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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD TYPE HUMAN PROCATHEPSIN K
 
Authors :  J. Sivaraman, M. Lalumiere, R. Menard, M. Cygler
Date :  21 Oct 98  (Deposition) - 25 Oct 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase (Thiol Protease), Procathepsin K, Cysteine Proteases, Proregion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Sivaraman, M. Lalumiere, R. Menard, M. Cygler
Crystal Structure Of Wild-Type Human Procathepsin K.
Protein Sci. V. 8 283 1999
PubMed-ID: 10048321
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (PROCATHEPSIN K)
    Chains: A, B, C, D
    EC Number: 3.4.22.38
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 7PCK)

(-) Sites  (0, 0)

(no "Site" information available for 7PCK)

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:63
2A:56 -A:96
3A:155 -A:204
4B:22 -B:63
5B:56 -B:96
6B:155 -B:204
7C:22 -C:63
8C:56 -C:96
9C:155 -C:204
10D:22 -D:63
11D:56 -D:96
12D:155 -D:204

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 7PCK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 7PCK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 7PCK)

(-) Exons   (0, 0)

(no "Exon" information available for 7PCK)

(-) 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:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d7pcka_ A: (Pro)cathepsin K                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 7pckA00 A:1P-215 Cysteine proteinases                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.........hhhhhhhh................................................hhhhhhhhhhhhhhhhhh.......hhhhhhh.....hhh...hhhhhhhhhhh.....hhh.............hhh.......eee.....hhhhhhhhhh...eeeee....hhhh.eeee.............eeeeeeeeeee..eeeeeee...........eeeee.....hhh.....eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 7pck A  1P LYPEEILDTHWELWKKTHRKQYNNKVDEISRRLIWEKNLKYISIHNLEASLGVHTYELAMNHLGDMTSEEVVQKMTGLKVPLSHSRSNDTLYIPEWEGRAPDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 215
                            |||||||10P|||||||20P|||||||30P|||||||40P|||||||50P|||||||60P|||||||70P|||||||80P|||||||90P|||||||||1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211    
                            |||||||9P||||||18P||||||27P||||||36P||||||45P||||||54P||||||63P||||||72P||||||81P||||||90P||||||99P|                                                                                                                                                                                                                      
                           1P||||||10P||||||19P||||||28P||||||37P||||||46P||||||55P||||||64P||||||73P||||||82P||||||91P||||||| 1                                                                                                                                                                                                                      
                            2P||||||11P||||||20P||||||29P||||||38P||||||47P||||||56P||||||65P||||||74P||||||83P||||||92P||||||                                                                                                                                                                                                                        
                             3P||||| 12P||||| 21P||||| 30P||||| 39P||||| 48P||||| 57P||||| 66P||||| 75P||||| 84P||||| 93P|||||                                                                                                                                                                                                                        
                              4P||||  13P||||  22P||||  31P||||  40P||||  49P||||  58P||||  67P||||  76P||||  85P||||  94P||||                                                                                                                                                                                                                        
                               5P|||   14P|||   23P|||   32P|||   41P|||   50P|||   59P|||   68P|||   77P|||   86P|||   95P|||                                                                                                                                                                                                                        
                                6P||    15P||    24P||    33P||    42P||    51P||    60P||    69P||    78P||    87P||    96P||                                                                                                                                                                                                                        
                                 7P|     16P|     25P|     34P|     43P|     52P|     61P|     70P|     79P|     88P|     97P|                                                                                                                                                                                                                        
                                  8P      17P      26P      35P      44P      53P      62P      71P      80P      89P      98P                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d7pckb_ B: (Pro)cathepsin K                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 7pckB00 B:1P-215 Cysteine proteinases                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.........hhhhhhhh.............................................hhhhhhhhhhhhhhhhhh.......hhhhhhh.....hhh...hhhhhhhhhhh...............................eee.....hhhhhhhhhh...eeeee....hhhh.eeee.............eeeeeeeeeee..eeeeeee...........eeeee.....hhh.....eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 7pck B  1P LYPEEILDTHWELWKKTHRKQYNNKVDEISRRLIWEKNLKYISIHNLEASLGVHTYELAMNHLGDMTSEEVVQKMTGLKVPLRSNDTLYIPEWEGRAPDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 215
                            |||||||10P|||||||20P|||||||30P|||||||40P|||||||50P|||||||60P|||||||70P|||||||80P|||||||93P|||||||  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214 
                           1P||||||10P||||||19P||||||28P||||||37P||||||46P||||||55P||||||64P||||||73P||||||82P||||||94P||||||                                                                                                                                                                                                                      
                            2P||||||11P||||||20P||||||29P||||||38P||||||47P||||||56P||||||65P||||||74P||||||86P||||||95P|||||                                                                                                                                                                                                                      
                             3P||||||12P||||||21P||||||30P||||||39P||||||48P||||||57P||||||66P||||||75P||||||87P||||||96P||||                                                                                                                                                                                                                      
                              4P||||| 13P||||| 22P||||| 31P||||| 40P||||| 49P||||| 58P||||| 67P||||| 76P||||| 88P||||| 97P|||                                                                                                                                                                                                                      
                               5P||||  14P||||  23P||||  32P||||  41P||||  50P||||  59P||||  68P||||  77P||||  89P||||  98P||                                                                                                                                                                                                                      
                                6P|||   15P|||   24P|||   33P|||   42P|||   51P|||   60P|||   69P|||   78P|||   90P|||   99P|                                                                                                                                                                                                                      
                                 7P||    16P||    25P||    34P||    43P||    52P||    61P||    70P||    79P||    91P||      1                                                                                                                                                                                                                      
                                  8P|     17P|     26P|     35P|     44P|     53P|     62P|     71P|     80P|     92P|                                                                                                                                                                                                                             
                                   9P      18P      27P      36P      45P      54P      63P      72P      81P      93P                                                                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d7pckc_ C: (Pro)cathepsin K                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 7pckC00 C:1P-215 Cysteine proteinases                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.........hhhhhhhh...........................................hhhhhhhhhhhhhhhhhh.......hhhhhhh.....hhh...hhhhhhhhhhh.....hhh.......................eee.....hhhhhhhhhh...eeeee....hhhh.eeee.............eeeeeeeeeee..eeeeeee...........eeeee.....hhh.....eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 7pck C  1P LYPEEILDTHWELWKKTHRKQYNNKVDEISRRLIWEKNLKYISIHNLEASLGVHTYELAMNHLGDMTSEEVVQKMTGLKVPLNDTLYIPEWEGRAPDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 215
                            |||||||10P|||||||20P|||||||30P|||||||40P|||||||50P|||||||60P|||||||70P|||||||80P|||||||95P|||||    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206         
                           1P||||||10P||||||19P||||||28P||||||37P||||||46P||||||55P||||||64P||||||73P||||||82P||||||96P||||                                                                                                                                                                                                                      
                            2P||||||11P||||||20P||||||29P||||||38P||||||47P||||||56P||||||65P||||||74P||||||88P||||||97P|||                                                                                                                                                                                                                      
                             3P||||||12P||||||21P||||||30P||||||39P||||||48P||||||57P||||||66P||||||75P||||||89P||||||98P||                                                                                                                                                                                                                      
                              4P||||| 13P||||| 22P||||| 31P||||| 40P||||| 49P||||| 58P||||| 67P||||| 76P||||| 90P||||| 99P|                                                                                                                                                                                                                      
                               5P||||  14P||||  23P||||  32P||||  41P||||  50P||||  59P||||  68P||||  77P||||  91P||||    1                                                                                                                                                                                                                      
                                6P|||   15P|||   24P|||   33P|||   42P|||   51P|||   60P|||   69P|||   78P|||   92P|||                                                                                                                                                                                                                           
                                 7P||    16P||    25P||    34P||    43P||    52P||    61P||    70P||    79P||    93P||                                                                                                                                                                                                                           
                                  8P|     17P|     26P|     35P|     44P|     53P|     62P|     71P|     80P|     94P|                                                                                                                                                                                                                           
                                   9P      18P      27P      36P      45P      54P      63P      72P      81P      95P                                                                                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d7pckd_ D: (Pro)cathepsin K                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 7pckD00 D:1P-215 Cysteine proteinases                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.........hhhhhhhh................................hhhhhhhhhhhhhhhhhh.......hhhhhhh.....hhh...hhhhhhhhhhh.....hhh.............hhh.......eee.....hhhhhhhhhh...eeeee....hhhh.eeee.............eeeeeeeeeee..eeeeeee...........eeeee.....hhh.....eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 7pck D  1P LYPEEILDTHWELWKKTHRKQYNNKVDEISRRLIWEKNLKYISIHNLEASLGVHTYELAMNHLGDMTSEEVVQKMTGLKVLYIAPDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 215
                            |||||||10P|||||||20P|||||||30P|||||||40P|||||||50P|||||||60P|||||||70P|||||||80P||||     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207        
                           1P||||||10P||||||19P||||||28P||||||37P||||||46P||||||55P||||||64P||||||73P||||||92P||                                                                                                                                                                                                                      
                            2P||||||11P||||||20P||||||29P||||||38P||||||47P||||||56P||||||65P||||||74P||||||93P|                                                                                                                                                                                                                      
                             3P||||||12P||||||21P||||||30P||||||39P||||||48P||||||57P||||||66P||||||75P||||||  1                                                                                                                                                                                                                      
                              4P||||| 13P||||| 22P||||| 31P||||| 40P||||| 49P||||| 58P||||| 67P||||| 76P|||||                                                                                                                                                                                                                         
                               5P||||  14P||||  23P||||  32P||||  41P||||  50P||||  59P||||  68P||||  77P||||                                                                                                                                                                                                                         
                                6P|||   15P|||   24P|||   33P|||   42P|||   51P|||   60P|||   69P|||   78P|||                                                                                                                                                                                                                         
                                 7P||    16P||    25P||    34P||    43P||    52P||    61P||    70P||    79P||                                                                                                                                                                                                                         
                                  8P|     17P|     26P|     35P|     44P|     53P|     62P|     71P|     80P|                                                                                                                                                                                                                         
                                   9P      18P      27P      36P      45P      54P      63P      72P      91P
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 7PCK)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)

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  CATK_HUMAN | P43235
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 Related Entries

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

UniProtKB/Swiss-Prot
        CATK_HUMAN | P43235: 1atk 1au0 1au2 1au3 1au4 1ayu 1ayv 1ayw 1bgo 1by8 1mem 1nl6 1nlj 1q6k 1snk 1tu6 1u9v 1u9w 1u9x 1vsn 1yk7 1yk8 1yt7 2ato 2aux 2auz 2bdl 2r6n 3c9e 3h7d 3kw9 3kwb 3kwz 3kx1 3o0u 3o1g 3ovz 4dmx 4dmy 4n79 4n8w 4x6h 4x6i 4x6j 4yv8 4yva 5j94 5ja7 5jh3 5tdi 5tun

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 7PCK)