5DLW - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AUTOTAXIN (ENPP2) WITH TAUROURSODEOXYCHOLIC ACID (TUDCA) AND LYSOPHOSPHATIDIC ACID (LPA)

Authors :   W. J. Keune, T. Heidebrecht, R. P. Joosten, A. Perrakis

Date :   07 Sep 15 (Deposition) - 13 Apr 16 (Release) - 27 Apr 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Autotaxin, Enpp2, Lpa, Steroids, Bile Salts, Tudca, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. J. Keune, J. Hausmann, R. Bolier, D. Tolenaars, A. Kremer, T. Heidebrecht, R. P. Joosten, M. Sunkara, A. J. Morris, E. Matas-Rico W. H. Moolenaar, R. P. Oude Elferink, A. Perrakis
Steroid Binding To Autotaxin Links Bile Salts And Lysophosphatidic Acid Signalling.
Nat Commun V. 7 11248 2016
PubMed-ID: 27075612 | Reference-DOI: 10.1038/NCOMMS11248

Molecule 1 - ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 2
	Chains	:	A
	EC Number	:	3.1.4.39
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Fragment	:	UNP RESIDUES 36-862
	Gene	:	ENPP2, ATX, NPPS2
	Mutation	:	YES
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	E-NPP 2,AUTOTAXIN,EXTRACELLULAR LYSOPHOSPHOLIPASE D,LYSOPLD

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (11, 31)

No.	Name	Count	Type	Full Name
1	5D5	1	Ligand/Ion	2-{[(3ALPHA,5BETA,7ALPHA,8ALPHA,14BETA,17ALPHA)-3,7-DIHYDROXY-24-OXOCHOLAN-24-YL]AMINO}ETHANESULFONIC ACID
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	CA	1	Ligand/Ion	CALCIUM ION
4	GOL	2	Ligand/Ion	GLYCEROL
5	IOD	13	Ligand/Ion	IODIDE ION
6	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
7	NA	2	Ligand/Ion	SODIUM ION
8	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
9	NKP	1	Ligand/Ion	(2R)-2-HYDROXY-3-(PHOSPHONOOXY)PROPYL (9E)-OCTADEC-9-ENOATE
10	SCN	2	Ligand/Ion	THIOCYANATE ION
11	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (22, 22)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:171 , THR A:209 , ASP A:358 , HIS A:359 , NKP A:904	binding site for residue ZN A 901
02	AC2	SOFTWARE	ASP A:311 , HIS A:315 , HIS A:474 , NKP A:904	binding site for residue ZN A 902
03	AC3	SOFTWARE	ASP A:739 , ASN A:741 , ASP A:743 , LEU A:745 , ASP A:747 , HOH A:1209	binding site for residue CA A 903
04	AC4	SOFTWARE	ILE A:167 , ASP A:171 , THR A:209 , PHE A:210 , LEU A:213 , LEU A:216 , ASN A:230 , TRP A:254 , TYR A:306 , ASP A:311 , HIS A:315 , HIS A:359 , HIS A:474 , ZN A:901 , ZN A:902 , 5D5 A:905	binding site for residue NKP A 904
05	AC5	SOFTWARE	LEU A:78 , SER A:81 , TYR A:82 , ARG A:246 , LYS A:248 , PHE A:249 , HIS A:251 , TRP A:254 , TRP A:260 , VAL A:277 , GLU A:646 , HIS A:647 , NKP A:904 , HOH A:1017	binding site for residue 5D5 A 905
06	AC6	SOFTWARE	ASN A:801 , SER A:804 , SER A:807 , HOH A:1158 , HOH A:1244 , HOH A:1279	binding site for residue NA A 906
07	AC7	SOFTWARE	TYR A:669 , ASP A:672 , MET A:675 , HOH A:1240 , HOH A:1267 , HOH A:1280	binding site for residue NA A 907
08	AC8	SOFTWARE	ASN A:230 , ARG A:391	binding site for residue IOD A 915
09	AC9	SOFTWARE	ASP A:782 , GOL A:931	binding site for residue IOD A 917
10	AD1	SOFTWARE	HIS A:281 , SER A:307 , THR A:334	binding site for residue IOD A 919
11	AD2	SOFTWARE	CYS A:85	binding site for residue IOD A 920
12	AD3	SOFTWARE	LEU A:788	binding site for residue IOD A 921
13	AD4	SOFTWARE	MET A:232	binding site for residue IOD A 922
14	AD5	SOFTWARE	SER A:846	binding site for residue IOD A 923
15	AD6	SOFTWARE	HOH A:1016 , HOH A:1092	binding site for residue IOD A 924
16	AD7	SOFTWARE	GLN A:559	binding site for residue IOD A 925
17	AD8	SOFTWARE	GLY A:271	binding site for residue IOD A 926
18	AD9	SOFTWARE	LYS A:499	binding site for residue SCN A 928
19	AE1	SOFTWARE	TYR A:496 , ARG A:535	binding site for residue SCN A 929
20	AE2	SOFTWARE	GLY A:661 , SER A:663 , ASN A:665 , SER A:759 , SER A:760	binding site for residue GOL A 930
21	AE3	SOFTWARE	ARG A:594 , HIS A:595 , THR A:634 , SER A:636 , ASP A:782 , IOD A:917	binding site for residue GOL A 931
22	AE4	SOFTWARE	GLU A:223 , SER A:224 , HIS A:225 , GLY A:255 , GLY A:256 , ASN A:436 , ASN A:437 , PRO A:522 , ASN A:524 , LEU A:745 , HIS A:831 , HOH A:1011 , HOH A:1021 , HOH A:1028 , HOH A:1032 , HOH A:1047 , HOH A:1057 , HOH A:1059 , HOH A:1104 , HOH A:1239	binding site for Poly-Saccharide residues NAG A 908 through MAN A 914 bound to ASN A 524

Asymmetric/Biological Unit

No.	Residues
1	A:58	-	A:75
2	A:62	-	A:93
3	A:73	-	A:86
4	A:79	-	A:85
5	A:102	-	A:119
6	A:107	-	A:137
7	A:117	-	A:130
8	A:123	-	A:129
9	A:148	-	A:194
10	A:156	-	A:350
11	A:366	-	A:468
12	A:413	-	A:805
13	A:566	-	A:666
14	A:568	-	A:651
15	A:774	-	A:784

Asymmetric/Biological Unit

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

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

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

(no "Exon" information available for 5DLW)

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
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Chain A from PDB  Type:PROTEIN  Length:781
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhhh....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.......................hhhhh.........hhhhhh.....ee.....eeeee....eeeee.....eeeeeeee.........hhhhh.........hhhhh.hhhhhhhh...eeee..hhhhh.hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..........hhhhh.............eeeeeeeee.....hhhhh...eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhhee.......hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dlw A  56 GSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIKVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSYDPKTIIAALTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRRWHVARKPLDVYKKPSGKCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPGIMYLQSEFDLGCTCDDSTKERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWAYFQRVLVKKYASERNGVNVISGPIFDYNYDGLRDTEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCASSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYES 860
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395||     410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570|      599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859 
                                                                                                                                                                                                                                                                                                                                                                              396|                                                                                                                                                                     570|                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                               402                                                                                                                                                                      590

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5DLW)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gln A:309 - Pro A:310	[ RasMol ]
		Pro A:70 - Pro A:71	[ RasMol ]
		Tyr A:205 - Pro A:206	[ RasMol ]

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	5dlw
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	ENPP2_RAT \| Q64610
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	3.1.4.39
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	ENPP2_RAT \| Q64610	:	2xr9 2xrg 5dlt 5dlv 5ijq 5ijs 5l0b 5l0e 5l0k 5lqq

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (11, 31)

Sites (22, 22)

SS Bonds (15, 15)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (36, 36)

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