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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF AUTOTAXIN WITH ORTHOVANADATE BOUND AS A TRIGONAL BIPYRAMIDAL INTERMEDIATE ANALOG

Authors :   J. Hausmann, R. P. Joosten, A. Perrakis

Date :   02 Mar 16 (Deposition) - 15 Jun 16 (Release) - 13 Jul 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Lysophosphatidylcholine, Somatomedin, Inflammation, Metastasis, Neuropathic Pain, Vascular Development, Neural Development (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Hausmann, W. J. Keune, A. L. Hipgrave Ederveen, L. Van Zeijl, R. P. Joosten, A. Perrakis
Structural Snapshots Of The Catalytic Cycle Of The Phosphodiesterase Autotaxin.
J. Struct. Biol. V. 195 199 2016
PubMed-ID: 27268273 | Reference-DOI: 10.1016/J.JSB.2016.06.002

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 Taxid	:	9606
	Gene	:	ENPP2, ATX, NPPS2
	Organism Common	:	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 (7, 15)

No.	Name	Count	Type	Full Name
1	5JK	1	Ligand/Ion	7ALPHA-HYDROXYCHOLESTEROL
2	6BR	1	Mod. Amino Acid	THREONINEVANADATE
3	CA	1	Ligand/Ion	CALCIUM ION
4	IOD	6	Ligand/Ion	IODIDE ION
5	NA	2	Ligand/Ion	SODIUM ION
6	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:214 , LYS A:248 , TRP A:254 , PRO A:258 , TRP A:260 , ILE A:261 , PHE A:274 , TRP A:275 , PHE A:777 , THR A:778	binding site for residue 5JK A 903
02	AC2	SOFTWARE	6BR A:209 , ASP A:311 , HIS A:315 , HIS A:474	binding site for residue ZN A 904
03	AC3	SOFTWARE	ASP A:171 , 6BR A:209 , ASP A:358 , HIS A:359	binding site for residue ZN A 905
04	AC4	SOFTWARE	ASP A:739 , ASN A:741 , ASP A:743 , LEU A:745 , ASP A:747 , HOH A:1062	binding site for residue CA A 906
05	AC5	SOFTWARE	ARG A:393	binding site for residue IOD A 907
06	AC6	SOFTWARE	HIS A:251	binding site for residue IOD A 908
07	AC7	SOFTWARE	ASN A:230	binding site for residue IOD A 909
08	AC8	SOFTWARE	ASP A:782	binding site for residue IOD A 910
09	AC9	SOFTWARE	LEU A:788 , GLU A:847	binding site for residue IOD A 911
10	AD1	SOFTWARE	TYR A:669 , ASP A:672 , MET A:675 , HOH A:1106 , HOH A:1145	binding site for residue NA A 913
11	AD2	SOFTWARE	ASN A:801 , SER A:804 , SER A:807	binding site for residue NA A 914
12	AD3	SOFTWARE	PRO A:522 , ASN A:524 , LEU A:745 , HOH A:1010 , HOH A:1033 , HOH A:1091	binding site for Poly-Saccharide residues NAG A 901 through NAG A 902 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: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 5IJS)

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

(no "Exon" information available for 5IJS)

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:784
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................hhhhhh.........hhhhh..............hhhhhh....hhhhhhh...hhhhh..................eeeeeee..hhhhhhhhhhhhhhhhhhhhhhee...ee.....hhhhhhhhhhhh.hhhhhh.....eee....eee....hhhhhhhhh...hhhhhhhhh.............hhhhhhhhhhhhhh........eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....ee.....eee.hhh..hhh.eeee...eeeeee........hhhhhhhhhh.......eeeee.hhhhhhhh.........eeeee....eee.......ee......hhhhh..eeee.......ee...ee..hhhhhhhhhh.............hhhhh.............................................hhhhhhh.....ee.....eeeee....eeeee....eeeeeeeee.........hhhhh...............hhhhhhhh...eeee..hhhhh...hhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..........hhhhh.............eeeeeeeee.....hhhhh...eeeeeeeee.............hhhhhhhhhhhhh..hhhhhhhhhhee.......hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ijs A  56 GSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIKVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKtFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSINNSKYDPKTIIAALTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRRWHVARKPCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPGIMYLQSEFDLGCTCEEFNKRLHTKGSTKERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWAYFQRVLVKKYASERNGVNVISGPIFDYNYDGLRDTEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCASSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYE 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  ||   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    
                                                                                                                                                                                   209-6BR                                                                                                                                                                                                                                                 457|                                                                                                 568|                                                                                                                                                                                                                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                                                                            468                                                                                                  579

Legend:		→ Mismatch	(orange background)
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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 '\|'

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

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		5JK	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		6BR	[ 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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	5ijs
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	3.1.4.39
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	ENPP2_RAT \| Q64610	:	2xr9 2xrg 5dlt 5dlv 5dlw 5ijq 5l0b 5l0e 5l0k 5lqq

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 15)

Sites (12, 12)

SS Bonds (14, 14)

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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