4QN9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF HUMAN NAPE-PLD

Authors :   G. Garau

Date :   17 Jun 14 (Deposition) - 17 Jun 15 (Release) - 17 Jun 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

Chains :   Asym./Biol. Unit : A,B

Keywords :   Pld, Nape, Anandamide, Bile Acid, Phospholipase, Inflammation, Pain, Complex, Nae, Aea, Oea, Pea, Mbl, Pe, Cannabinoid, Fat, Acyl, Deoxycholate, Obesity, Phospholipid, Membrane, Steroid, Drug, Alpha- Beta-Beta-Alpha Fold, Phosphodiesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Magotti, I. Bauer, M. Igarashi, M. Babagoli, R. Marotta, D. Piomelli, G. Garau
Structure Of Human N-Acylphosphatidylethanolamine-Hydrolyzing Phospholipase D: Regulation Of Fatty Acid Ethanolamide Biosynthesis By Bile Acids.
Structure V. 23 598 2015
PubMed-ID: 25684574 | Reference-DOI: 10.1016/J.STR.2014.12.018

Molecule 1 - N-ACYL-PHOSPHATIDYLETHANOLAMINE-HYDROLYZING PHOSPHOLIPASE D
	Chains	:	A, B
	EC Number	:	3.1.4.54
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	C7ORF18, NAPEPLD
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	N-ACYL PHOSPHATIDYLETHANOLAMINE PHOSPHOLIPASE D, NAPE-PLD, NAPE-HYDROLYZING PHOSPHOLIPASE D

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 20)

No.	Name	Count	Type	Full Name
1	3PE	2	Ligand/Ion	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
2	DXC	11	Ligand/Ion	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
3	SO4	3	Ligand/Ion	SULFATE ION
4	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:185 , HIS A:187 , HIS A:253 , ASP A:284 , ZN A:502 , 3PE A:503	BINDING SITE FOR RESIDUE ZN A 501
02	AC2	SOFTWARE	ASP A:189 , HIS A:190 , ASP A:284 , HIS A:343 , ZN A:501 , 3PE A:503	BINDING SITE FOR RESIDUE ZN A 502
03	AC3	SOFTWARE	ALA A:154 , PRO A:156 , HIS A:187 , TYR A:188 , ASP A:189 , HIS A:253 , TRP A:254 , LYS A:256 , ARG A:257 , ASP A:284 , MET A:317 , GLN A:320 , HIS A:321 , HIS A:343 , ZN A:501 , ZN A:502 , DXC A:507 , 3PE B:606	BINDING SITE FOR RESIDUE 3PE A 503
04	AC4	SOFTWARE	TYR A:193 , TRP A:218 , LYS A:221 , CYS A:222 , TYR B:159 , MET B:160 , DXC B:602 , DXC B:607 , DXC B:610	BINDING SITE FOR RESIDUE DXC A 504
05	AC5	SOFTWARE	TYR A:159 , MET A:160 , DXC A:506 , HOH A:623 , TYR B:193 , TRP B:218 , LYS B:221 , CYS B:222 , HOH B:701	BINDING SITE FOR RESIDUE DXC A 505
06	AC6	SOFTWARE	DXC A:505 , MET B:260 , DXC B:603	BINDING SITE FOR RESIDUE DXC A 506
07	AC7	SOFTWARE	THR A:258 , LEU A:259 , 3PE A:503 , DXC B:602 , DXC B:607	BINDING SITE FOR RESIDUE DXC A 507
08	AC8	SOFTWARE	ARG A:166 , ARG A:167 , SER B:173 , HOH B:736	BINDING SITE FOR RESIDUE SO4 A 508
09	AC9	SOFTWARE	SER A:152 , HOH A:617 , SER B:151 , SER B:152	BINDING SITE FOR RESIDUE SO4 A 509
10	BC1	SOFTWARE	TYR A:159 , HOH A:614 , TYR B:188 , TRP B:218 , ARG B:257 , DXC B:603 , HOH B:740	BINDING SITE FOR RESIDUE DXC B 601
11	BC2	SOFTWARE	MET A:260 , DXC A:504 , DXC A:507 , HOH B:743 , HOH B:748	BINDING SITE FOR RESIDUE DXC B 602
12	BC3	SOFTWARE	DXC A:506 , THR B:258 , LEU B:259 , DXC B:601 , 3PE B:606	BINDING SITE FOR RESIDUE DXC B 603
13	BC4	SOFTWARE	HIS B:185 , HIS B:187 , HIS B:253 , ASP B:284 , ZN B:605 , 3PE B:606	BINDING SITE FOR RESIDUE ZN B 604
14	BC5	SOFTWARE	ASP B:189 , HIS B:190 , ASP B:284 , HIS B:343 , ZN B:604 , 3PE B:606	BINDING SITE FOR RESIDUE ZN B 605
15	BC6	SOFTWARE	3PE A:503 , ALA B:154 , PRO B:156 , HIS B:187 , TYR B:188 , ASP B:189 , HIS B:253 , TRP B:254 , LYS B:256 , ARG B:257 , ASP B:284 , MET B:317 , GLN B:320 , HIS B:321 , HIS B:343 , DXC B:603 , ZN B:604 , ZN B:605	BINDING SITE FOR RESIDUE 3PE B 606
16	BC7	SOFTWARE	TYR A:188 , TRP A:218 , ARG A:257 , DXC A:504 , DXC A:507 , TYR B:159 , HOH B:721 , HOH B:740	BINDING SITE FOR RESIDUE DXC B 607
17	BC8	SOFTWARE	LEU A:259 , LYS B:256 , LEU B:259 , MET B:260 , DXC B:609	BINDING SITE FOR RESIDUE DXC B 608
18	BC9	SOFTWARE	LYS A:256 , LEU A:259 , MET A:260 , LEU B:259 , DXC B:608 , DXC B:610	BINDING SITE FOR RESIDUE DXC B 609
19	CC1	SOFTWARE	DXC A:504 , GLY B:161 , PRO B:162 , ALA B:348 , DXC B:609	BINDING SITE FOR RESIDUE DXC B 610
20	CC2	SOFTWARE	THR A:171 , SER A:173 , HOH A:611 , ARG B:166 , ARG B:167	BINDING SITE FOR RESIDUE SO4 B 611

(no "SS Bond" information available for 4QN9)

Asymmetric/Biological Unit

No.	Residues
1	Asp A:62	-	Gly A:63
2	Arg A:121	-	Glu A:122
3	Gly A:124	-	Leu A:125
4	Ile A:178	-	Asp A:179
5	Gly A:299	-	Pro A:300
6	Glu A:312	-	Pro A:313
7	Asp B:62	-	Gly B:63
8	Arg B:121	-	Glu B:122
9	Gly B:124	-	Leu B:125
10	Ile B:178	-	Asp B:179
11	Gly B:299	-	Pro B:300
12	Glu B:312	-	Pro B:313

(no "SAP(SNP)/Variant" information available for 4QN9)

(no "PROSITE Motif" information available for 4QN9)

(no "Exon" information available for 4QN9)

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:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................hhhhhhhhh.....................eeee.....eeeee..eeeee................................eeee.........hhhhhhhhhhhh....eeeee..hhhhhhhh....eeee....eeee..eeeeeeeee...................eeeee....eeee........hhhhhhhhh....eeeee.....hhhhhh....hhhhhhhhhhhh....eeee............hhhhhhhhhhhhhhh.....ee......eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qn9 A  57 SKKGKDGRFVNPWPTWKNPSIPNSSVPSSKEELDKELPVLKPYFITNPEEAGVREAGLRVTWLGHATVMVEMDELIFLTDPIFSSRASPSQYMGPKRFRRSPCTISELPPIDAVLISHNHYDHLDYNSVIALNERFGNELRWFVPLGLLDWMQKCGCENVIELDWWEENCVPGHDKVTFVFTPSQHWCKRTLMDDNKVLWGSWSVLGPWNRFFFAGDTGYCPAFEEIGKRFGPFDLAAIPIGAYEPRWFMKYQHVDPEEAVRIHTDVQTKKSMAIHWGTFALANEHYLEPPVKLNEALERYGLNAEDFFVLKHGESRYLNN 388
                                    66        76  ||    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 
                                                 79|                                                                                                                                                                                                                                                                                                         
                                                  91

Chain B from PDB  Type:PROTEIN  Length:322
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................hhhhhhhhh.....................eeee.....eeeee..eeeee................................eeee.........hhhhhhhhhhhh....eeeee..hhhhhhhh....eeee....eeee..eeeeeeeee...................eeeee....eeee........hhhhhhhhh....eeeee.....hhhhhh....hhhhhhhhhhhhh...eeee............hhhhhhhhhhhhhh......ee......eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qn9 B  57 SKKGKDGRFVNPWPTWKNPSIPNSSVPSSKEELDKELPVLKPYFITNPEEAGVREAGLRVTWLGHATVMVEMDELIFLTDPIFSSRASPSQYMGPKRFRRSPCTISELPPIDAVLISHNHYDHLDYNSVIALNERFGNELRWFVPLGLLDWMQKCGCENVIELDWWEENCVPGHDKVTFVFTPSQHWCKRTLMDDNKVLWGSWSVLGPWNRFFFAGDTGYCPAFEEIGKRFGPFDLAAIPIGAYEPRWFMKYQHVDPEEAVRIHTDVQTKKSMAIHWGTFALANEHYLEPPVKLNEALERYGLNAEDFFVLKHGESRYLNND 389
                                    66        76  ||    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  
                                                 79|                                                                                                                                                                                                                                                                                                          
                                                  91

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 4QN9)

(no "CATH Domain" information available for 4QN9)

(no "Pfam Domain" information available for 4QN9)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Arg A:121 - Glu A:122	[ RasMol ]
		Arg B:121 - Glu B:122	[ RasMol ]
		Asp A:62 - Gly A:63	[ RasMol ]
		Asp B:62 - Gly B:63	[ RasMol ]
		Glu A:312 - Pro A:313	[ RasMol ]
		Glu B:312 - Pro B:313	[ RasMol ]
		Gly A:124 - Leu A:125	[ RasMol ]
		Gly A:299 - Pro A:300	[ RasMol ]
		Gly B:124 - Leu B:125	[ RasMol ]
		Gly B:299 - Pro B:300	[ RasMol ]
		Ile A:178 - Asp A:179	[ RasMol ]
		Ile B:178 - Asp B:179	[ RasMol ]

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	4qn9
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 20)

Sites (20, 20)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (13, 13)

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