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(-) Description

Title :  ASMASE WITH ZINC
 
Authors :  Y. F. Zhou, R. R. Wei
Date :  18 Feb 16  (Deposition) - 07 Sep 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Acid Sphingomyelinase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. F. Zhou, M. C. Metcalf, S. C. Garman, T. Edmunds, H. Qiu, R. R. Wei
Human Acid Sphingomyelinase Structures Provide Insight To Molecular Basis Of Niemann-Pick Disease.
Nat Commun V. 7 13082 2016
PubMed-ID: 27725636  |  Reference-DOI: 10.1038/NCOMMS13082

(-) Compounds

Molecule 1 - SPHINGOMYELIN PHOSPHODIESTERASE
    Chains: A
    EC Number: 3.1.4.12
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Plasmid: PIRES2
    Expression System Strain: HEK293S GNT1-
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: SMPD1, ASM
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ACID SPHINGOMYELINASE,ASMASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 27)

Asymmetric Unit (5, 27)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2MAN1Ligand/IonALPHA-D-MANNOSE
3NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO411Ligand/IonSULFATE ION
5ZN2Ligand/IonZINC ION
Biological Unit 1 (4, 25)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2MAN1Ligand/IonALPHA-D-MANNOSE
3NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO411Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 50)
No.NameCountTypeFull Name
1BMA6Ligand/IonBETA-D-MANNOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG20Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO422Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:173 , ASN A:175binding site for residue NAG A 702
02AC2SOFTWARENAG A:704binding site for residue BMA A 705
03AC3SOFTWARENAG A:711binding site for residue NAG A 712
04AC4SOFTWARENAG A:713binding site for residue NAG A 714
05AC5SOFTWAREASP A:206 , ASP A:278 , ASN A:318 , HIS A:425 , HIS A:457 , ZN A:716 , HOH A:891binding site for residue ZN A 715
06AC6SOFTWAREASP A:206 , HIS A:208 , ASP A:278 , HIS A:459 , ZN A:715 , HOH A:891binding site for residue ZN A 716
07AC7SOFTWAREHIS A:430 , HIS A:457 , HOH A:802binding site for residue SO4 A 717
08AC8SOFTWARELYS A:105 , ASN A:108binding site for residue SO4 A 718
09AC9SOFTWAREGLN A:132 , SER A:133 , HIS A:136binding site for residue SO4 A 719
10AD1SOFTWARELYS A:187 , SER A:190 , ARG A:608 , HIS A:609binding site for residue SO4 A 720
11AD2SOFTWAREARG A:148 , PHE A:331 , ILE A:332 , GLU A:333 , HIS A:336binding site for residue SO4 A 721
12AD3SOFTWARESER A:172 , SER A:173binding site for residue SO4 A 722
13AD4SOFTWAREPRO A:583 , GLY A:585 , THR A:586 , PRO A:587 , CYS A:588binding site for residue SO4 A 723
14AD5SOFTWAREPRO A:235 , ALA A:236 , PRO A:580 , SER A:581 , GLU A:582binding site for residue SO4 A 724
15AD6SOFTWARETHR A:458 , TYR A:488 , ILE A:489 , HOH A:804binding site for residue SO4 A 725
16AD7SOFTWAREASP A:563 , MET A:564 , GLN A:565binding site for residue SO4 A 726
17AD8SOFTWAREPRO A:194 , ARG A:561 , GLY A:562binding site for residue SO4 A 727
18AD9SOFTWAREASN A:86 , LYS A:124 , ILE A:125binding site for Mono-Saccharide NAG A 701 bound to ASN A 86
19AE1SOFTWARETHR A:288 , ARG A:289 , ASN A:335 , BMA A:705binding site for Poly-Saccharide residues NAG A 703 through NAG A 704 bound to ASN A 335
20AE2SOFTWAREASN A:395 , MAN A:709 , BMA A:710binding site for Poly-Saccharide residues NAG A 706 through BMA A 708 bound to ASN A 395
21AE3SOFTWAREASN A:503 , NAG A:712 , HOH A:801binding site for Mono-Saccharide NAG A 711 bound to ASN A 503
22AE4SOFTWAREASN A:520 , THR A:522 , GLN A:523 , GLN A:534 , NAG A:714 , HOH A:803 , HOH A:887binding site for Mono-Saccharide NAG A 713 bound to ASN A 520
23AE5SOFTWAREASN A:175 , ILE A:176 , SER A:177 , NAG A:707 , BMA A:708binding site for Poly-Saccharide residues MAN A 709 through BMA A 710

(-) SS Bonds  (8, 8)

Asymmetric 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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:268 -Pro A:269
2Thr A:322 -Pro A:323
3Tyr A:488 -Ile A:489

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I81)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I81)

(-) Exons   (0, 0)

(no "Exon" information available for 5I81)

(-) 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:528
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...................................eeeeeee................................................hhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhhhhhhhhhhhh...eee.......................hhhhhhhhhhhh....hhhhhhhhhhhh.eeeeee..eeeee.hhhhhh..hhhhhh...hhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhhhhh...eeeeee......eeeeee.......eeeeeee............eeeeeeee.........eeeeeeee.hhhhhh........eeeeehhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh....hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5i81 A  84 WGNLTCPICKGLFTAINLGLKKEPNVARVGSVAIKLCNLLKIAPPAVCQSIVHLFEDDMVEVWRRSVLSPSEACGLLLGSTCGHWDIFSSWNISLPTVPKPPPKPPSPPAPGAPVSRILFLTDLHWDHDYLEGTDPDCADPLCCRRGSGLPPASRPGAGYWGEYSKCDLPLRTLESLLSGLGPAGPFDMVYWTGDIPAHDVWHQTRQDQLRALTTVTALVRKFLGPVPVYPAVGNHESTPVNSFPPPFIEGNHSSRWLYEAMAKAWEPWLPAEALRTLRIGGFYALSPYPGLRLISLNMNFCSRENFWLLINSTDPAGQLQWLVGELQAAEDRGDKVHIIGHIPPGHCLKSWSWNYYRIVARYENTLAAQFFGHTHVDEFEVFYDEETLSRPLAVAFLAPSATTYIGLNPGYRVYQIDGNYSGSSHVVLDHETYILNLTQANIPGAIPHWQLLYRARETYGLPNTLPTAWHNLVYRMRGDMQLFQTFWFLYHKGHPPSEPCGTPCRLATLCAQLSARADSPALCRHLM 611
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603
   Legend:   → Mismatch (orange background)
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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)

(no "SCOP Domain" information available for 5I81)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I81)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I81)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ASM_HUMAN | P17405: 1x9o 5i85 5i8r 5jg8

(-) Related Entries Specified in the PDB File

5i85 5i8r