5LQQ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF AUTOTAXIN (ENPP2) WITH LM350

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

Date :   17 Aug 16 (Deposition) - 28 Dec 16 (Release) - 08 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A

Keywords :   Autotaxin, Enpp2, Inhibitor, Lm350, Ectonucleotide Pyrophosphatase/Phosphodiesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. M. Miller, W. J. Keune, D. Castagna, L. C. Young, E. L. Duffy, F. Potjewyd, F. Salgado-Polo, P. Engel Garcia, D. Semaan, J. M. Pritchard, A. Perrakis, S. J. Macdonald, C. Jamieson, A. J. Watso
Structure-Activity Relationships Of Small Molecule Autotaxi Inhibitors With A Discrete Binding Mode.
J. Med. Chem. V. 60 722 2017
PubMed-ID: 27982588 | Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01597

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 Organ	:	KIDNEY
	Expression System Plasmid	:	PCDNA5
	Expression System Taxid	:	9606
	Expression System Variant	:	FLP-IN
	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 (8, 23)

No.	Name	Count	Type	Full Name
1	72P	1	Ligand/Ion	3-(6-CHLORANYL-2-METHYL-1-PHENYL-INDOL-3-YL)SULFANYLBENZOIC ACID
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	CA	1	Ligand/Ion	CALCIUM ION
4	IOD	10	Ligand/Ion	IODIDE ION
5	MAN	5	Ligand/Ion	ALPHA-D-MANNOSE
6	NA	1	Ligand/Ion	SODIUM ION
7	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:311 , HIS A:315 , HIS A:474 , HOH A:1073	binding site for residue ZN A 909
02	AC2	SOFTWARE	ASP A:171 , THR A:209 , ASP A:311 , ASP A:358 , HIS A:359	binding site for residue ZN A 910
03	AC3	SOFTWARE	ASP A:739 , ASN A:741 , ASP A:743 , LEU A:745 , ASP A:747 , HOH A:1037	binding site for residue CA A 911
04	AC4	SOFTWARE	ASN A:230	binding site for residue IOD A 912
05	AC5	SOFTWARE	HIS A:281 , SER A:307 , THR A:334	binding site for residue IOD A 914
06	AC6	SOFTWARE	ASP A:782	binding site for residue IOD A 916
07	AC7	SOFTWARE	GLU A:847	binding site for residue IOD A 917
08	AC8	SOFTWARE	SER A:846	binding site for residue IOD A 919
09	AC9	SOFTWARE	SER A:81 , LYS A:248 , PHE A:249 , HIS A:251 , TRP A:254 , TRP A:260 , PHE A:274 , TRP A:275 , VAL A:277	binding site for residue 72P A 922
10	AD1	SOFTWARE	TYR A:669 , ASP A:672 , LYS A:673 , MET A:675 , HOH A:1042 , HOH A:1074	binding site for residue NA A 923
11	AD2	SOFTWARE	LEU A:220 , GLU A:223 , SER A:224 , GLY A:255 , GLY A:256 , GLN A:257 , ASN A:436 , ASN A:437 , PRO A:522 , ASN A:524 , LEU A:745 , HIS A:831 , HOH A:1007 , HOH A:1010 , HOH A:1020 , HOH A:1022 , HOH A:1023	binding site for Poly-Saccharide residues NAG A 901 through MAN A 908 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:413	-	A:805
12	A:566	-	A:666
13	A:568	-	A:651
14	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 5LQQ)

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

(no "Exon" information available for 5LQQ)

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:775
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................hhhhhhh........hhhhh..............hhhhhh....hhhhhhh...hhhhh..................eeeeeee..hhhhhhhhhhhhhhhhhhhhhhee...ee.....hhhhhhhhhhhh.hhhhhh.....eee....eee....hhhhhhhhh...hhhhhhhhh.............hhhhhhhhhhhhhh........eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....ee.....eee.hhh......eeee...eeeeee........hhhhhhhhhh.......eeeee.hhhhhhhh.........eeeee....eee.......ee......hhhhh..eeee.......ee...ee..hhhhhhhhhh.............hhhhh.......................hhhhh.......hhhhhhhh.....ee.....eeeee....eeeee....eeeeeeeee.........hhhhh...............hhhhhhhh...eeee..hhhhh....hhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee............................eeeeeeeee.....hhhhh...eeeeeeeee.............hhhhhhhhhhhhh..hhhhhhhhhhee.......hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lqq A  56 GSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIKVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSINNSKYDPKTIIAALTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRRWHVARKPLDFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPGIMYLQSEFDLGCTCKGSTKERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWAYFQRVLVKKYASERNGVNVISGPIFDYNYDGLRDTEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCASSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYE 859
                                    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       405       415       425       435       445       455   ||  475       485       495       505       515       525       535       545       555       565  ||   594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854     
                                                                                                                                                                                                                                                                                                                                                                                                                                             459|                                                                                               568|                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                                                                                                                                                                                                              470                                                                                                588

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 '\|'

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

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		72P	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		BMA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		IOD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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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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	5lqq
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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	ENPP2_RAT \| Q64610
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	3.1.4.39
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	ENPP2_RAT \| Q64610
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	ENPP2_RAT \| Q64610	:	2xr9 2xrg 5dlt 5dlv 5dlw 5ijq 5ijs 5l0b 5l0e 5l0k

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 23)

Sites (11, 11)

SS Bonds (14, 14)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (36, 36)

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