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(-) Description

Title :  CRYSTAL STRUCTURE OF A CLOSTRIPAIN (PARMER_00083) FROM PARABACTEROIDES MERDAE ATCC 43184 IN COMPLEX WITH PEPTIDE INHIBITOR AC-VLTK-AOMK
 
Authors :  D. W. Wolan, G. E. Gonzalez-Paez, S. Chatterjee
Date :  24 Feb 15  (Deposition) - 16 Mar 16  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.12
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Clostripain, Microbiome, Secreted Protease, Inhibitor, Unknown Function-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Roncase, C. Moon, S. Chatterjee, G. E. Gonzalez-Paez, C. S. Craik A. J. O'Donoghue, D. W. Wolan
Substrate Profiling And High Resolution Co-Complex Crystal Structure Of A Secreted C11 Protease Conserved Across Commensal Bacteria.
Acs Chem. Biol. V. 12 1556 2017
PubMed-ID: 28414448  |  Reference-DOI: 10.1021/ACSCHEMBIO.7B00143

(-) Compounds

Molecule 1 - CLOSTRIPAIN FAMILY
    Atcc: 43184
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Taxid: 866768
    Fragment: UNP RESIDUES 23-146
    Gene: PARMER_00083
    Organism Scientific: PARABACTEROIDES MERDAE ATCC 43184
    Organism Taxid: 411477
 
Molecule 2 - CLOSTRIPAIN FAMILY
    Atcc: 43184
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Taxid: 866768
    Fragment: UNP RESIDUES 148-375
    Gene: PARMER_00083
    Organism Scientific: PARABACTEROIDES MERDAE ATCC 43184
    Organism Taxid: 411477
 
Molecule 3 - PEPTIDE INHIBITOR AC-VLTK-AOMK
    Chains: C
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CKC1Mod. Amino Acid(3S)-3,7-DIAMINOHEPTAN-2-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:42 , LEU A:43 , ASP A:108 , TRP A:131 , SER A:132 , HIS A:133 , GLY A:134 , ASP B:177 , CYS B:179 , GLU B:203 , THR B:204 , MET B:205 , ALA B:206 , THR B:221 , ASP B:222 , TYR B:241 , ALA B:333 , HOH B:467 , HOH C:501 , HOH C:502 , HOH C:503BINDING SITE FOR CHAIN C OF PEPTIDE INHIBITOR AC -VLTK-AOMK

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YEC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YEC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YEC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YEC)

(-) Exons   (0, 0)

(no "Exon" information available for 4YEC)

(-) 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:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeee......eeeeeeee..eeeeeeeee.......hhhhhhhhhhhhhhhh.eeeeeeeee.........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yec A  22 METPEPRTTRTILVYMMANNSLNSFASKNIESMIEGATSKNLNGGNLIVYYAPAGSPPELLRIKEENGVVKKIHLKDYEKQNSADPDVMRSVIGEVVSQYPADSYGLVLWSHGTAWLPSDYQNKLK 147
                                    31        41        51        61        71        81        91       101       111       121       131       141      


Chain B from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeehhhhhhhhh....eeeeeee.....hhhhhhhh...eeeeee..........hhhhhhhhhh....hhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhhhh..hhhhhhhhhhhhh............eeehhhhhhh..hhhhhhhhhhhhhhheeeeee..eeee....eeee.......eee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yec B 148 AFGQDGNNWMEIDDLAKGLPDDLFDFILFDACYMASVECTYELRNKAEYILASPTETMADGWPYEEMMPQLFATDLQLEKVGETFYNHYLNNTYPYATVSLTKTSELDNLKSAIHDILADKTESDIYSLDPKNMQRLEYLYRSPGMLYDFNDYIKQLATAEQYDRFISCLDKAVVYKAHTPKSYYAAIGNALPIKSYCGLTIFVPQESLPKMLEWYKQRVGWYKAVYE 375
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367        


Chain C from PDB  Type:PROTEIN  Length:5
                                     
               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
                 4yec C 401 xVLTx 405
                            |   |
                          401-ACE
                              405-CKC
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4YEC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YEC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YEC)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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