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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PPCA (TRIGONAL CRYSTAL FORM 2)
 
Authors :  N. Kolli, S. C. Garman
Date :  25 Sep 13  (Deposition) - 12 Mar 14  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cathepsin A, Glycoprotein, Serine Protease, Carboxypeptidase, Protective Protein, N-Linked Glycosylation, Proteolytically Activated Form, Lysosomal Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Kolli, S. C. Garman
Proteolytic Activation Of Human Cathepsin A.
J. Biol. Chem. V. 289 11592 2014
PubMed-ID: 24599961  |  Reference-DOI: 10.1074/JBC.M113.524280

(-) Compounds

Molecule 1 - LYSOSOMAL PROTECTIVE PROTEIN
    Chains: A, B
    EC Number: 3.4.16.5
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: PIB/V5-HIS-TOPO TA
    Expression System Strain: HI-FIVE
    Expression System Taxid: 7111
    Expression System Vector Type: STABLE CELL LINE
    Gene: CTSA, PPGB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CARBOXYPEPTIDASE C, CARBOXYPEPTIDASE L, CATHEPSIN A, PROTECTIVE PROTEIN CATHEPSIN A, PPCA, PROTECTIVE PROTEIN FOR BETA- GALACTOSIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:117 , GLU A:120 , ARG A:343 , LEU A:345 , NAG A:502BINDING SITE FOR RESIDUE NAG A 501
2AC2SOFTWARENAG A:501 , BMA A:503BINDING SITE FOR RESIDUE NAG A 502
3AC3SOFTWAREGLN A:165 , NAG A:502BINDING SITE FOR RESIDUE BMA A 503
4AC4SOFTWAREPRO A:77 , GLY A:255 , ASN A:305 , THR A:307BINDING SITE FOR RESIDUE NAG A 504
5AC5SOFTWAREASN B:117 , GLU B:120 , ARG B:343 , LEU B:345BINDING SITE FOR RESIDUE NAG B 501
6AC6SOFTWAREPRO B:77 , ASN B:305 , THR B:307BINDING SITE FOR RESIDUE NAG B 502

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:60 -A:334
2A:212 -A:228
3A:213 -A:218
4A:253 -A:303
5B:60 -B:334
6B:212 -B:228
7B:213 -B:218
8B:253 -B:303

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:57 -Pro A:58
2Ser A:100 -Pro A:101
3Gly B:57 -Pro B:58
4Ser B:100 -Pro B:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MWT)

(-) 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:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..............eeeeeee....eeeeeeee....hhhhh.eeeee.......hhhhhhhh...eee......eee...hhhhh.eeeee.........ee.......hhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhhhhhhh............hhhhhhh.......hhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh.........eeeeeee...eeeeeeeeeee..eeeeee.....hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mwt A   1 APDQDEIQRLPGLAKQPSFRQYSGYLKGSGSKHLHYWFVESQKDPENSPVVLWLNGGPGCSSLDGLLTEHGPFLVQPDGVTLEYNPYSWNLIANVLYLESPAGVGFSYSDDKFYATNDTEVAQSNFEALQDFFRLFPEYKNNKLFLTGESYAGIYIPTLAVLVMQDPSMNLQGLAVGNGLSSYEQNDNSLVYFAYYHGLLGNRLWSSLQTHCCSQNKCNFYDNKDLECVTNLQEVARIVGNSGLNIYNLYAPCAGGVPRMDPPCTNTTAASTYLNNPYVRKALNIPEQLPQWDMCNFLVNLQYRRLYRSMNSQYLKLLSSQKYQILLYNGDVDMACNFMGDEWFVDSLNQKMEVQRRPWLVKYGDSGEQIAGFVKEFSHIAFLTIKGAGHMVPTDKPLAAFTMFSRFLNKQPY 452
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449   
                                                                                                                                                                                                                                                                                           258|                                                                                                                                                          
                                                                                                                                                                                                                                                                                            298                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..............eeeeeee....eeeeeeee....hhhhh.eeeee.......hhhhhhhh...eee......eee...hhhhh.eeeee.........ee.......hhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhee..ee......hhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhhhhhhh............hhhhhhh.......hhhhhhhhhhhh..eeeeeee......hhhhhhhhhhh.........eeeeeee...eeeeeeeeeee..eeeeee.....hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mwt B   1 APDQDEIQRLPGLAKQPSFRQYSGYLKGSGSKHLHYWFVESQKDPENSPVVLWLNGGPGCSSLDGLLTEHGPFLVQPDGVTLEYNPYSWNLIANVLYLESPAGVGFSYSDDKFYATNDTEVAQSNFEALQDFFRLFPEYKNNKLFLTGESYAGIYIPTLAVLVMQDPSMNLQGLAVGNGLSSYEQNDNSLVYFAYYHGLLGNRLWSSLQTHCCSQNKCNFYDNKDLECVTNLQEVARIVGNSGLNIYNLYAPCAGGVPRMDPPCTNTTAASTYLNNPYVRKALNIPEQLPQWDMCNFLVNLQYRRLYRSMNSQYLKLLSSQKYQILLYNGDVDMACNFMGDEWFVDSLNQKMEVQRRPWLVKYGDSGEQIAGFVKEFSHIAFLTIKGAGHMVPTDKPLAAFTMFSRFLNKQPY 452
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449   
                                                                                                                                                                                                                                                                                           258|                                                                                                                                                          
                                                                                                                                                                                                                                                                                            298
   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 4MWT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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  4mwt
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  3.4.16.5
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 Related Entries

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

UniProtKB/Swiss-Prot
        PPGB_HUMAN | P10619: 1ivy 3bp4 3bp7 3bxn 4az0 4az3 4ci9 4cia 4cib 4mws

(-) Related Entries Specified in the PDB File

1ivy ZYMOGEN FORM
4mws