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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  ENDOTHIAPEPSIN-DB5 COMPLEX.
 
Authors :  D. Bailey, J. Sanz-Aparicio, A. Albert, J. B. Cooper
Date :  22 Nov 11  (Deposition) - 18 Apr 12  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase-Hydrolase Inhibitor Complex, Aspartic Proteinase Mechanism, Transition State Analogue. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Bailey, E. P. Carpenter, A. Coker, S. Coker, J. Read, A. T. Jones, P. Erskine, C. F. Aguilar, M. Badasso, L. Toldo, F. Rippmann, J. Sanz-Aparicio, A. Albert, T. L. Blundell, N. B. Roberts, S. P. Wood, J. B. Cooper
An Analysis Of Subdomain Orientation, Conformational Change And Disorder In Relation To Crystal Packing Of Aspartic Proteinases.
Acta Crystallogr. , Sect. D V. 68 541 2012
PubMed-ID: 22525752  |  Reference-DOI: 10.1107/S0907444912004817

(-) Compounds

Molecule 1 - ENDOTHIAPEPSIN
    Chains: A
    EC Number: 3.4.23.22
    Organism Common: CHESNUT BLIGHT FUNGUS
    Organism Scientific: CRYPHONECTRIA PARASITICA
    Organism Taxid: 5116
    Synonym: ASPARTATE PROTEASE
 
Molecule 2 - DB5 PEPTIDE
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
113E1Mod. Amino AcidN-[(2S)-2-AMINO-3-PHENYLPROPYL]-L-METHIONINE
2SUI1Mod. Amino Acid(3-AMINO-2,5-DIOXO-1-PYRROLIDINYL)ACETIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 3URI)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:254 -A:289

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:25 -Pro A:26
2Ser A:136 -Pro A:137

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3URI)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.CARP_CRYPA106-417  1A:17-327
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.CARP_CRYPA121-132
305-316		  2A:32-43
A:215-226

(-) Exons   (0, 0)

(no "Exon" information available for 3URI)

(-) 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:329
 aligned with CARP_CRYPA | P11838 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:330
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419
           CARP_CRYPA    90 STGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTASEVDGQTIYTPSKSTTAKLLSGATWSISYGDGSSSSGDVYTDTVSVGGLTVTGQAVESAKKVSSSFTEDSTIDGLLGLAFSTLNTVSPTQQKTFFDNAKASLDSPVFTADLGYHAPGTYNFGFIDTTAYTGSITYTAVSTKQGFWEWTSTGYAVGSGTFKSTSIDGIADTGTTLLYLPATVVSAYWAQVSGAKSSSSVGGYVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSSCFGGIQSSAGIGINIFGDVALKAAFVVFNGATTPTLGFASK 419
               SCOP domains d3uria_ A: Endothiapepsin                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee.......eeeeeee....eeeeeeee......eee....hhhhh.-....hhhhh...eeeeeeeeeee.....eeeeeeeeeeeee..eeeeeeeeeeeeeehhhhhhh....eeee..hhhhh........hhhhhhhhhh...eeeee......eeeee...hhhhheeeeeeee........eeeeeeeee.....eeeeeeeee......eeehhhhhhhhhh.....eee....eeeee.......eeeee..eeeeehhhhheeee......eeee.eee......eeehhhhhh.eeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------PEPTIDASE_A1  PDB: A:17-327 UniProt: 106-417                                                                                                                                                                                                                                                                            -- PROSITE (1)
                PROSITE (2) -------------------------------ASP_PROTEASE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3uri A   1 STGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTASEVd-QTIYTPSKSTTAKLLSGATWSISYGDGSSSSGDVYTDTVSVGGLTVTGQAVESAKKVSSSFTEDSTIDGLLGLAFSTLNTVSPTQQKTFFDNAKASLDSPVFTADLGYHAPGTYNFGFIDTTAYTGSITYTAVSTKQGFWEWTSTGYAVGSGTFKSTSIDGIADTGTTLLYLPATVVSAYWAQVSGAKSSSSVGGYVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSSCFGGIQSSAGIGINIFGDVALKAAFVVFNGATTPTLGFASK 329
                                    10        20        30        40        50   | |  59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329
                                                                                54-SUI                                                                                                                                                                                                                                                                                
                                                                                  55                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 3uri B 401 PHLSxAH 408
                                || 
                              405-13E
                               407
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3URI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3URI)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CARP_CRYPA | P11838)
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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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  Cis Peptide Bonds
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  3uri
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  CARP_CRYPA | P11838
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  3.4.23.22
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 Related Entries

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

UniProtKB/Swiss-Prot
        CARP_CRYPA | P11838: 1e5o 1e80 1e81 1e82 1eed 1ent 1epl 1epm 1epn 1epo 1epp 1epq 1epr 1er8 1gkt 1gvt 1gvu 1gvv 1gvw 1gvx 1od1 1oew 1oex 2er0 2er6 2er7 2er9 2jji 2jjj 2v00 2vs2 3er3 3er5 3lzy 3pb5 3pbd 3pbz 3pcw 3pcz 3pgi 3pi0 3pld 3pll 3pm4 3pmu 3pmy 3prs 3psy 3pww 3q6y 3t6i 3t7p 3t7q 3t7x 3urj 3url 3wz6 3wz7 3wz8 4ape 4er1 4er2 4er4 4kup 4l6b 4lap 4lbt 4lhh 4lp9 4y35 4y36 4y37 4y38 4y39 4y3a 4y3d 4y3e 4y3f 4y3g 4y3h 4y3j 4y3l 4y3m 4y3n 4y3p 4y3q 4y3r 4y3s 4y3t 4y3w 4y3x 4y3y 4y3z 4y41 4y43 4y44 4y45 4y47 4y48 4y4a 4y4b 4y4d 4y4e 4y4g 4y4j 4y4t 4y4u 4y4w 4y4x 4y4z 4y50 4y51 4y53 4y54 4y56 4y57 4y58 4y5a 4y5b 4y5c 4y5e 4y5g 4y5k 4y5l 4y5m 4y5n 4y5p 4yck 4yct 4ycy 4yd3 4yd4 4yd5 4yd6 4yd7 4ze6 4zea 5dpz 5dq1 5dq2 5dq4 5dq5 5dr0 5dr1 5dr3 5dr4 5dr7 5dr8 5er1 5er2 5hco 5hct 5is4 5isj 5isk 5j25 5oyq 5oyr 5oys 5oyt 5oyu 5oyv 5oyw 5oyx 5oyy 5oyz 5oz0 5oz1 5oz2 5oz3 5oz4 5oz5 5oz6 5oz7 5oz8 5oz9 5oza 5ozb 5ozc 5ozd 5oze 5ozf 5ozg 5ozh 5ozi 5ozj 5ozk 5ozl 5ozm 5ozn 5ozo 5ozp 5ozq 5ozr 5ozs 5ozt 5ozu 5ozv 5ozw 5ozx 5ozy 5ozz 5p00 5p01 5p02 5p03 5p04 5p05 5p06 5p07 5p08 5p09 5p0a 5p0b 5p0c 5p0d 5p0e 5p0f 5p0g 5p0h 5p0i 5p0j 5p0k 5p0l 5p0m 5p0n 5p0o 5p0p 5p0q 5p0r 5p0s 5p0t 5p0u 5p0v 5p0w 5p0x 5p0y 5p0z 5p10 5p11 5p12 5p13 5p14 5p15 5p16 5p17 5p18 5p19 5p1a 5p1b 5p1c 5p1d 5p1e 5p1f 5p1g 5p1h 5p1i 5p1j 5p1k 5p1l 5p1m 5p1n 5p1o 5p1p 5p1q 5p1r 5p1s 5p1t 5p1u 5p1v 5p1w 5p1x 5p1y 5p1z 5p20 5p22 5p23 5p24 5p25 5p26 5p27 5p28 5p29 5p2a 5p2b 5p2c 5p2d 5p2e 5p2f 5p2g 5p2h 5p2i 5p2j 5p2k 5p2l 5p2m 5p2n 5p2o 5p2q 5p2r 5p2s 5p2t 5p2u 5p2v 5p2w 5p2x 5p2y 5p2z 5p30 5p31 5p32 5p33 5p34 5p35 5p36 5p37 5p38 5p39 5p3a 5p3b 5p3c 5p3d 5p3e 5p3f 5p3g 5p3h 5p3i 5p3j 5p3k 5p3l 5p3m 5p3n 5p3o 5p3p 5p3q 5p3r 5p3s 5p3t 5p3u 5p3v 5p3w 5p3x 5p3y 5p3z 5p40 5p41 5p42 5p43 5p44 5p45 5p46 5p47 5p48 5p49 5p4a 5p4b 5p4c 5p4d 5p4e 5p4f 5p4g 5p4h 5p4i 5p4j 5p4k 5p4l 5p4m 5p4n 5p4o 5p4p 5p4q 5p4r 5p4s 5p4t 5p4u 5p4v 5p4w 5p4x 5p4y 5p4z 5p50 5p51 5p52 5p53 5p54 5p55 5p56 5p57 5p58 5p59 5p5a 5p5b 5p5c 5p5d 5p5e 5p5f 5p5g 5p5h 5p5i 5p5j 5p5k 5p5l 5p5m 5p5n 5p5o 5p5p 5p5q 5p5r 5p5s 5p5t 5p5u 5p5v 5p5w 5p5x 5p5y 5p5z 5p60 5p61 5p62 5p63 5p64 5p65 5p66 5p67 5p68 5p69 5p6a 5p6b 5p6c 5p6d 5p6e 5p6f 5p6g 5p6h 5p6i 5p6j 5p6k 5p6l 5p6m 5p6n 5p6o 5p6p 5p6q 5p6r 5p6s 5p6t 5p6u 5p6v 5p6w 5p6x 5p6y 5p6z 5p70 5p71 5p72 5p73 5p74 5p75 5p76 5p77 5p78 5p79 5p7a 5p7b 5p7c 5p7d 5p7e 5p7f 5p7g 5p7h 5p7i 5p7j 5p7k 5p7l 5p7m 5p7n 5p7o 5p7p 5p7q 5p7r 5p7s 5p7t 5p7u 5p7v 5p7w 5p7x 5p7y 5p7z 5p80 5p81 5p82 5p83 5p84 5p85 5p86 5p87 5p88 5p89 5p8a 5p8b 5p8c 5p8d 5p8e 5p8f 5p8g 5p8h 5p8i 5p8j 5p8k 5p8l 5p8m 5p8n 5p8o 5p8p 5p8q 5p8r 5p8s 5p8t 5p8u 5p8v

(-) Related Entries Specified in the PDB File

3urj 3url