BINDING SITE FOR RESIDUE ACP C1123
05AC5SOFTWAREARG A:81 , GLU B:88 , LEU B:89 , SER B:90 , ARG B:92BINDING SITE FOR RESIDUE MPD B1122
06AC6SOFTWAREGLU A:28 , GLU A:76 , ACT A:1123BINDING SITE FOR RESIDUE NA A1122
07AC7SOFTWAREGLU A:28 , GLU A:76 , NA A:1122BINDING SITE FOR RESIDUE ACT A1123
08AC8SOFTWAREARG B:9 , ILE B:10 , ALA C:30 , GLN C:33 , GLU C:34 , CYS C:113 , OLC C:1125BINDING SITE FOR RESIDUE OLC C1124
09AC9SOFTWARESER A:17 , CYS A:113 , TRP A:117 , GLU B:34 , ALA B:37 , ILE B:44 , GLU B:69 , ASN B:72 , LEU B:102 , OLC B:1124BINDING SITE FOR RESIDUE OLC B1123
10BC1SOFTWAREILE A:10 , TRP A:117 , GLN B:33 , GLU B:34 , TRP B:112 , TRP B:117 , OLC B:1123BINDING SITE FOR RESIDUE OLC B1124
11BC2SOFTWARETRP A:18 , TRP A:25 , ILE A:26BINDING SITE FOR RESIDUE OLC A1124
12BC3SOFTWAREGLN A:33 , GLU A:34 , ALA A:37 , ILE A:44 , VAL A:62 , ALA A:108 , VAL A:109 , TRP A:112 , LEU A:116 , LEU B:39 , LEU B:40 , TRP B:47BINDING SITE FOR RESIDUE OLC A1125
13BC4SOFTWAREALA B:13 , SER B:17 , GLU C:69 , ASN C:72 , SER C:98 , LEU C:102 , ILE C:106 , VAL C:109 , ACP C:1123 , OLC C:1124BINDING SITE FOR RESIDUE OLC C1125
14BC5SOFTWAREGLU B:76 , GLY B:83 , SER B:84 , GLU B:85 , TYR B:86 , HIS B:87 , LYS B:94 , NA B:1126BINDING SITE FOR RESIDUE ACT B1125
15BC6SOFTWAREGLU B:28 , GLU B:76 , ACT B:1125BINDING SITE FOR RESIDUE NA B1126
16BC7SOFTWAREGLU C:88BINDING SITE FOR RESIDUE NA C1126
17BC8SOFTWAREHIS A:119BINDING SITE FOR RESIDUE ACT A1126

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UXX)

(-) 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:115
                                                                                                                                                   
               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
                 4uxx A   7 FTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLAVVIACWLDVDACTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWCILLWSHFG 121
                                    16        26        36        46        56        66        76        86        96       106       116     


Chain B from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4uxx B   6 GFTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLAVVIACWLDVDACTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWCILLWSHFG 121
                                    15        25        35        45        55        65        75        85        95       105       115      


Chain C from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               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
                 4uxx C  16 YSWKGLRAAWINEAAFRQEGVAVLLAVVIACWLDVDACTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWCILLWSHF 120
                                    25        35        45        55        65        75        85        95       105       115
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4UXX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4uxz 4uyo 5d56 5d57 5d6i 5dwk

(-) Related Entries Specified in the PDB File

4uxw STRUCTURE OF DELTA4-DGKA-APO IN 9.9 MAG
4uxz STRUCTURE OF DELTA7-DGKA-SYN IN 7.9 MAG TO 2.18 ANGSTROM RESOLUTION