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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CLASS I HUMAN ENDOPLASMIC RETICULUM 1,2-ALPHA-MANNOSIDASE AND MAN9GLCNAC2-PA COMPLEX
 
Authors :  K. Karaveg, Y. Xiang, K. W. Moremen
Date :  16 Jun 16  (Deposition) - 10 May 17  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Alpha-Barrel, Cation Replacement, Protein-Glycan Interaction, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Xiang, K. Karaveg, K. W. Moremen
Substrate Recognition And Catalysis By Gh47 Alpha-Mannosidases Involved In Asn-Linked Glycan Maturation In The Mammalian Secretory Pathway.
Proc. Natl. Acad. Sci. V. 113 E7890 2016 U. S. A.
PubMed-ID: 27856750  |  Reference-DOI: 10.1073/PNAS.1611213113

(-) Compounds

Molecule 1 - ENDOPLASMIC RETICULUM MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA- MANNOSIDASE
    ChainsA
    EC Number3.2.1.113
    EngineeredYES
    Expression SystemKOMAGATAELLA PASTORIS
    Expression System Taxid4922
    GeneMAN1B1, UNQ747/PRO1477
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymER ALPHA-1,2-MANNOSIDASE,ER MANNOSIDASE 1,ERMAN1, MAN9GLCNAC2-SPECIFIC-PROCESSING ALPHA-MANNOSIDASE,MANNOSIDASE ALPHA CLASS 1B MEMBER 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 17)

Asymmetric/Biological Unit (7, 17)
No.NameCountTypeFull Name
11PS1Ligand/Ion3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
2BMA1Ligand/IonBETA-D-MANNOSE
3BU14Ligand/Ion1,4-BUTANEDIOL
4LA1Ligand/IonLANTHANUM (III) ION
5MAN7Ligand/IonALPHA-D-MANNOSE
6NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SO42Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:688 , MAN A:707 , HOH A:864 , HOH A:892 , HOH A:927 , HOH A:1038 , HOH A:1082binding site for residue LA A 701
2AC2SOFTWARELYS A:262 , LYS A:266 , HIS A:452 , LEU A:453 , HOH A:865 , HOH A:994 , HOH A:1022binding site for residue SO4 A 702
3AC3SOFTWARELEU A:576 , TYR A:577 , GLN A:579binding site for residue SO4 A 703
4AC4SOFTWARESER A:278 , TRP A:473 , VAL A:488 , GLY A:540 , ASP A:654 , HOH A:847binding site for residue BU1 A 704
5AC5SOFTWAREASN A:360 , PRO A:364 , ARG A:367 , ILE A:379 , HOH A:846 , HOH A:1053binding site for residue BU1 A 705
6AC6SOFTWAREARG A:265 , TRP A:269 , GLU A:309 , TRP A:313 , LYS A:317 , HOH A:801binding site for residue 1PS A 715
7AC7SOFTWAREARG A:597 , MAN A:707 , BMA A:709 , MAN A:710 , HOH A:871 , HOH A:1000 , HOH A:1257binding site for residue BU1 A 716
8AC8SOFTWAREHIS A:515 , ARG A:632 , PRO A:634 , HOH A:803 , HOH A:827 , HOH A:1084binding site for residue BU1 A 717
9AC9SOFTWAREASN A:327 , PHE A:329 , ARG A:334 , SER A:375 , ASP A:376 , PRO A:387 , ARG A:388 , TRP A:389 , GLU A:397 , ALA A:460 , ARG A:461 , ASP A:463 , LYS A:521 , ASP A:523 , LEU A:525 , GLU A:570 , ALA A:590 , ASP A:591 , HIS A:593 , ARG A:597 , GLU A:599 , PHE A:659 , GLU A:663 , THR A:688 , GLU A:689 , LA A:701 , BU1 A:716 , HOH A:811 , HOH A:821 , HOH A:856 , HOH A:860 , HOH A:864 , HOH A:867 , HOH A:871 , HOH A:927 , HOH A:951 , HOH A:955 , HOH A:1009 , HOH A:1019 , HOH A:1038 , HOH A:1051 , HOH A:1059 , HOH A:1108 , HOH A:1134binding site for Poly-Saccharide residues NAG A 706 through MAN A 714

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:527 -A:556

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:503 -Pro A:504

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KIJ)

(-) 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:452
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh....eee....eee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee.....ee.......eehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...........ee......ee...ee.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhheee......eee.eee..eee.eee...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh........eeee..........ee.hhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhh..........eee.....eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kij A 245 HLNYRQKGVIDVFLHAWKGYRKFAWGHDELKPVSRSFSEWFGLGLTLIDALDTMWILGLRKEFEEARKWVSKKLHFEKDVDVNLFESTIRILGGLLSAYHLSGDSLFLRKAEDFGNRLMPAFRTPSKIPYSDVNIGTGVAHPPRWTSDSTVAEVTSIQLEFRELSRLTGDKKFQEAVEKVTQHIHGLSGKKDGLVPMFINTHSGLFTHLGVFTLGARADSYYEYLLKQWIQGGKQETQLLEDYVEAIEGVRTHLLRHSEPSKLTFVGELAHGRFSAKMDHLVCFLPGTLALGVYHGLPASHMELAQELMETCYQMNRQMETGLSPEIVHFNLYPQPGRRDVEVKPADRHNLLRPETVESLFYLYRVTGDRKYQDWGWEILQSFSRFTRVPSGGYSSINNVQDPQKPEPRDKMESFFLGETLKYLFLLFSDDPNLLSLDAYVFNTEAHPLPIW 696
                                   254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694  

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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 5KIJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        MA1B1_HUMAN | Q9UKM71fmi 1fo2 1fo3 1x9d 5kk7

(-) Related Entries Specified in the PDB File

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