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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE AUTOTAXIN IN COMPLEX WITH A DNA APTAMER
 
Authors :  K. Kato, H. Nishimasu, J. Morita, R. Ishitani, O. Nureki
Date :  24 Jan 16  (Deposition) - 06 Apr 16  (Release) - 25 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phospholipase D, Dna Aptamer, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Kato, H. Ikeda, S. Miyakawa, S. Futakawa, Y. Nonaka, M. Fujiwara, S. Okudaira, K. Kano, J. Aoki, J. Morita, R. Ishitani, H. Nishimasu, Y. Nakamura, O. Nureki
Structural Basis For Specific Inhibition Of Autotaxin By A Dna Aptamer
Nat. Struct. Mol. Biol. V. 23 395 2016
PubMed-ID: 27043297  |  Reference-DOI: 10.1038/NSMB.3200

(-) Compounds

Molecule 1 - ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 2
    Chains: A
    EC Number: 3.1.4.39
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 36-862
    Gene: ENPP2, NPPS2, PDNP2
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: E-NPP 2,AUTOTAXIN,EXTRACELLULAR LYSOPHOSPHOLIPASE D,LYSOPLD
 
Molecule 2 - MODIFIED DNA (34-MER)
    Chains: B
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (12, 37)

Asymmetric/Biological Unit (12, 37)
No.NameCountTypeFull Name
1A2M3Mod. Nucleotide2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2BMA2Ligand/IonBETA-D-MANNOSE
3CA2Ligand/IonCALCIUM ION
4CL1Ligand/IonCHLORIDE ION
5GOL10Ligand/IonGLYCEROL
6K1Ligand/IonPOTASSIUM ION
7MAN5Ligand/IonALPHA-D-MANNOSE
8NA1Ligand/IonSODIUM ION
9NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
10OMC2Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
11OMG4Mod. NucleotideO2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
12ZN2Ligand/IonZINC ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:171 , THR A:209 , ASP A:358 , HIS A:359binding site for residue ZN A 912
02AC2SOFTWAREASP A:311 , HIS A:315 , HIS A:474 , HOH B:2206binding site for residue ZN A 913
03AC3SOFTWAREASP A:735 , ASN A:737 , ASN A:739 , LEU A:741 , ASP A:743 , HOH A:1155binding site for residue CA A 914
04AC4SOFTWAREASN A:797 , ASP A:798 , SER A:800 , SER A:803 , HOH A:1193 , HOH A:1298 , HOH A:1392binding site for residue NA A 915
05AC5SOFTWAREGLY A:229 , ASN A:230 , ARG A:391binding site for residue CL A 916
06AC6SOFTWAREASP A:147 , TYR A:665 , ASP A:668 , MET A:671 , HOH A:1136 , HOH A:1368binding site for residue K A 917
07AC7SOFTWAREGLU A:799 , SER A:800 , GLU A:813 , LEU A:814 , MET A:817 , HOH A:1004 , HOH A:1016binding site for residue GOL A 918
08AC8SOFTWARELEU A:593 , ALA A:777 , ASP A:778 , LYS A:779 , CYS A:780binding site for residue GOL A 919
09AC9SOFTWAREILE A:640 , GLY A:674 , PHE A:675 , PRO A:679 , TRP A:708 , THR A:709 , GLN A:712 , GOL A:925 , HOH A:1011binding site for residue GOL A 920
10AD1SOFTWAREGLN A:418 , PHE A:420 , LYS A:421 , LEU A:446 , GLU A:448 , GOL A:926binding site for residue GOL A 921
11AD2SOFTWAREGLU A:150 , ARG A:152 , ASP A:798 , HOH A:1350binding site for residue GOL A 922
12AD3SOFTWAREPRO A:544 , LEU A:600 , ARG A:823 , GLU A:826 , GLY A:830 , LEU A:831 , ASP A:832 , HOH A:1264 , HOH A:1271 , HOH A:1333binding site for residue GOL A 923
13AD4SOFTWARESER A:231 , MET A:232 , TYR A:233 , VAL A:385 , ARG A:393 , GLU A:441binding site for residue GOL A 924
14AD5SOFTWARETHR A:645 , TYR A:673 , LYS A:705 , GOL A:920binding site for residue GOL A 925
15AD6SOFTWAREGLU A:448 , ARG A:449 , ASP A:477 , GOL A:921binding site for residue GOL A 926
16AD7SOFTWAREASN A:737 , ASN A:739 , LEU A:741 , ILE A:744 , GLU A:747 , HOH A:1148 , HOH A:1155binding site for residue GOL A 927
17AD8SOFTWAREOMG B:2009 , DG B:2025 , HOH B:2207 , HOH B:2213 , HOH B:2214 , HOH B:2215 , HOH B:2218binding site for residue CA B 2101
18AD9SOFTWARELEU A:376 , THR A:377 , ASN A:410 , THR A:837 , SER A:838 , ARG A:839 , SER A:840 , HOH A:1087 , HOH A:1145 , HOH A:1283binding site for Poly-Saccharide residues NAG A 908 through MAN A 911 bound to ASN A 410
19AE1SOFTWARELEU A:220 , GLU A:223 , SER A:224 , GLY A:255 , ASN A:436 , ASN A:437 , PRO A:522 , ASN A:524 , HIS A:827 , HOH A:1025 , HOH A:1060 , HOH A:1063 , HOH A:1107 , HOH A:1113 , HOH A:1123 , HOH A:1129 , HOH A:1153 , HOH A:1174 , HOH A:1184 , HOH A:1241 , HOH A:1269 , HOH A:1334binding site for Poly-Saccharide residues NAG A 901 through MAN A 907 bound to ASN A 524
20AE2SOFTWAREARG A:244 , DC B:2013 , DA B:2016 , DT B:2023 , DT B:2024 , DG B:2025binding site for residues A2M B 2014 and OMG B 2015
21AE3SOFTWAREARG A:246 , DA B:2017 , DT B:2018 , DT B:2021binding site for residues A2M B 2019 and OMC B 2020
22AE4SOFTWAREDC B:2002 , DT B:2003 , DG B:2004 , DC B:2031 , OMG B:2034binding site for residues A2M B 2032 and OMG B 2033
23AE5SOFTWAREDC B:2001 , DC B:2002 , DT B:2003 , A2M B:2032binding site for residues OMG B 2033 and OMG B 2034

(-) SS Bonds  (15, 15)

Asymmetric/Biological Unit
No.Residues
1A:58 -A:75
2A:62 -A:93
3A:73 -A:86
4A:79 -A:85
5A:102 -A:119
6A:107 -A:137
7A:117 -A:130
8A:123 -A:129
9A:148 -A:194
10A:156 -A:350
11A:366 -A:468
12A:413 -A:801
13A:566 -A:662
14A:568 -A:647
15A:770 -A:780

(-) Cis Peptide Bonds  (2, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr A:205 -Pro A:206
2Gln A:309 -Pro A:310

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HRT)

(-) 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:786
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....................hhhhhh....hhhhhhh........hhhhh..............hhhhhh....hhhhhhhh..hhhhh..................eeeeeee..hhhhhhhhhhhhhhhhhhhhhheeeeeee.....hhhhhhhhhhhh.hhhhhh.....eee....eee....hhhhhhhhh...hhhhhhhhh.............hhhhhhhhhhhhhh........eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....ee.....eee.hhh..hhh.eeee...eeeeee........hhhhhhhhh........eeeee.hhhhhhhh.........eeeee....eee.................ee......hhhhheeeeee.......ee...ee..hhhhhhhhhh.............hhhhh.......................hhhhh........hhhhhh.....ee.....eeeee....eeeee.....eeeeeeee.........hhhhh.........hhhhh.hhhhhhhh...eeee..hhhhh.hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee............................eeeeeeeee.....hhhhh...eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhhee.......hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5hrt A   52 TNTSGSCKGRCFELQDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIRVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDATFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLKLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRPKIPNNLKYDPKAIIANLTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDLHLLVERRWHVARKPLDVYKKPSGKCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTLPEEVSRPNYPGIMYLQSDFDLGCTCDSTEERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWTYFQRVLVKKYASERNGVNVISGPIFDYNYNGLRDIEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCNSSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYESEI  858
                                    61    ||  76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566  ||   592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852      
                                         66|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              569|                                                                                                                                                                                                                                                                                
                                          72                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               586                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:DNA/RNA  Length:34
                                                                   
                5hrt B 2001 CCTGGAcGgAACCxgAATxcTTTTGGTCTCCxgg 2034
                                  2010   || 2020      2030 |||
                               2007-OMC  ||   ||        2032-A2M
                                 2009-OMG||   ||         2033-OMG
                                      2014-A2M||          2034-OMG
                                       2015-OMG|              
                                           2019-A2M           
                                            2020-OMC
   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 5HRT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)

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  5hrt
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  ENPP2_MOUSE | Q9R1E6
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  3.1.4.39
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 Related Entries

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UniProtKB/Swiss-Prot
        ENPP2_MOUSE | Q9R1E6: 3nkm 3nkn 3nko 3nkp 3nkq 3nkr 3wav 3waw 3wax 3way 4gtw 4gtx 4gty 4gtz 5inh 5jvg 5lia

(-) Related Entries Specified in the PDB File

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