4GTW - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MOUSE ENPP1 IN COMPLEX WITH AMP

Authors :   K. Kato, H. Nishimasu, R. Ishitani, O. Nureki

Date :   29 Aug 12 (Deposition) - 07 Nov 12 (Release) - 07 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Bone Mineralization, Phosphodiesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Kato, H. Nishimasu, S. Okudaira, E. Mihara, R. Ishitani, J. Takagi, J. Aoki, O. Nureki
Crystal Structure Of Enpp1, An Extracellular Glycoprotein Involved In Bone Mineralization And Insulin Signaling.
Proc. Natl. Acad. Sci. Usa V. 109 16876 2012
PubMed-ID: 23027977 | Reference-DOI: 10.1073/PNAS.1208017109

Molecule 1 - ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 2, ALKALINE PHOSPHODIESTERASE I
	Chains	:	A, B
	EC Number	:	3.1.4.39
	Engineered	:	YES
	Expression System Plasmid	:	MODIFIED PCDNA3.1
	Expression System Strain	:	HEK293S GNT1-
	Expression System Vector Type	:	PLASMID
	Gene	:	ENPP2, NPPS2, PDNP2, ENPP1, MCG_9001
	Mutation	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	THE FUSION PROTEIN OF ENPP2 (UNP RESIDUES 51-59) AND ENPP1 (UNP RESIDUES 92-905)
	Synonym	:	E-NPP 2, AUTOTAXIN, EXTRACELLULAR LYSOPHOSPHOLIPASE D, LYSOPLD, ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE 1, ISOFORM CRA_D

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (7, 44)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	CA	2	Ligand/Ion	CALCIUM ION
4	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
5	MSE	24	Mod. Amino Acid	SELENOMETHIONINE
6	NAG	8	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (5, 21)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	CA	-1	Ligand/Ion	CALCIUM ION
4	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
5	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
6	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 17)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	BMA	-1	Ligand/Ion	BETA-D-MANNOSE
3	CA	-1	Ligand/Ion	CALCIUM ION
4	MAN	-1	Ligand/Ion	ALPHA-D-MANNOSE
5	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
6	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MAN A:1005	BINDING SITE FOR RESIDUE MAN A 1006
02	AC2	SOFTWARE	ASN A:267	BINDING SITE FOR RESIDUE NAG A 1007
03	AC3	SOFTWARE	ASN A:323 , SER A:325 , VAL A:326 , HOH A:1129 , HOH A:1161	BINDING SITE FOR RESIDUE NAG A 1008
04	AC4	SOFTWARE	ASP A:200 , THR A:238 , PHE A:239 , ASN A:259 , LEU A:272 , LYS A:277 , TYR A:322 , TYR A:353 , ASP A:358 , HIS A:362 , HIS A:406 , HIS A:517 , ZN A:1010 , ZN A:1011 , HOH A:1169	BINDING SITE FOR RESIDUE AMP A 1009
05	AC5	SOFTWARE	ASP A:200 , THR A:238 , ASP A:358 , ASP A:405 , HIS A:406 , AMP A:1009	BINDING SITE FOR RESIDUE ZN A 1010
06	AC6	SOFTWARE	ASP A:358 , HIS A:362 , HIS A:517 , AMP A:1009	BINDING SITE FOR RESIDUE ZN A 1011
07	AC7	SOFTWARE	ASP A:780 , ASP A:782 , ASP A:784 , ARG A:786 , TYR A:787 , ASP A:788	BINDING SITE FOR RESIDUE CA A 1012
08	AC8	SOFTWARE	ASN B:267	BINDING SITE FOR RESIDUE NAG B 1003
09	AC9	SOFTWARE	ASN B:323 , VAL B:326	BINDING SITE FOR RESIDUE NAG B 1004
10	BC1	SOFTWARE	ASP B:200 , THR B:238 , PHE B:239 , ASN B:259 , LEU B:272 , LYS B:277 , TYR B:322 , TYR B:353 , GLU B:355 , ASP B:358 , HIS B:362 , HIS B:406 , HIS B:517 , ZN B:1006 , ZN B:1007 , HOH B:1149	BINDING SITE FOR RESIDUE AMP B 1005
11	BC2	SOFTWARE	ASP B:200 , THR B:238 , ASP B:405 , HIS B:406 , AMP B:1005	BINDING SITE FOR RESIDUE ZN B 1006
12	BC3	SOFTWARE	ASP B:358 , HIS B:362 , HIS B:517 , AMP B:1005	BINDING SITE FOR RESIDUE ZN B 1007
13	BC4	SOFTWARE	ASP B:780 , ASP B:782 , ASP B:784 , ARG B:786 , TYR B:787 , ASP B:788	BINDING SITE FOR RESIDUE CA B 1008
14	BC5	SOFTWARE	LEU A:249 , SER A:253 , PRO A:565 , ASN A:567 , ASP A:784 , ARG A:786 , LEU A:874 , MAN A:1006 , HOH A:1154 , HOH A:1157 , SER B:802	BINDING SITE FOR LINKED RESIDUES A 1001 to 1005
15	BC6	SOFTWARE	LEU B:249 , PRO B:565 , ASN B:567 , ASP B:784 , ARG B:786 , LEU B:874	BINDING SITE FOR LINKED RESIDUES B 1001 to 1002

Asymmetric Unit

No.	Residues
1	A:177	-	A:223
2	A:185	-	A:397
3	A:413	-	A:512
4	A:462	-	A:848
5	A:596	-	A:652
6	A:607	-	A:706
7	A:609	-	A:691
8	A:818	-	A:828
9	B:177	-	B:223
10	B:185	-	B:397
11	B:413	-	B:512
12	B:462	-	B:848
13	B:596	-	B:652
14	B:607	-	B:706
15	B:609	-	B:691
16	B:818	-	B:828

Asymmetric Unit

No.	Residues
1	Tyr A:234	-	Pro A:235
2	Glu A:356	-	Pro A:357
3	Val A:444	-	Pro A:445
4	Thr A:601	-	Ser A:602
5	Lys A:647	-	Gln A:648
6	Tyr B:234	-	Pro B:235
7	Glu B:356	-	Pro B:357
8	Val B:444	-	Pro B:445
9	Lys B:647	-	Gln B:648

(no "SAP(SNP)/Variant" information available for 4GTW)

(no "PROSITE Motif" information available for 4GTW)

(no "Exon" information available for 4GTW)

Asymmetric 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:706
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eeeeee...hhhhhhhhhhhhhhhhhhhhh.eee..ee.....hhhhhhhhhhhh.hhhhhh.....eee....eee...hhhhhh.......hhhhhhhhh...ee..........................hhhhhhhhhhhhh.........eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.....ee.....eeehhhhhh....eeee.....eeee..........hhhhhhhhhh.......eeeee.hhhhhhhh.........eeeee....eee...........ee......hhhhh..eeee.......eee..ee..hhhhhhhhhhh............hhhhh..............eee..................hhhhhhhhh.....ee.....eeeeee...eeeeee....eeeeeeeee....................hhhhh.....eeeee..........hhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhh.eee..eee....eeeeeeeee............eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhhee.......hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gtw A 170 KSWVEETCESIDTPECPAEFESPPTLLFSLDGFRAEYLHTWGGLLPVISKLKNCGTYTKNmRPmYPTKTFPNHYSIVTGLYPESHGIIDNKmYDPKmNASFSLKSKEKFNPLWYKGQPIWVTANHQEVKSGTYFWPGSDVEIDGILPDIYKVYNGSVPFEERILAVLEWLQLPSHERPHFYTLYLEEPDSSGHSHGPVSSEVIKALQKVDRLVGmLmDGLKDLGLDKCLNLILISDHGmEQGSCKKYVYLNKYLGDVNNVKVVYGPAARLRPTDVPETYYSFNYEALAKNLSCREPNQHFRPYLKPFLPKRLHFAKSDRIEPLTFYLDPQWQLALNPSERKYCGSGFHGSDNLFSNmQALFIGYGPAFKHGAEVDSFENIEVYNLmCDLLGLIPAPNNGSHGSLNHLLKKPIYNPSHPKEEGFLSQCPIKSTSNDLGCTCDPEDDDIYHmTVPYGRPRILLKQHRVCLLQQQQFLTGYSLDLLmPLWASYTFLSNDSNCLYQDLRIPLSPVHKCSYYKSNSKLSYGFLTPPRLNHIYSEALLTSNIVPmYQSFQVIWHYLHDTLLQRYAHERNGINVVSGPVFDFDYDGRYDSLEILKQNSRVIRSQEILIPTHFFIVLTSCKQLSETPLECSALESSAYILPHRPDNIESCTHGKRESSWVEELLTLHRARVTDVELITGLSFYQDRQESVSELLRLKTHLPIFS 902
                                   179       189       199       209       219       229|  |   239       249       259 |    |269       279       289       299       309       319       329       339       349       359       369       379    | |389       399       409       419       429       439       449       459       469       479       489       499       509       519      |529       539       549     | 559       569       579       589       599       609 ||    635       645       655       665   |   675     ||692       702       712       722   ||  736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896      
                                                                                      230-MSE                        261-MSE|                                                                                                                   384-MSE                 408-MSE                                                                                                               526-MSE                      555-MSE                                                 611|      |                               669-MSE     681|                                  726|           745-MSE                                                                                                                                                         
                                                                                         233-MSE                          266-MSE                                                                                                                 386-MSE                                                                                                                                                                                                                           628      |                                            689                                   731                                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           635-MSE

Chain B from PDB  Type:PROTEIN  Length:697
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eeeeee...hhhhhhhhhhhhhhhhhhhhh.eee..ee.....hhhhhhhhhhhh.hhhhhh.....eee....eee...hhhhhh.......hhhhhhhhh...ee..........................hhhhhhhhhhhhh.........eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.....ee.....eeehhhhhh....eeee.....eeee..........hhhhhhhhhh.......eeeee.hhhhhhhh.........eeeee....eee........ee......hhhhh..eeee.......eee..ee..hhhhhhhhhhh............hhhhh..............eee..................hhhhhhhh.....ee.....eeeeee...eeeeee....eeeeeeeee...................hhhhh..eeee..........hhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhh.eee..eee....eeeeeeeee............eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhhee.......hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gtw B 170 KSWVEETCESIDTPECPAEFESPPTLLFSLDGFRAEYLHTWGGLLPVISKLKNCGTYTKNmRPmYPTKTFPNHYSIVTGLYPESHGIIDNKmYDPKmNASFSLKSKEKFNPLWYKGQPIWVTANHQEVKSGTYFWPGSDVEIDGILPDIYKVYNGSVPFEERILAVLEWLQLPSHERPHFYTLYLEEPDSSGHSHGPVSSEVIKALQKVDRLVGmLmDGLKDLGLDKCLNLILISDHGmEQGSCKKYVYLNKYLGDVNNVKVVYGPAARLRPTDVPETYYSFNYEALAKNLSCREPNQHFRPYLKPFLPKRLHFAKSDRIEPLTFYLDPQWQLALNPSYCGSGFHGSDNLFSNmQALFIGYGPAFKHGAEVDSFENIEVYNLmCDLLGLIPAPNNGSHGSLNHLLKKPIYNPSHPKEEGFLSQCPIKSTSNDLGCTCDPDDDIYHmTVPYGRPRILLKQHRVCLLQQQQFLTGYSLDLLmPLWASYTFLSNDNCLYQDLRIPLSPVHKCSYYKLSYGFLTPPRLNHIYSEALLTSNIVPmYQSFQVIWHYLHDTLLQRYAHERNGINVVSGPVFDFDYDGRYDSLEILKQNSRVIRSQEILIPTHFFIVLTSCKQLSETPLECSALESSAYILPHRPDNIESCTHGKRESSWVEELLTLHRARVTDVELITGLSFYQDRQESVSELLRLKTHLPIFS 902
                                   179       189       199       209       219       229|  |   239       249       259 |    |269       279       289       299       309       319       329       339       349       359       369       379    | |389       399       409       419       429       439       449       459       469       479       489       499       512       522   |   532       542       552  |    562       572       582       592       602       629     | 639       649       659       669       679 ||    697       707  ||   721    || 735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       
                                                                                      230-MSE                        261-MSE|                                                                                                                   384-MSE                 408-MSE                                                                                            507|            526-MSE                      555-MSE                                                 611|     |                               669-MSE     681|                 710|        726|           745-MSE                                                                                                                                                         
                                                                                         233-MSE                          266-MSE                                                                                                                 386-MSE                                                                                                                   511                                                                                                  629     |                                            690                  715         731                                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       635-MSE

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 4GTW)

(no "CATH Domain" information available for 4GTW)

(no "Pfam Domain" information available for 4GTW)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		AMP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		BMA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Sites
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		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu A:356 - Pro A:357	[ RasMol ]
		Glu B:356 - Pro B:357	[ RasMol ]
		Lys A:647 - Gln A:648	[ RasMol ]
		Lys B:647 - Gln B:648	[ RasMol ]
		Thr A:601 - Ser A:602	[ RasMol ]
		Tyr A:234 - Pro A:235	[ RasMol ]
		Tyr B:234 - Pro B:235	[ RasMol ]
		Val A:444 - Pro A:445	[ RasMol ]
		Val B:444 - Pro B:445	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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	4gtw
		Family and Domain Information	:	ProDom \| SYSTERS
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
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Access by UniProt ID/Accession number
	ENPP1_MOUSE \| P06802
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	ENPP2_MOUSE \| Q9R1E6
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	G3X9S2_MOUSE \| G3X9S2
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		Protein-protein Interaction	:	DIP
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	3.1.4.39
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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	G3X9S2_MOUSE \| G3X9S2
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ENPP1_MOUSE \| P06802	:	4b56 4gtx 4gty 4gtz
	ENPP2_MOUSE \| Q9R1E6	:	3nkm 3nkn 3nko 3nkp 3nkq 3nkr 3wav 3waw 3wax 3way 4gtx 4gty 4gtz 5hrt 5inh 5jvg 5lia
	G3X9S2_MOUSE \| G3X9S2	:	4gtx 4gty 4gtz

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 44)

Sites (15, 15)

SS Bonds (16, 16)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

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Gene Ontology (57, 89)

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Related Entries Specified in the PDB File