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(-) Description

Title :  CRYSTAL STRUCTURE OF AUTOTAXIN/ENPP2 WITH A COVALENT FRAGMENT
 
Authors :  M. G. Klein, R. Tjhen
Date :  07 Mar 16  (Deposition) - 15 Mar 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A
Keywords :  Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Lanier, D. C. Cole, Y. Istratiy, M. G. Klein, P. A. Schwartz, R. Tjhen A. Jennings, M. S. Hixon
Repurposing Suzuki Coupling Reagents As A Directed Fragment Library Targeting Serine Hydrolases And Related Enzymes.
J. Med. Chem. V. 60 5209 2017
PubMed-ID: 28564542  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01224

(-) Compounds

Molecule 1 - ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 2
    ChainsA
    EC Number3.1.4.39
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    GeneENPP2, NPPS2, PDNP2
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymE-NPP 2,AUTOTAXIN,EXTRACELLULAR LYSOPHOSPHOLIPASE D,LYSOPLD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 14)

Asymmetric/Biological Unit (7, 14)
No.NameCountTypeFull Name
16C11Ligand/Ion{2-[(3-CHLOROPHENYL)METHOXY]PHENYL}BORONIC ACID
2ACT1Ligand/IonACETATE ION
3BMA1Ligand/IonBETA-D-MANNOSE
4CA1Ligand/IonCALCIUM ION
5MAN3Ligand/IonALPHA-D-MANNOSE
6NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
7ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:171 , THR A:209 , ASP A:358 , HIS A:359 , 6C1 A:914binding site for residue ZN A 901
2AC2SOFTWAREASP A:311 , HIS A:315 , HIS A:474 , ACT A:913 , 6C1 A:914binding site for residue ZN A 902
3AC3SOFTWAREASP A:735 , ASN A:737 , ASN A:739 , LEU A:741 , ASP A:743 , HOH A:1213binding site for residue CA A 903
4AC4SOFTWAREASN A:230 , ASP A:311 , HIS A:315 , HIS A:474 , ZN A:902 , 6C1 A:914 , HOH A:1015 , HOH A:1162binding site for residue ACT A 913
5AC5SOFTWAREASP A:171 , THR A:209 , PHE A:210 , ASN A:230 , TYR A:306 , GLU A:308 , ASP A:311 , PHE A:312 , HIS A:359 , HIS A:474 , ZN A:901 , ZN A:902 , ACT A:913binding site for residue 6C1 A 914
6AC6SOFTWAREASN A:53 , SER A:55binding site for Poly-Saccharide residues NAG A 911 through NAG A 912 bound to ASN A 53
7AC7SOFTWARELEU A:376 , THR A:377 , ASN A:410 , ARG A:540 , HOH A:1050binding site for Mono-Saccharide NAG A 910 bound to ASN A 410
8AC8SOFTWARELEU A:220 , SER A:224 , HIS A:225 , HIS A:251 , ARG A:252 , TRP A:254 , GLY A:255 , GLY A:256 , ARG A:439 , PRO A:522 , ASN A:524 , LEU A:741 , HIS A:827 , HOH A:1002 , HOH A:1069 , HOH A:1071 , HOH A:1076 , HOH A:1100 , HOH A:1102 , HOH A:1132 , HOH A:1169 , HOH A:1179 , HOH A:1209binding site for Poly-Saccharide residues NAG A 904 through MAN A 909 bound to ASN A 524

(-) 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  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:70 -Pro A:71
2Tyr A:205 -Pro A:206
3Gln A:309 -Pro A:310

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5INH)

(-) 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:780
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...................................hhhhhhh........hhhhh..............hhhhhh....hhhhhhh...hhhhh..................eeeeeee..hhhhhhhhhhhhhhhhhhhhhheeeeeee.....hhhhhhhhhhhh.hhhhhh.....eee....eee....hhhhhhhhh...hhhhhhhhh.............hhhhhhhhhhhhhh........eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....ee.....eee.hhh..hhh.eeee...eeeeee........hhhhhhhhh........eeeee.hhhhhhhh.........eeeee....eee.hhhhh...........ee......hhhhheeeeee.......ee...ee..hhhhhhhhhh.............hhhhh............................hhhhhhh.....ee.....eeeee....eeeee.....eeeeeeee.......................hhhhh.hhhhhhhh...eeee..hhhhh.hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..........hhhhh.............eeeeeeeee.....hhhhh...eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhhee.......hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5inh A  53 NTSGSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIRVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDATFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLKLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRPKIPNNLKYDPKAIIANLTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDLHLLVERRWHVARKPLDVYKKPSGKCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTLPEEVSRPNYPGIMGCTCDGSTEERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWTYFQRVLVKKYASERNGVNVISGPIFDYNYNGLRDIEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCNSSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYE 855
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552   ||  585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 556| 569|                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  565  585                                                                                                                                                                                                                                                                              

   Legend:   → Mismatch (orange background)
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  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 5INH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

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
        ENPP2_MOUSE | Q9R1E63nkm 3nkn 3nko 3nkp 3nkq 3nkr 3wav 3waw 3wax 3way 4gtw 4gtx 4gty 4gtz 5hrt 5jvg 5lia

(-) Related Entries Specified in the PDB File

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