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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ACID SPHINGOMYELINASE
 
Authors :  Z. J. Xiong, G. G. Prive
Date :  19 Apr 16  (Deposition) - 06 Jul 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lysosomal Hydrolase, Neimann-Pick Disease, Sphingolipid, Saposin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. J. Xiong, J. Huang, G. Poda, R. Pomes, G. G. Prive
Structure Of Human Acid Sphingomyelinase Reveals The Role O The Saposin Domain In Activating Substrate Hydrolysis.
J. Mol. Biol. V. 428 3026 2016
PubMed-ID: 27349982  |  Reference-DOI: 10.1016/J.JMB.2016.06.012

(-) Compounds

Molecule 1 - SPHINGOMYELIN PHOSPHODIESTERASE
    ChainsA, B
    EC Number3.1.4.12
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System CommonHUMAN
    Expression System Taxid9606
    FragmentUNP RESIDUES 47-629
    GeneSMPD1, ASM
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymACID SPHINGOMYELINASE,ASMASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 27)

Asymmetric/Biological Unit (4, 27)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG19Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN4Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:206 , HIS A:208 , ASP A:278 , HIS A:459 , ZN A:702 , ACT A:703binding site for residue ZN A 701
02AC2SOFTWAREASP A:206 , ASP A:278 , ASN A:318 , HIS A:425 , HIS A:457 , ZN A:701 , ACT A:703binding site for residue ZN A 702
03AC3SOFTWAREASP A:206 , ASP A:278 , ASN A:318 , HIS A:319 , HIS A:457 , HIS A:459 , ZN A:701 , ZN A:702binding site for residue ACT A 703
04AC4SOFTWAREASP B:206 , HIS B:208 , ASP B:278 , HIS B:459 , ZN B:702 , ACT B:703binding site for residue ZN B 701
05AC5SOFTWAREASP B:206 , ASP B:278 , ASN B:318 , HIS B:425 , HIS B:457 , ZN B:701 , ACT B:703binding site for residue ZN B 702
06AC6SOFTWAREASP B:206 , HIS B:208 , ASP B:278 , HIS B:282 , ASN B:318 , HIS B:457 , HIS B:459 , ZN B:701 , ZN B:702binding site for residue ACT B 703
07AC7SOFTWAREASN A:86 , ILE B:125binding site for Mono-Saccharide NAG A 704 bound to ASN A 86
08AC8SOFTWARESER A:173 , TRP A:174 , ASN A:175 , SER A:434binding site for Mono-Saccharide NAG A 705 bound to ASN A 175
09AC9SOFTWAREARG A:289 , ASN A:335 , HIS A:336binding site for Poly-Saccharide residues NAG A 710 through NAG A 711 bound to ASN A 335
10AD1SOFTWAREASN A:395binding site for Mono-Saccharide NAG A 712 bound to ASN A 395
11AD2SOFTWAREPRO A:371 , TYR A:372 , ASN A:503binding site for Poly-Saccharide residues NAG A 708 through NAG A 709 bound to ASN A 503
12AD3SOFTWAREASN A:520 , GLN A:523 , GLN A:534binding site for Poly-Saccharide residues NAG A 706 through NAG A 707 bound to ASN A 520
13AD4SOFTWAREILE A:125 , PHE B:82 , ASN B:86binding site for Mono-Saccharide NAG B 704 bound to ASN B 86
14AD5SOFTWAREASN B:175binding site for Mono-Saccharide NAG B 705 bound to ASN B 175
15AD6SOFTWARELEU B:137 , THR B:288 , ARG B:289 , ASN B:335binding site for Poly-Saccharide residues NAG B 709 through MAN B 711 bound to ASN B 335
16AD7SOFTWAREASN B:395binding site for Poly-Saccharide residues NAG B 712 through NAG B 713 bound to ASN B 395
17AD8SOFTWARETYR B:372 , ASN B:503binding site for Poly-Saccharide residues NAG B 714 through NAG B 715 bound to ASN B 503
18AD9SOFTWAREARG A:559 , ASN B:520 , GLN B:523 , GLN B:534 , GLY B:577binding site for Poly-Saccharide residues NAG B 706 through MAN B 708 bound to ASN B 520

(-) SS Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1A:89 -A:165
2A:92 -A:157
3A:120 -A:131
4A:221 -A:226
5A:227 -A:250
6A:385 -A:431
7A:584 -A:588
8A:594 -A:607
9B:89 -B:165
10B:92 -B:157
11B:120 -B:131
12B:221 -B:226
13B:227 -B:250
14B:385 -B:431
15B:584 -B:588
16B:594 -B:607

(-) Cis Peptide Bonds  (15, 15)

Asymmetric/Biological Unit
No.Residues
1Ile A:125 -Ala A:126
2Pro A:153 -Ser A:154
3Ser A:154 -Glu A:155
4Pro A:266 -Ala A:267
5Ala A:267 -Gly A:268
6Gly A:268 -Pro A:269
7Thr A:322 -Pro A:323
8Gly A:334 -Asn A:335
9Ile B:125 -Ala B:126
10Pro B:153 -Ser B:154
11Ser B:154 -Glu B:155
12Pro B:266 -Ala B:267
13Ala B:267 -Gly B:268
14Thr B:322 -Pro B:323
15Gly B:334 -Asn B:335

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JG8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JG8)

(-) Exons   (0, 0)

(no "Exon" information available for 5JG8)

(-) Sequences/Alignments

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
(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:529
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh....................................eeeeeee................................................hhhhhhhhhhh........eeee............hhhhhhhhhhhhhhhhhhhhh...eee.......................hhhhhhhh........hhhhhhhhhhh..eee.....eeeee.hhhhhh..hhhhhh...hhhhhhhhhhhhhhhhhhhhheeeeee........hhhhhhhhhhhhhh...eeeeeeeeee..eeeeee.......eeeeeeeee..........eeeeeeee.........eeeeeeeeehhhhhh.......ee...hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh....hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jg8 A  83 GWGNLTCPICKGLFTAINLGLKKEPNVARVGSVAIKLCNLLKIAPPAVCQSIVHLFEDDMVEVWRRSVLSPSEACGLLLGSTCGHWDIFSSWNISLPTVPKPPPKPPSPPAPGAPVSRILFLTDLHWDHDYLEGTDPDCADPLCCRRGSGLPPASRPGAGYWGEYSKCDLPLRTLESLLSGLGPAGPFDMVYWTGDIPAHDVWHQTRQDQLRALTTVTALVRKFLGPVPVYPAVGNHESTPVNSFPPPFIEGNHSSRWLYEAMAKAWEPWLPAEALRTLRIGGFYALSPYPGLRLISLNMNFCSRENFWLLINSTDPAGQLQWLVGELQAAEDRGDKVHIIGHIPPGHCLKSWSWNYYRIVARYENTLAAQFFGHTHVDEFEVFYDEETLSRPLAVAFLAPSATTYIGLNPGYRVYQIDGNYSGSSHVVLDHETYILNLTQANIPGAIPHWQLLYRARETYGLPNTLPTAWHNLVYRMRGDMQLFQTFWFLYHKGHPPSEPCGTPCRLATLCAQLSARADSPALCRHLM 611
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602         

Chain B from PDB  Type:PROTEIN  Length:530
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh....................................eeeeeee................................................hhhhhhhhhhh........eeee............hhhhhhhhhhhhhhhhhhhhh...eee.......................hhhhhhhh........hhhhhhhhhhh..eee.....eeeee.hhhhhh..hhhhhh...hhhhhhhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhhhhhh...eeeeeeeeee..eeeeee.......eeeeeeeee..........eeeeeeee.........eeeeeeeeehhhhhh.......ee...hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jg8 B  82 FGWGNLTCPICKGLFTAINLGLKKEPNVARVGSVAIKLCNLLKIAPPAVCQSIVHLFEDDMVEVWRRSVLSPSEACGLLLGSTCGHWDIFSSWNISLPTVPKPPPKPPSPPAPGAPVSRILFLTDLHWDHDYLEGTDPDCADPLCCRRGSGLPPASRPGAGYWGEYSKCDLPLRTLESLLSGLGPAGPFDMVYWTGDIPAHDVWHQTRQDQLRALTTVTALVRKFLGPVPVYPAVGNHESTPVNSFPPPFIEGNHSSRWLYEAMAKAWEPWLPAEALRTLRIGGFYALSPYPGLRLISLNMNFCSRENFWLLINSTDPAGQLQWLVGELQAAEDRGDKVHIIGHIPPGHCLKSWSWNYYRIVARYENTLAAQFFGHTHVDEFEVFYDEETLSRPLAVAFLAPSATTYIGLNPGYRVYQIDGNYSGSSHVVLDHETYILNLTQANIPGAIPHWQLLYRARETYGLPNTLPTAWHNLVYRMRGDMQLFQTFWFLYHKGHPPSEPCGTPCRLATLCAQLSARADSPALCRHLM 611
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5JG8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JG8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JG8)

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:267 - Gly A:268   [ RasMol ]  
    Ala B:267 - Gly B:268   [ RasMol ]  
    Gly A:268 - Pro A:269   [ RasMol ]  
    Gly A:334 - Asn A:335   [ RasMol ]  
    Gly B:334 - Asn B:335   [ RasMol ]  
    Ile A:125 - Ala A:126   [ RasMol ]  
    Ile B:125 - Ala B:126   [ RasMol ]  
    Pro A:153 - Ser A:154   [ RasMol ]  
    Pro A:266 - Ala A:267   [ RasMol ]  
    Pro B:153 - Ser B:154   [ RasMol ]  
    Pro B:266 - Ala B:267   [ RasMol ]  
    Ser A:154 - Glu A:155   [ RasMol ]  
    Ser B:154 - Glu B:155   [ RasMol ]  
    Thr A:322 - Pro A:323   [ RasMol ]  
    Thr B:322 - Pro B:323   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ASM_HUMAN | P174051x9o 5i81 5i85 5i8r

(-) Related Entries Specified in the PDB File

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