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(-) Description

Title :  HUMAN CATHEPSIN K MUTANT C25S IN COMPLEX WITH THE ALLOSTERIC EFFECTOR NSC94914
 
Authors :  M. Novinec, M. Korenc, B. Lenarcic
Date :  12 Apr 16  (Deposition) - 30 Nov 16  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Allostery Cysteine Peptidase Proteolysis Enzyme Regulation Collagenase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Novinec, M. Rebernik, B. Lenarcic
An Allosteric Site Enables Fine-Tuning Of Cathepsin K By Diverse Effectors.
Febs Lett. V. 590 4507 2016
PubMed-ID: 27859061  |  Reference-DOI: 10.1002/1873-3468.12495

(-) Compounds

Molecule 1 - CATHEPSIN K
    Chains: A, B
    EC Number: 3.4.22.38
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CTSK, CTSO, CTSO2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CATHEPSIN O,CATHEPSIN O2,CATHEPSIN X

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
16HM2Ligand/Ion[([1,1'-BIPHENYL]-2-YL)METHYL]PROPANEDIOIC ACID
2ACT1Ligand/IonACETATE ION
3GOL1Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
16HM1Ligand/Ion[([1,1'-BIPHENYL]-2-YL)METHYL]PROPANEDIOIC ACID
2ACT-1Ligand/IonACETATE ION
3GOL-1Ligand/IonGLYCEROL
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
16HM1Ligand/Ion[([1,1'-BIPHENYL]-2-YL)METHYL]PROPANEDIOIC ACID
2ACT1Ligand/IonACETATE ION
3GOL1Ligand/IonGLYCEROL
4SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:-1 , ALA A:1 , LYS A:119 , LYS A:122 , ARG A:123 , LYS A:176 , ARG A:198 , ASN A:199 , HOH A:430 , HOH A:468binding site for residue 6HM A 301
2AC2SOFTWAREGLN A:19 , GLY A:23 , SER A:24 , SER A:25 , ASN A:161 , HIS A:162 , HOH A:404binding site for residue SO4 A 302
3AC3SOFTWAREARG B:0 , ALA B:1 , LYS B:119 , LYS B:122 , ARG B:123 , ARG B:198 , ASN B:199 , HOH B:438 , HOH B:490binding site for residue 6HM B 301
4AC4SOFTWAREARG B:8 , THR B:14 , PRO B:15 , VAL B:16 , GLU B:59 , ASN B:60 , TYR B:67 , ASN B:70 , TYR B:193 , HOH B:468 , HOH B:494binding site for residue GOL B 302
5AC5SOFTWAREASN B:18 , GLY B:185 , GLU B:186 , ASN B:187 , HOH B:419binding site for residue SO4 B 303
6AC6SOFTWARESER A:95 , CYS A:96 , LYS B:176 , HOH B:465binding site for residue ACT B 304

(-) SS Bonds  (6, 6)

Asymmetric 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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JA7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JA7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JA7)

(-) Exons   (0, 0)

(no "Exon" information available for 5JA7)

(-) 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:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh.ee................hhh.eee...eeee....hhhhhhhhhhhh..eeeee...hhhhhh....ee...........eeeeeeeeeee..eeeeeee...........eeeee....hhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ja7 A  -6 IPEWEGRAPDSVDYRKKGYVTPVKNQGQCGSSWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 215
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213  


Chain B from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh.ee................hhh.eee....eee....hhhhhhhhhhhh..eeeee...hhhhhh....ee...........eeeeeeeeeee..eeeeeee...........eeeee....hhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ja7 B  -7 YIPEWEGRAPDSVDYRKKGYVTPVKNQGQCGSSWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM 215
                                     2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5JA7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JA7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JA7)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)

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  5ja7
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  CATK_HUMAN | P43235
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  3.4.22.38
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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 5jh3 5tdi 5tun 7pck

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5JA7)