4WGK - JenaLib

Title :   CRYSTAL STRUCTURE OF HUMAN NEUTRAL CERAMIDASE WITH ZN-BOUND PHOSPHATE

Authors :   M. V. Airola, M. J. Pulkoski-Gross, L. M. Obeid, Y. A. Hannun

Date :   18 Sep 14 (Deposition) - 08 Jul 15 (Release) - 19 Aug 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.58

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

Keywords :   Ceramidase, Amidase, Zinc, Phosphate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. V. Airola, W. J. Allen, M. J. Pulkoski-Gross, L. M. Obeid, R. C. Rizzo Y. A. Hannun
Structural Basis For Ceramide Recognition And Hydrolysis By Human Neutral Ceramidase.
Structure V. 23 1482 2015
PubMed-ID: 26190575 | Reference-DOI: 10.1016/J.STR.2015.06.013

Compounds

Molecule 1 - NEUTRAL CERAMIDASE
	Chains	:	A, B
	EC Number	:	3.5.1.23
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF9
	Expression System Taxid	:	7108
	Gene	:	ASAH2, HNAC1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NCDASE, ACYLSPHINGOSINE DEACYLASE 2, BCDASE, LCDASE, HCD, N- ACYLSPHINGOSINE AMIDOHYDROLASE 2, NON-LYSOSOMAL CERAMIDASE

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (8, 25)

Asymmetric Unit (8, 25)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	CA	2	Ligand/Ion	CALCIUM ION
3	CIT	4	Ligand/Ion	CITRIC ACID
4	CL	1	Ligand/Ion	CHLORIDE ION
5	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
6	NAG	11	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	PO4	2	Ligand/Ion	PHOSPHATE ION
8	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 10)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	CIT	2	Ligand/Ion	CITRIC ACID
4	CL	-1	Ligand/Ion	CHLORIDE ION
5	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
6	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	PO4	1	Ligand/Ion	PHOSPHATE ION
8	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 10)

No.	Name	Count	Type	Full Name
1	BMA	-1	Ligand/Ion	BETA-D-MANNOSE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	CIT	2	Ligand/Ion	CITRIC ACID
4	CL	-1	Ligand/Ion	CHLORIDE ION
5	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
6	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	PO4	1	Ligand/Ion	PHOSPHATE ION
8	ZN	-1	Ligand/Ion	ZINC ION

Sites (21, 21)

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:194 , HIS A:303 , GLU A:540 , TYR A:579 , PO4 A:810	binding site for residue ZN A 801
02	AC2	SOFTWARE	LEU A:134 , ASP A:712 , SER A:714 , THR A:717 , HOH A:977	binding site for residue CA A 802
03	AC3	SOFTWARE	GLY A:122 , MET A:162 , HIS A:194 , HIS A:196 , HIS A:303 , GLU A:540 , TYR A:579 , TYR A:591 , ZN A:801 , HOH A:926 , HOH A:1082	binding site for residue PO4 A 810
04	AC4	SOFTWARE	ASN A:249 , TYR A:273 , SER A:274 , SER A:275 , THR A:277 , ASP A:278 , LYS A:279 , GLU A:280 , ARG A:547	binding site for residue CIT A 811
05	AC5	SOFTWARE	GLU A:556 , HIS A:560 , ARG A:611 , LYS A:615 , HOH A:952	binding site for residue CIT A 812
06	AC6	SOFTWARE	HIS B:194 , HIS B:303 , GLU B:540 , TYR B:579 , PO4 B:808	binding site for residue ZN B 801
07	AC7	SOFTWARE	LEU B:134 , ASP B:712 , SER B:714 , THR B:717	binding site for residue CA B 802
08	AC8	SOFTWARE	GLY B:122 , MET B:162 , HIS B:194 , HIS B:196 , HIS B:303 , GLU B:540 , TYR B:579 , TYR B:591 , ZN B:801 , HOH B:1027	binding site for residue PO4 B 808
09	AC9	SOFTWARE	ARG B:184 , SER B:425	binding site for residue CL B 809
10	AD1	SOFTWARE	ASN B:249 , TYR B:273 , SER B:274 , SER B:275 , THR B:277 , ASP B:278 , LYS B:279 , GLU B:280 , ARG B:547 , HOH B:919	binding site for residue CIT B 810
11	AD2	SOFTWARE	GLU B:556 , HIS B:560 , ARG B:611 , LEU B:725	binding site for residue CIT B 811
12	AD3	SOFTWARE	GLY B:107 , ARG B:108 , GLY B:339	binding site for residue EDO B 812
13	AD4	SOFTWARE	ASN B:311 , HIS B:312	binding site for residue EDO B 813
14	AD5	SOFTWARE	ASN A:217 , GLN A:221	binding site for Mono-Saccharide NAG A 806 bound to ASN A 217
15	AD6	SOFTWARE	ASN A:308 , ASN A:309 , SER A:310 , ASP A:392 , MET A:393 , HOH A:1009 , HOH A:1061 , HOH A:1076 , HOH A:1087	binding site for Poly-Saccharide residues NAG A 807 through BMA A 809 bound to ASN A 308
16	AD7	SOFTWARE	ASN A:440 , HOH A:913	binding site for Mono-Saccharide NAG A 805 bound to ASN A 440
17	AD8	SOFTWARE	ALA A:558 , GLN A:563 , GLN A:660 , ILE A:675 , HIS A:722 , GLY A:724 , ASN A:730	binding site for Poly-Saccharide residues NAG A 803 through NAG A 804 bound to ASN A 730
18	AD9	SOFTWARE	SER B:150 , ASN B:151 , ARG B:184 , HOH B:960 , HOH B:1075	binding site for Mono-Saccharide NAG B 807 bound to ASN B 151
19	AE1	SOFTWARE	ASN B:217 , GLN B:686 , HOH B:909 , HOH B:941	binding site for Mono-Saccharide NAG B 806 bound to ASN B 217
20	AE2	SOFTWARE	ASN B:308 , ASN B:309 , SER B:310 , ASP B:392 , MET B:393 , HOH B:901 , HOH B:928	binding site for Mono-Saccharide NAG B 803 bound to ASN B 308
21	AE3	SOFTWARE	ALA B:558 , GLN B:563 , HIS B:722 , GLY B:724 , ASN B:730 , HOH B:938 , HOH B:1029 , HOH B:1069	binding site for Poly-Saccharide residues NAG B 804 through NAG B 805 bound to ASN B 730

SS Bonds (6, 6)

Cis Peptide Bonds (6, 6)

Asymmetric Unit

No.	Residues
1	Lys A:500	-	Pro A:501
2	Lys A:513	-	Pro A:514
3	Lys B:500	-	Pro B:501
4	Lys B:513	-	Pro B:514
5	Gln B:686	-	Asn B:687
6	Asn B:687	-	Gln B:688

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:670
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.....eeeeee.......eeeee....eeeeeeee.......eeeeee.....hhhhhhhhhhhhhhhhh.......eeeee.....ee.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.....ee.hhhhhh..hhhhhh........eeeeeeeee....eeeeeee.............ee.hhhhhhhhhhhhhhhh..........eeeee......ee.....eee................hhhh.eee.....hhhhhhhhhhhhhhhhhhhhhhh..eee...eeeeeeeee....eee.....eee.....ee.hhh.ee..ee............hhhhhhhhhhhh...hhhhhhhhh...eeehhhhh.........eeeeeeeee..eeeee...eehhhhhhhhhhhhhhhhhhh.....eeeee........ee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhh...........................eee....eee...eeeeeee..hhhhhh......eeeeeee....eeeeeee.....eeeeeee.....eeeeeeee.......eeeeeeeeeeeee...eeeeeeee...eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wgk A 100 SGYHIGVGRADCTGQVADINLMGYGKSGQNAQGILTRLYSRAFIMAEPDGSNRTVFVSIDIGMVSQRLRLEVLNRLQSKYGSLYRRDNVILSGTHTHSGPAGYFQYTVFVIASEGFSNQTFQHMVTGILKSIDIAHTNMKPGKIFINKGNVDGVQINRSPYSYLQNPQSERARYSSNTDKEMIVLKMVDLNGDDLGLISWFAIHPVSMNNSNHLVNSDNVGYASYLLEQEKNKGYLPGQGPFVAAFASSNLGDVSPNILGPRCINTGESCDNANSTCPIGGPSMCIAKGPGQDMFDSTQIIGRAMYQRAKELYASASQEVTGPLASAHQWVDMTDVTVWLNSTHASKTCKPALGYSFAAGTIDGVGGLNFTQGKTEGDPFWDTIRDQILGKPSEEIKECHKPKPILLHTGELSKPHPWHPDIVDVQIITLGSLAITAIPGEFTTMSGRRLREAVQAEFASHGMQNMTVVISGLCNVYTHYITTYEEYQAQRYEAASTIYGPHTLSAYIQLFRNLAKAIATDTVANLSRGPEPPFFKQIPSIVDRAPKGRTFGDVLQPAKPEYRVGEVAEVIFVGANPKNSVQTHQTFLTVEKYEATSTSWQIVCNDASWETRFYWHKGLLGLSNATVEWHIPDTAQPGIYRIRYFGHNRKQPAVILSFEGTSPAFEVVTI 780
                                   109       119       129       139       149       159       169       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       619       629      |644       654       664       674       684||     696       706       716       726       736       746       756||     770       780
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  636|                                        685|                                                                  757|                  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   642                                         688                                                                   762

Chain B from PDB  Type:PROTEIN  Length:672
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee.....eeeeee.......eeeee....eeeeeeee.......eeeeee.....hhhhhhhhhhhhhhhhh.......eeeee.....ee.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee.....ee.hhhhhh..hhhhhh........eeeeeeeee....eeeeeee.............ee.hhhhhhhhhhhhhhhh..........eeeee......ee.....eee.................hhh.eee.....hhhhhhhhhhhhhhhhhhhhhhh..eee...eeeeeeeee....eee.....eee.....ee.hhh.ee..ee............hhhhhhhhhhhh...hhhhhhhhh...eeehhhhh.........eeeeeeeee..eeeee...eehhhhhhhhhhhhhhhhhhh.....eeeee........ee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhh............................eee....eee...eeeeeee..hhhhhh........eeeeeee....eeeeeee.....eeeeeee.....eeeeeeee.......eeeeeeeeeeeee..eeeeeeee...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wgk B  99 FSGYHIGVGRADCTGQVADINLMGYGKSGQNAQGILTRLYSRAFIMAEPDGSNRTVFVSIDIGMVSQRLRLEVLNRLQSKYGSLYRRDNVILSGTHTHSGPAGYFQYTVFVIASEGFSNQTFQHMVTGILKSIDIAHTNMKPGKIFINKGNVDGVQINRSPYSYLQNPQSERARYSSNTDKEMIVLKMVDLNGDDLGLISWFAIHPVSMNNSNHLVNSDNVGYASYLLEQEKNKGYLPGQGPFVAAFASSNLGDVSPNILGPRCINTGESCDNANSTCPIGGPSMCIAKGPGQDMFDSTQIIGRAMYQRAKELYASASQEVTGPLASAHQWVDMTDVTVWLNSTHASKTCKPALGYSFAAGTIDGVGGLNFTQGKTEGDPFWDTIRDQILGKPSEEIKECHKPKPILLHTGELSKPHPWHPDIVDVQIITLGSLAITAIPGEFTTMSGRRLREAVQAEFASHGMQNMTVVISGLCNVYTHYITTYEEYQAQRYEAASTIYGPHTLSAYIQLFRNLAKAIATDTVANLSRGPEPPFFKQLIPSIVDRAPKGRTFGDVLQPAKPEYRVGEVAEVIFVGANPKNSVQNQTHQTFLTVEKYEATSTSWQIVCNDASWETRFYWHKGLLGLSNATVEWHIPDTAQPGIYRIRYFGHNRKQAVILSFEGTSPAFEVVT 779
                                   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638|      652       662       672       682       692       702       712       722       732       742       752    || 767       777  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     638|                                                                                                               757|                
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      643                                                                                                                763

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

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	Cis Peptide Bonds
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