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(-) Description

Title :  CRYSTAL STRUCTURE OF PROPHYTEPSIN, A ZYMOGEN OF A BARLEY VACUOLAR ASPARTIC PROTEINASE.
 
Authors :  J. Kervinen, G. J. Tobin, J. Costa, D. S. Waugh, A. Wlodawer, A. Zdanov
Date :  19 May 99  (Deposition) - 16 Jul 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Aspartic Proteinases, Phytepsin, Saposin-Like Domain, Zymogen Structure, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kervinen, G. J. Tobin, J. Costa, D. S. Waugh, A. Wlodawer, A. Zdanov
Crystal Structure Of Plant Aspartic Proteinase Prophytepsin: Inactivation And Vacuolar Targeting.
Embo J. V. 18 3947 1999
PubMed-ID: 10406799  |  Reference-DOI: 10.1093/EMBOJ/18.14.3947
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROPHYTEPSIN
    Chains: A, B, C
    EC Number: 3.4.23.40
    Organism Scientific: HORDEUM VULGARE
    Organism Taxid: 4513

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1QDM)

(-) Sites  (0, 0)

(no "Site" information available for 1QDM)

(-) SS Bonds  (18, 18)

Asymmetric Unit
No.Residues
1A:6S-A:100S
2A:31S-A:72S
3A:37S-A:69S
4A:49 -A:55
5A:214 -A:218
6A:257 -A:294
7B:6S-B:100S
8B:31S-B:72S
9B:37S-B:69S
10B:49 -B:55
11B:214 -B:218
12B:257 -B:294
13C:6S-C:100S
14C:31S-C:72S
15C:37S-C:69S
16C:49 -C:55
17C:214 -C:218
18C:257 -C:294

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Thr A:26 -Pro A:27
2Thr B:26 -Pro B:27
3Thr C:26 -Pro C:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QDM)

(-) PROSITE Motifs  (3, 15)

Asymmetric Unit (3, 15)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.ASPR_HORVU84-505
 
 		  3A:18-335
B:18-335
C:18-335
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.ASPR_HORVU99-110
 
 
286-297
 
 		  6A:33-44
B:33-44
C:33-44
A:220-231
B:220-231
C:220-231
3SAP_BPS50015 Saposin B type domain profile.ASPR_HORVU314-354
 
 
378-419
 
 		  6A:1S-38S
B:1S-38S
C:1S-38S
A:65S-249
B:65S-249
C:65S-249
Biological Unit 1 (3, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.ASPR_HORVU84-505
 
 		  1A:18-335
-
-
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.ASPR_HORVU99-110
 
 
286-297
 
 		  2A:33-44
-
-
A:220-231
-
-
3SAP_BPS50015 Saposin B type domain profile.ASPR_HORVU314-354
 
 
378-419
 
 		  2A:1S-38S
-
-
A:65S-249
-
-
Biological Unit 2 (3, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.ASPR_HORVU84-505
 
 		  1-
B:18-335
-
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.ASPR_HORVU99-110
 
 
286-297
 
 		  2-
B:33-44
-
-
B:220-231
-
3SAP_BPS50015 Saposin B type domain profile.ASPR_HORVU314-354
 
 
378-419
 
 		  2-
B:1S-38S
-
-
B:65S-249
-
Biological Unit 3 (3, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.ASPR_HORVU84-505
 
 		  1-
-
C:18-335
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.ASPR_HORVU99-110
 
 
286-297
 
 		  2-
-
C:33-44
-
-
C:220-231
3SAP_BPS50015 Saposin B type domain profile.ASPR_HORVU314-354
 
 
378-419
 
 		  2-
-
C:1S-38S
-
-
C:65S-249

(-) Exons   (0, 0)

(no "Exon" information available for 1QDM)

(-) 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:433
 aligned with ASPR_HORVU | P42210 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:478
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500        
          ASPR_HORVU     31 VRIALKKRPIDRNSRVATGLSGGEEQPLLSGANPLRSEEEGDIVALKNYMNAQYFGEIGVGTPPQKFTVIFDTGSSNLWVPSAKCYFSIACYLHSRYKAGASSTYKKNGKPAAIQYGTGSIAGYFSEDSVTVGDLVVKDQEFIEATKEPGITFLVAKFDGILGLGFKEISVGKAVPVWYKMIEQGLVSDPVFSFWLNRHVDEGEGGEIIFGGMDPKHYVGEHTYVPVTQKGYWQFDMGDVLVGGKSTGFCAGGCAAIADSGTSLLAGPTAIITEINEKIGAAGVVSQECKTIVSQYGQQILDLLLAETQPKKICSQVGLCTFDGTRGVSAGIRSVVDDEPVKSNGLRADPMCSACEMAVVWMQNQLAQNKTQDLILDYVNQLCNRLPSPMGESAVDCGSLGSMPDIEFTIGGKKFALKPEEYILKVGEGAAAQCISGFTAMDIPPPRGPLWILGDVFMGPYHTVFDYGKLRIGFAKAA  508
               SCOP domains ----------------------               d1qdma2 A:2-247,A:248-338 Plant acid proteinase, phytepsin                                                                                                                                                                                            d1qdma1 A:1S-104S (Pro)phytepsin                                                                        d1qdma2 A:2-247,A:248-338 Plant acid proteinase, phytepsin                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhh..---------------.....hhhhhhhhhh...................................hhhhhhh...hhhhh................................................hhhhhh.........hhhhhhhhh.hhhhhhh..................----.............................eeee..eee..ee.......eeeee......eeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....--------------------------hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..........eehhhhhh....eeeee..eeeeehhhhheee..hhhhh.eee.eee.........eeeehhhhhh................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------PEPTIDASE_A1  PDB: A:18-335 UniProt: 84-505                                                                                                                                                                                                                                                                                                                                                                                           --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------ASP_PROTEASE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE----------------SAP_B  PDB: A:1S-38S UniProt: 314-354    -----------------------SAP_B  PDB: A:65S-249 UniProt: 378-419    ----------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1qdm A   6P VRIALKKRPIDRNSRVATGLSG---------------EEEGDIVALKNYMNAQYFGEIGVGTPPQKFTVIFDTGSSNLWVPSAKCYFSIACYLHSRYKAGASSTYKKNGKPAAIQYGTGSIAGYFSEDSVTVGDLVVKDQEFIEATKEPGITFLVAKFDGILGLGFKEISVGKAVPVWYKMIEQGLVSDPVFSFWLNRHV----GGEIIFGGMDPKHYVGEHTYVPVTQKGYWQFDMGDVLVGGKSTGFCAGGCAAIADSGTSLLAGPTAIITEINEKIGAAGVVSQECKTIVSQYGQQILDLLLAETQPKKICSQVGLCT--------------------------ADPMCSACEMAVVWMQNQLAQNKTQDLILDYVNQLCNRLPSPMGESAVDCGSLGSMPDIEFTIGGKKFALKPEEYILKVGEGAAAQCISGFTAMDIPPPRGPLWILGDVFMGPYHTVFDYGKLRIGFAKAA  338
                            |||||||15P|||||||25P||       -       | 4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164    |  174       184       194       204       214       224       234       244  ||||||7S|||||||17S|||||||27S|||||||37S|        -         -       67S|||||||77S|||||||87S|||||||97S|||||||250       260       270       280       290       300       310       320       330        
                            ||||||14P||||||23P||||               2                                                                                                                                                               164  169                                                                           247|||||||9S||||||18S||||||27S||||||36S||                        65S||||||74S||||||83S||||||92S|||||101S||||                                                                                          
                           6P||||||15P||||||24P|||                                                                                                                                                                                                                                                                    1S||||||10S||||||19S||||||28S||||||37S|                         66S||||||75S||||||84S||||||93S|||||102S|||                                                                                          
                            7P||||||16P||||||25P||                                                                                                                                                                                                                                                                     2S||||||11S||||||20S||||||29S||||||38S                          67S||||||76S||||||85S||||||94S|||||103S||                                                                                          
                             8P||||| 17P||||| 26P|                                                                                                                                                                                                                                                                      3S||||| 12S||||| 21S||||| 30S|||||                              68S||||| 77S||||| 86S||||| 95S|||||104S|                                                                                          
                              9P||||  18P||||  27P                                                                                                                                                                                                                                                                       4S||||  13S||||  22S||||  31S||||                               69S||||  78S||||  87S||||  96S||||  248                                                                                          
                              10P|||   19P|||                                                                                                                                                                                                                                                                             5S|||   14S|||   23S|||   32S|||                                70S|||   79S|||   88S|||   97S|||                                                                                               
                               11P||    20P||                                                                                                                                                                                                                                                                              6S||    15S||    24S||    33S||                                 71S||    80S||    89S||    98S||                                                                                               
                                12P|     21P|                                                                                                                                                                                                                                                                               7S|     16S|     25S|     34S|                                  72S|     81S|     90S|     99S|                                                                                               
                                 13P      22P                                                                                                                                                                                                                                                                                8S      17S      26S      35S                                   73S      82S      91S     100S                                                                                               


Chain B from PDB  Type:PROTEIN  Length:433
 aligned with ASPR_HORVU | P42210 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:478
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500        
          ASPR_HORVU     31 VRIALKKRPIDRNSRVATGLSGGEEQPLLSGANPLRSEEEGDIVALKNYMNAQYFGEIGVGTPPQKFTVIFDTGSSNLWVPSAKCYFSIACYLHSRYKAGASSTYKKNGKPAAIQYGTGSIAGYFSEDSVTVGDLVVKDQEFIEATKEPGITFLVAKFDGILGLGFKEISVGKAVPVWYKMIEQGLVSDPVFSFWLNRHVDEGEGGEIIFGGMDPKHYVGEHTYVPVTQKGYWQFDMGDVLVGGKSTGFCAGGCAAIADSGTSLLAGPTAIITEINEKIGAAGVVSQECKTIVSQYGQQILDLLLAETQPKKICSQVGLCTFDGTRGVSAGIRSVVDDEPVKSNGLRADPMCSACEMAVVWMQNQLAQNKTQDLILDYVNQLCNRLPSPMGESAVDCGSLGSMPDIEFTIGGKKFALKPEEYILKVGEGAAAQCISGFTAMDIPPPRGPLWILGDVFMGPYHTVFDYGKLRIGFAKAA  508
               SCOP domains ----------------------               d1qdmb2 B:2-247,B:248-338 Plant acid proteinase, phytepsin                                                                                                                                                                                            d1qdmb1 B:1S-104S (Pro)phytepsin                                                                        d1qdmb2 B:2-247,B:248-338 Plant acid proteinase, phytepsin                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhh...---------------.....hhhhh........................................hhhhhhh.......................................................hhhhhhh.........hhhhhhhhh.hhhhhhhhhh...............----.............................eeee...ee..ee.......eeeee......eeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...--------------------------hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhh..ee...hhhhh..eeeee..eeeeehhhhheeee.hhhhheeee.eee.........eeeehhhhhh................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------PEPTIDASE_A1  PDB: B:18-335 UniProt: 84-505                                                                                                                                                                                                                                                                                                                                                                                           --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------ASP_PROTEASE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE----------------SAP_B  PDB: B:1S-38S UniProt: 314-354    -----------------------SAP_B  PDB: B:65S-249 UniProt: 378-419    ----------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1qdm B   6P VRIALKKRPIDRNSRVATGLSG---------------EEEGDIVALKNYMNAQYFGEIGVGTPPQKFTVIFDTGSSNLWVPSAKCYFSIACYLHSRYKAGASSTYKKNGKPAAIQYGTGSIAGYFSEDSVTVGDLVVKDQEFIEATKEPGITFLVAKFDGILGLGFKEISVGKAVPVWYKMIEQGLVSDPVFSFWLNRHV----GGEIIFGGMDPKHYVGEHTYVPVTQKGYWQFDMGDVLVGGKSTGFCAGGCAAIADSGTSLLAGPTAIITEINEKIGAAGVVSQECKTIVSQYGQQILDLLLAETQPKKICSQVGLCT--------------------------ADPMCSACEMAVVWMQNQLAQNKTQDLILDYVNQLCNRLPSPMGESAVDCGSLGSMPDIEFTIGGKKFALKPEEYILKVGEGAAAQCISGFTAMDIPPPRGPLWILGDVFMGPYHTVFDYGKLRIGFAKAA  338
                            |||||||15P|||||||25P||       -       | 4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164    |  174       184       194       204       214       224       234       244  ||||||7S|||||||17S|||||||27S|||||||37S|        -         -       67S|||||||77S|||||||87S|||||||97S|||||||250       260       270       280       290       300       310       320       330        
                           6P||||||15P||||||24P|||               2                                                                                                                                                               164  169                                                                           247|||||||9S||||||18S||||||27S||||||36S||                        65S||||||74S||||||83S||||||92S|||||101S||||                                                                                          
                            7P||||||16P||||||25P||                                                                                                                                                                                                                                                                    1S||||||10S||||||19S||||||28S||||||37S|                         66S||||||75S||||||84S||||||93S|||||102S|||                                                                                          
                             8P||||||17P||||||26P|                                                                                                                                                                                                                                                                     2S||||||11S||||||20S||||||29S||||||38S                          67S||||||76S||||||85S||||||94S|||||103S||                                                                                          
                              9P||||| 18P||||| 27P                                                                                                                                                                                                                                                                      3S||||| 12S||||| 21S||||| 30S|||||                              68S||||| 77S||||| 86S||||| 95S|||||104S|                                                                                          
                              10P||||  19P||||                                                                                                                                                                                                                                                                           4S||||  13S||||  22S||||  31S||||                               69S||||  78S||||  87S||||  96S||||  248                                                                                          
                               11P|||   20P|||                                                                                                                                                                                                                                                                            5S|||   14S|||   23S|||   32S|||                                70S|||   79S|||   88S|||   97S|||                                                                                               
                                12P||    21P||                                                                                                                                                                                                                                                                             6S||    15S||    24S||    33S||                                 71S||    80S||    89S||    98S||                                                                                               
                                 13P|     22P|                                                                                                                                                                                                                                                                              7S|     16S|     25S|     34S|                                  72S|     81S|     90S|     99S|                                                                                               
                                  14P      23P                                                                                                                                                                                                                                                                               8S      17S      26S      35S                                   73S      82S      91S     100S                                                                                               


Chain C from PDB  Type:PROTEIN  Length:431
 aligned with ASPR_HORVU | P42210 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:478
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500        
          ASPR_HORVU     31 VRIALKKRPIDRNSRVATGLSGGEEQPLLSGANPLRSEEEGDIVALKNYMNAQYFGEIGVGTPPQKFTVIFDTGSSNLWVPSAKCYFSIACYLHSRYKAGASSTYKKNGKPAAIQYGTGSIAGYFSEDSVTVGDLVVKDQEFIEATKEPGITFLVAKFDGILGLGFKEISVGKAVPVWYKMIEQGLVSDPVFSFWLNRHVDEGEGGEIIFGGMDPKHYVGEHTYVPVTQKGYWQFDMGDVLVGGKSTGFCAGGCAAIADSGTSLLAGPTAIITEINEKIGAAGVVSQECKTIVSQYGQQILDLLLAETQPKKICSQVGLCTFDGTRGVSAGIRSVVDDEPVKSNGLRADPMCSACEMAVVWMQNQLAQNKTQDLILDYVNQLCNRLPSPMGESAVDCGSLGSMPDIEFTIGGKKFALKPEEYILKVGEGAAAQCISGFTAMDIPPPRGPLWILGDVFMGPYHTVFDYGKLRIGFAKAA  508
               SCOP domains ----------------------                d1qdmc2 C:3-247,C:248-338 Plant acid proteinase, phytepsin                                                                                                                                                                                           d1qdmc1 C:1S-104S (Pro)phytepsin                                                                        d1qdmc2 C:3-247,C:248-338 Plant acid protei nase, phytepsin                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------                --------------Asp-1qdmC01 C:17-337                                                                                                                                                                                                                                                                                                                                                                                                                     - Pfam domains (1)
           Pfam domains (2) ----------------------                --------------Asp-1qdmC02 C:17-337                                                                                                                                                                                                                                                                                                                                                                                                                     - Pfam domains (2)
           Pfam domains (3) ----------------------                --------------Asp-1qdmC03 C:17-337                                                                                                                                                                                                                                                                                                                                                                                                                     - Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SapB_2-1qdmC07 C:3S-37S            ----------------------------SapB_1-1qdmC04 C:66S-104S              ------------------------------------------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SapB_2-1qdmC08 C:3S-37S            ----------------------------SapB_1-1qdmC05 C:66S-104S              ------------------------------------------------------------------------------------------- Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SapB_2-1qdmC09 C:3S-37S            ----------------------------SapB_1-1qdmC06 C:66S-104S              ------------------------------------------------------------------------------------------- Pfam domains (6)
         Sec.struct. author ...............hhhhhh.----------------...hhhhhhhhhhh....................................hhhhhh...hhhhh...............................................hhhhhh..........hhhhhhhhh.hhhhhhhhh................----.........hhh.................eeee..eee..ee.......eeeee......eeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh...--------------------------hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..........ee...hhhhh..eeeee..eeeeehhhhhheee....-.eee..eee.........eeee......................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------PEPTIDASE_A1  PDB: C:18-335 UniProt: 84-505                                                                                                                                                                                                                                                                                                                                                                                           --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------ASP_PROTEASE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE----------------SAP_B  PDB: C:1S-38S UniProt: 314-354    -----------------------SAP_B  PDB: C:65S-249 UniProt: 378-419    ----------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1qdm C   6P VRIALKKRPIDRNSRVATGLSG----------------EEGDIVALKNYMNAQYFGEIGVGTPPQKFTVIFDTGSSNLWVPSAKCYFSIACYLHSRYKAGASSTYKKNGKPAAIQYGTGSIAGYFSEDSVTVGDLVVKDQEFIEATKEPGITFLVAKFDGILGLGFKEISVGKAVPVWYKMIEQGLVSDPVFSFWLNRHV----GGEIIFGGMDPKHYVGEHTYVPVTQKGYWQFDMGDVLVGGKSTGFCAGGCAAIADSGTSLLAGPTAIITEINEKIGAAGVVSQECKTIVSQYGQQILDLLLAETQPKKICSQVGLCT--------------------------ADPMCSACEMAVVWMQNQLAQNKTQDLILDYVNQLCNRLPSPMGESAVDCGSLGSMPDIEFTIGGKKFALKPEEYILKVGEGA-AQCISGFTAMDIPPPRGPLWILGDVFMGPYHTVFDYGKLRIGFAKAA  338
                            |||||||15P|||||||25P||       -        |4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164    |  174       184       194       204       214       224       234       244  ||||||7S|||||||17S|||||||27S|||||||37S|        -         -       67S|||||||77S|||||||87S|||||||97S|||||||250       260       270       280       290 |     300       310       320       330        
                           6P||||||15P||||||24P|||                3                                                                                                                                                              164  169                                                                           247|||||||9S||||||18S||||||27S||||||36S||                        65S||||||74S||||||83S||||||92S|||||101S||||                                       290 |                                              
                            7P||||||16P||||||25P||                                                                                                                                                                                                                                                                    1S||||||10S||||||19S||||||28S||||||37S|                         66S||||||75S||||||84S||||||93S|||||102S|||                                         292                                              
                             8P||||||17P||||||26P|                                                                                                                                                                                                                                                                     2S||||||11S||||||20S||||||29S||||||38S                          67S||||||76S||||||85S||||||94S|||||103S||                                                                                          
                              9P||||| 18P||||| 27P                                                                                                                                                                                                                                                                      3S||||| 12S||||| 21S||||| 30S|||||                              68S||||| 77S||||| 86S||||| 95S|||||104S|                                                                                          
                              10P||||  19P||||                                                                                                                                                                                                                                                                           4S||||  13S||||  22S||||  31S||||                               69S||||  78S||||  87S||||  96S||||  248                                                                                          
                               11P|||   20P|||                                                                                                                                                                                                                                                                            5S|||   14S|||   23S|||   32S|||                                70S|||   79S|||   88S|||   97S|||                                                                                               
                                12P||    21P||                                                                                                                                                                                                                                                                             6S||    15S||    24S||    33S||                                 71S||    80S||    89S||    98S||                                                                                               
                                 13P|     22P|                                                                                                                                                                                                                                                                              7S|     16S|     25S|     34S|                                  72S|     81S|     90S|     99S|                                                                                               
                                  14P      23P                                                                                                                                                                                                                                                                               8S      17S      26S      35S                                   73S      82S      91S     100S
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 Classification and Annotation

(-) SCOP Domains  (2, 6)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1QDM)

(-) Pfam Domains  (3, 9)

Asymmetric Unit
(-)
Clan: Peptidase_AA (368)
(-)
Family: Asp (155)
(-)
Hordeum vulgare (Barley) (1)
1aAsp-1qdmC01C:17-337
1bAsp-1qdmC02C:17-337
1cAsp-1qdmC03C:17-337
(-)
Clan: no clan defined [family: SapB_1] (11)
(-)
Family: SapB_1 (11)
(-)
Hordeum vulgare (Barley) (1)
2aSapB_1-1qdmC04C:66S-104S
2bSapB_1-1qdmC05C:66S-104S
2cSapB_1-1qdmC06C:66S-104S
(-)
Clan: no clan defined [family: SapB_2] (17)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (ASPR_HORVU | P42210)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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 Databases and Analysis Tools

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  1qdm
    Family and Domain Information: ProDom | SYSTERS
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  ASPR_HORVU | P42210
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  3.4.23.40
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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1QDM)

(-) Related Entries Specified in the PDB File

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