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(-) Description

Title :  PROTEINASE K BY LB NANOTEMPLATE METHOD AFTER THE FIRST STEP OF HIGH X-RAY DOSE ON ESRF ID14-2 BEAMLINE
 
Authors :  E. Pechkova, S. K. Tripathi, C. Nicolini
Date :  20 Jul 08  (Deposition) - 07 Jul 09  (Release) - 07 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.02
Chains :  Asym./Biol. Unit :  X
Keywords :  Alpha And Beta Proteins, Calcium, Hydrolase, Metal-Binding, Protease, Serine Protease, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Pechkova, S. K. Tripathi, C. Nicolini
Radiation Damage In Protein Structural Characterization By Synchrotron Radiation: State Of The Art And Nanotechnology-Based Perspective
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEINASE K
    Chains: X
    EC Number: 3.4.21.64
    Organism Common: ENGYODONTIUM ALBUM
    Organism Scientific: TRITIRACHIUM ALBUM
    Organism Taxid: 37998
    Synonym: TRITIRACHIUM ALKALINE PROTEINASE, ENDOPEPTIDASE K

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU X:174 , PRO X:175 , THR X:179 , ASP X:200 , HOH X:300 , HOH X:337BINDING SITE FOR RESIDUE CA X 280

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1X:34 -X:123
2X:178 -X:249

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser X:170 -Pro X:171

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUBTILASE_ASPPS00136 Serine proteases, subtilase family, aspartic acid active site.PRTK_PARAQ140-151  1X:35-46
2SUBTILASE_HISPS00137 Serine proteases, subtilase family, histidine active site.PRTK_PARAQ174-184  1X:69-79
3SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.PRTK_PARAQ327-337  1X:222-232

(-) Exons   (0, 0)

(no "Exon" information available for 3DVR)

(-) 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 X from PDB  Type:PROTEIN  Length:279
 aligned with PRTK_PARAQ | P06873 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:279
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375         
           PRTK_PARAQ   106 AAQTNAPWGLARISSTSPGTSTYYYDESAGQGSCVYVIDTGIEASHPEFEGRAQMVKTYYYSSRDGNGHGTHCAGTVGSRTYGVAKKTQLFGVKVLDDNGSGQYSTIIAGMDFVASDKNNRNCPKGVVASLSLGGGYSSSVNSAAARLQSSGVMVAVAAGNNNADARNYSPASEPSVCTVGASDRYDRRSSFSNYGSVLDIFGPGTSILSTWIGGSTRSISGTSMATPHVAGLAAYLMTLGKTTAASACRYIADTANKGDLSNIPFGTVNLLAYNNYQA 384
               SCOP domains d3dvrx_ X: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3dvrX00 X:1-279  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhhh........ee........eeeeeee......hhhhh..eeeeee.........hhhhhhhhhhhh.........eeeeee........hhhhhhhhhhhhhhhhhhh....eeeeee...ee.hhhhhhhhhhhhhh..eeeee......hhh.ee.......eeeeee.................eeee...eeeee...eeeee.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhee............ee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------SUBTILASE_AS----------------------SUBTILASE_H----------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S----------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dvr X   1 AAQTNAPWGLARISSTSPGTSTYYYDESAGQGSCVYVIDTGIEASHPEFEGRAQMVKTYYYSSRDGNGHGTHCAGTVGSRTYGVAKKTQLFGVKVLDDNGSGQYSTIIAGMDFVASDKNNRNCPKGVVASLSLGGGYSSSVNSAAARLQSSGVMVAVAAGNNNADARNYSPASEPSVCTVGASDRYDRRSSFSNYGSVLDIFGPGTSILSTWIGGSTRSISGTSMATPHVAGLAAYLMTLGKTTAASACRYIADTANKGDLSNIPFGTVNLLAYNNYQA 279
                                    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       260       270
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (PRTK_PARAQ | P06873)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
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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  3dvr
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRTK_PARAQ | P06873: 1bjr 1cnm 1egq 1ht3 1ic6 1oyo 1p7v 1p7w 1pek 1pfg 1pj8 1ptk 2dp4 2dqk 2duj 2g4v 2hd4 2hpz 2id8 2pkc 2pq2 2prk 2pwa 2pwb 2pyz 2v8b 3aj8 3aj9 3d9q 3ddz 3de0 3de1 3de2 3de3 3de4 3de5 3de6 3de7 3dvq 3dvs 3dw1 3dw3 3dwe 3dyb 3gt3 3gt4 3i2y 3i30 3i34 3i37 3l1k 3osz 3prk 3ptl 3q40 3q5g 3qmp 4b5l 4dj5 4fon 4wob 4woc 4zar 5amx 5avj 5avk 5b1d 5b1e 5cw1 5i9s 5k7s 5kxu 5kxv 5uvl

(-) Related Entries Specified in the PDB File

1ptk PROTEINASE K
3dvq PROTEINASE K
3dvs PROTEINASE K
3dw1 PROTEINASE K
3dw3 PROTEINASE K