2OXE - JenaLib

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Title :   STRUCTURE OF THE HUMAN PANCREATIC LIPASE-RELATED PROTEIN 2

Authors :   J. R. Walker, T. Davis, A. Seitova, P. J. Finerty Jr. , C. Butler-Cole, I. Kozieradzki, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwa A. Bochkarev, S. Dhe-Paganon, Structural Genomics Consortium (S

Date :   20 Feb 07 (Deposition) - 27 Mar 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Glycoprotein, Hydrolase, Lipid Degradation, Pancreatic Lipase, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Eydoux, S. Spinelli, T. L. Davis, J. R. Walker, A. Seitova, S. Dhe-Paganon, A. De Caro, C. Cambillau, F. Carriere
Structure Of Human Pancreatic Lipase-Related Protein 2 With The Lid In An Open Conformation.
Biochemistry V. 47 9553 2008
PubMed-ID: 18702514 | Reference-DOI: 10.1021/BI8005576
(for further references see the PDB file header)

Molecule 1 - PANCREATIC LIPASE-RELATED PROTEIN 2
	Chains	:	A, B
	EC Number	:	3.1.1.3
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Plasmid	:	PAB-BEE
	Expression System Strain	:	HIGH5
	Expression System Taxid	:	7108
	Expression System Vector Type	:	PLASMID
	Gene	:	PNLIPRP2, PLRP2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Tissue	:	PANCREAS

		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 (4, 17)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	CL	5	Ligand/Ion	CHLORIDE ION
3	MAN	6	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:353 , THR A:355 , PHE A:410 , NAG A:501 , HOH A:624	BINDING SITE FOR RESIDUE NAG A 500
02	AC2	SOFTWARE	GLU A:384 , ASN A:385 , ASP A:409 , PHE A:410 , NAG A:500 , MAN A:502	BINDING SITE FOR RESIDUE NAG A 501
03	AC3	SOFTWARE	ASN A:385 , NAG A:501 , MAN A:503 , MAN A:504	BINDING SITE FOR RESIDUE MAN A 502
04	AC4	SOFTWARE	MAN A:502	BINDING SITE FOR RESIDUE MAN A 503
05	AC5	SOFTWARE	ASN A:385 , MAN A:502	BINDING SITE FOR RESIDUE MAN A 504
06	AC6	SOFTWARE	ASN B:295 , ASN B:353 , THR B:355 , ASP B:409 , NAG B:501	BINDING SITE FOR RESIDUE NAG B 500
07	AC7	SOFTWARE	ASP B:409 , NAG B:500 , MAN B:502 , HOH B:614	BINDING SITE FOR RESIDUE NAG B 501
08	AC8	SOFTWARE	ASN B:385 , NAG B:501 , MAN B:503 , MAN B:504 , HOH B:630	BINDING SITE FOR RESIDUE MAN B 502
09	AC9	SOFTWARE	MAN B:502 , HOH B:615	BINDING SITE FOR RESIDUE MAN B 503
10	BC1	SOFTWARE	ASN B:383 , ASN B:385 , MAN B:502	BINDING SITE FOR RESIDUE MAN B 504
11	BC2	SOFTWARE	GLU A:206 , ARG A:209 , ASP A:211 , ASP A:214 , HOH A:617	BINDING SITE FOR RESIDUE CA A 600
12	BC3	SOFTWARE	GLU B:206 , ARG B:209 , ASP B:211 , ASP B:214	BINDING SITE FOR RESIDUE CA B 600
13	BC4	SOFTWARE	ASN A:66	BINDING SITE FOR RESIDUE CL A 1
14	BC5	SOFTWARE	GLY B:255	BINDING SITE FOR RESIDUE CL B 2
15	BC6	SOFTWARE	LYS A:99 , ARG B:126	BINDING SITE FOR RESIDUE CL A 3
16	BC7	SOFTWARE	PRO B:64 , ASN B:66	BINDING SITE FOR RESIDUE CL B 5

Asymmetric Unit

No.	Residues
1	A:21	-	A:27
2	A:109	-	A:120
3	A:256	-	A:280
4	A:304	-	A:315
5	A:318	-	A:323
6	A:453	-	A:469
7	B:21	-	B:27
8	B:109	-	B:120
9	B:256	-	B:280
10	B:304	-	B:315
11	B:318	-	B:323
12	B:453	-	B:469

Asymmetric Unit

No.	Residues
1	Lys A:32	-	Pro A:33
2	Val A:229	-	Pro A:230
3	Phe A:316	-	Pro A:317
4	Lys B:32	-	Pro B:33
5	Val B:229	-	Pro B:230
6	Phe B:316	-	Pro B:317

(no "SAP(SNP)/Variant" information available for 2OXE)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPASE_SER	PS00120	Lipases, serine active site.	LIPR2_HUMAN	165-174	2	A:165-174 B:165-174
2	PLAT	PS50095	PLAT domain profile.	LIPR2_HUMAN	357-469	2	A:357-469 B:357-469

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPASE_SER	PS00120	Lipases, serine active site.	LIPR2_HUMAN	165-174	1	A:165-174 -
2	PLAT	PS50095	PLAT domain profile.	LIPR2_HUMAN	357-469	1	A:357-469 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPASE_SER	PS00120	Lipases, serine active site.	LIPR2_HUMAN	165-174	1	- B:165-174
2	PLAT	PS50095	PLAT domain profile.	LIPR2_HUMAN	357-469	1	- B:357-469

(no "Exon" information available for 2OXE)

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:435
 aligned with LIPR2_HUMAN | P54317 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:452
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467  
          LIPR2_HUMAN    18 KEVCYGQLGCFSDEKPWAGTLQRPVKLLPWSPEDIDTRFLLYTNENPNNFQLITGTEPDTIEASNFQLDRKTRFIIHGFLDKAEDSWPSDMCKKMFEVEKVNCICVDWRHGSRAMYTQAVQNIRVVGAETAFLIQALSTQLGYSLEDVHVIGHSLGAHTAAEAGRRLGGRVGRITGLDPAGPCFQDEPEEVRLDPSDAVFVDVIHTDSSPIVPSLGFGMSQKVGHLDFFPNGGKEMPGCKKNVLSTITDIDGIWEGIGGFVSCNHLRSFEYYSSSVLNPDGFLGYPCASYDEFQESKCFPCPAEGCPKMGHYADQFKGKTSAVEQTFFLNTGESGNFTSWRYKVSVTLSGKEKVNGYIRIALYGSNENSKQYEIFKGSLKPDASHTCAIDVDFNVGKIQKVKFLWNKRGINLSEPKLGASQITVQSGEDGTEYNFCSSDTVEENVLQSLYPC 469
               SCOP domains d2oxea1 A:18-355 automated matches                                                                                                                                                                                                                                                                                                                d2oxea2 A:356-469 automated matches                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhh.eee..................hhhhhh.eeeeee..eeeeeeee....hhhhhhh......eeeeee.........hhhhhhhhhhh....eeeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee.hhhhhhhhhhhhh.....eeeee................hhhhh..eeee...ee........ee......eeeee.........-----------.......hhhhhhhhhhhhhhhhhhhhh......ee..hhhhhhh................hhhhh........eeeee..........eeeeeeeeeee...eeeeeeeeee....eeeeeeeeeeee....eeeeeeee........eeeeeee.------...eeeeeeeeee.....eeeee..........eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------LIPASE_SER--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PLAT  PDB: A:357-469 UniProt: 357-469                                                                             PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oxe A  18 KEVCYGQLGCFSDEKPWAGTLQRPVKLLPWSPEDIDTRFLLYTNENPNNFQLITGTEPDTIEASNFQLDRKTRFIIHGFLDKAEDSWPSDMCKKMFEVEKVNCICVDWRHGSRAMYTQAVQNIRVVGAETAFLIQALSTQLGYSLEDVHVIGHSLGAHTAAEAGRRLGGRVGRITGLDPAGPCFQDEPEEVRLDPSDAVFVDVIHTDSSPIVPSLGFGMSQKVGHLDFFPNGGKEMPGC-----------DGIWEGIGGFVSCNHLRSFEYYSSSVLNPDGFLGYPCASYDEFQESKCFPCPAEGCPKMGHYADQFKGKTSAVEQTFFLNTGESGNFTSWRYKVSVTLSGKEKVNGYIRIALYGSNENSKQYEIFKGSLKPDASHTCAIDVDFNVGKIQKVKFLWNK------EPKLGASQITVQSGEDGTEYNFCSSDTVEENVLQSLYPC 469
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247        |-         -|      277       287       297       307       317       327       337       347       357       367       377       387       397       407       417      |  -   |   437       447       457       467  
                                                                                                                                                                                                                                                                        256         268                                                                                                                                                         424    431

Chain B from PDB  Type:PROTEIN  Length:431
 aligned with LIPR2_HUMAN | P54317 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:452
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467  
          LIPR2_HUMAN    18 KEVCYGQLGCFSDEKPWAGTLQRPVKLLPWSPEDIDTRFLLYTNENPNNFQLITGTEPDTIEASNFQLDRKTRFIIHGFLDKAEDSWPSDMCKKMFEVEKVNCICVDWRHGSRAMYTQAVQNIRVVGAETAFLIQALSTQLGYSLEDVHVIGHSLGAHTAAEAGRRLGGRVGRITGLDPAGPCFQDEPEEVRLDPSDAVFVDVIHTDSSPIVPSLGFGMSQKVGHLDFFPNGGKEMPGCKKNVLSTITDIDGIWEGIGGFVSCNHLRSFEYYSSSVLNPDGFLGYPCASYDEFQESKCFPCPAEGCPKMGHYADQFKGKTSAVEQTFFLNTGESGNFTSWRYKVSVTLSGKEKVNGYIRIALYGSNENSKQYEIFKGSLKPDASHTCAIDVDFNVGKIQKVKFLWNKRGINLSEPKLGASQITVQSGEDGTEYNFCSSDTVEENVLQSLYPC 469
               SCOP domains d2oxeb1 B:18-355 automated matches                                                                                                                                                                                                                                                                                                                d2oxeb2 B:356-469 automated matches                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Lipase-2oxeB01 B:18-354                                                                                                                                                                                                                                                                                                                          ----PLAT-2oxeB03 B:359-467                                                                                       -- Pfam domains (1)
           Pfam domains (2) Lipase-2oxeB02 B:18-354                                                                                                                                                                                                                                                                                                                          ----PLAT-2oxeB04 B:359-467                                                                                       -- Pfam domains (2)
         Sec.struct. author .eee.hhh.eee..................hhhhhh.eeeee........eee....hhhhhh.......eeeeee.........hhhhhhhhhhhhhh.eeeeeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeehhhhhhhhhhhhhh.....eeeee................hhhhh.eeeee...ee........ee......eeeee.........----------------..hhhhh.....hhhhhhhhhhh......ee..hhhhhhh................hhhhh........eeeee..........eeeeeeeeeee...eeeeeeeeee........eeeeeeee....eeeeeeee........eeeeeee.-----....eeeeeeeeee.....eeeee..........eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------LIPASE_SER--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PLAT  PDB: B:357-469 UniProt: 357-469                                                                             PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oxe B  18 KEVCYGQLGCFSDEKPWAGTLQRPVKLLPWSPEDIDTRFLLYTNENPNNFQLITGTEPDTIEASNFQLDRKTRFIIHGFLDKAEDSWPSDMCKKMFEVEKVNCICVDWRHGSRAMYTQAVQNIRVVGAETAFLIQALSTQLGYSLEDVHVIGHSLGAHTAAEAGRRLGGRVGRITGLDPAGPCFQDEPEEVRLDPSDAVFVDVIHTDSSPIVPSLGFGMSQKVGHLDFFPNGGKEMPGC----------------GIGGFVSCNHLRSFEYYSSSVLNPDGFLGYPCASYDEFQESKCFPCPAEGCPKMGHYADQFKGKTSAVEQTFFLNTGESGNFTSWRYKVSVTLSGKEKVNGYIRIALYGSNENSKQYEIFKGSLKPDASHTCAIDVDFNVGKIQKVKFLWNK-----SEPKLGASQITVQSGEDGTEYNFCSSDTVEENVLQSLYPC 469
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247        |-         -     | 277       287       297       307       317       327       337       347       357       367       377       387       397       407       417      |  -  |    437       447       457       467  
                                                                                                                                                                                                                                                                        256              273                                                                                                                                                    424   430

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 "CATH Domain" information available for 2OXE)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: AB_hydrolase (347)

Family: Lipase (7)

Homo sapiens (Human) (6)

1a	Lipase-2oxeB01	B:18-354
1b	Lipase-2oxeB02	B:18-354

Clan: PLAT (25)

Family: PLAT (25)

Homo sapiens (Human) (7)

2a	PLAT-2oxeB03	B:359-467
2b	PLAT-2oxeB04	B:359-467

Asymmetric Unit(hide GO term definitions)

Chain A,B (LIPR2_HUMAN | P54317)

molecular function
	GO:0047372	acylglycerol lipase activity	Catalysis of the reaction: H2O + acylglycerol = a fatty acid + glycerol.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0052689	carboxylic ester hydrolase activity	Catalysis of the hydrolysis of a carboxylic ester bond.
	GO:0047714	galactolipase activity	Catalysis of the reaction: 1,2-diacyl-3-beta-D-galactosyl-sn-glycerol + 2 H2O = 3-beta-D-galactosyl-sn-glycerol + 2 carboxylates.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004620	phospholipase activity	Catalysis of the hydrolysis of a glycerophospholipid.
	GO:0004806	triglyceride lipase activity	Catalysis of the reaction: triacylglycerol + H2O = diacylglycerol + a carboxylate.
biological process
	GO:0019376	galactolipid catabolic process	The chemical reactions and pathways resulting in the breakdown of galactolipids, any glycolipid containing one of more residues of galactose and/or N-acetylgalactosamine.
	GO:0016042	lipid catabolic process	The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:0044241	lipid digestion	The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested lipids into components that may be easily absorbed and directed into metabolism.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0009395	phospholipid catabolic process	The chemical reactions and pathways resulting in the breakdown of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
	GO:0006641	triglyceride metabolic process	The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Asymmetric Unit
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	Cis Peptide Bonds
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		Phe A:316 - Pro A:317	[ RasMol ]
		Phe B:316 - Pro B:317	[ RasMol ]
		Val A:229 - Pro A:230	[ RasMol ]
		Val B:229 - Pro B:230	[ RasMol ]

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	2oxe
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	LIPR2_HUMAN \| P54317
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	LIPR2_HUMAN \| P54317
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	LIPR2_HUMAN \| P54317	:	2pvs

(no "Related Entries Specified in the PDB File" available for 2OXE)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 17)

Sites (16, 16)

SS Bonds (12, 12)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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