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(-) Description

Title :  STRUCTURE OF THE SUBTILISIN INDUCED SERPIN-TYPE PROTEINASE INHIBITOR, MIROPIN.
 
Authors :  T. Goulas, M. Ksiazek, I. Garcia-Ferrer, D. Mizgalska, J. Potempa, X. G
Date :  06 Mar 17  (Deposition) - 24 May 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Serpin-Type Proteinase Inhibitor, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Goulas, M. Ksiazek, I. Garcia-Ferrer, A. M. Sochaj-Gregorczyk, I. Waligorska, M. Wasylewski, J. Potempa, F. X. Gomis-Ruth
A Structure-Derived Snap-Trap Mechanism Of A Multispecific Serpin From The Dysbiotic Human Oral Microbiome.
J. Biol. Chem. V. 292 10883 2017
PubMed-ID: 28512127  |  Reference-DOI: 10.1074/JBC.M117.786533

(-) Compounds

Molecule 1 - SERPIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Gene: BFO_3114
    Organism Scientific: TANNERELLA FORSYTHIA
    Organism Taxid: 28112
    Other Details: THE AMINO-TERMINAL RESIDUES (GPLGS) ARE COMING FROM THE CLONING STRATEGY. WHERE CSX IS S-OXY CYSTEINE.
 
Molecule 2 - SERPIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Gene: BFO_3114
    Organism Scientific: TANNERELLA FORSYTHIA
    Organism Taxid: 28112
    Other Details: THE AMINO-TERMINAL RESIDUES (GPLGS) ARE COMING FROM THE CLONING STRATEGY. WHERE CSX IS S-OXY CYSTEINE.

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CSX1Mod. Amino AcidS-OXY CYSTEINE
3GOL4Ligand/IonGLYCEROL
4IOD6Ligand/IonIODIDE ION
5K1Ligand/IonPOTASSIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECL A:408binding site for residue K A 401
02AC2SOFTWAREILE A:187binding site for residue IOD A 403
03AC3SOFTWAREASN A:169binding site for residue IOD A 404
04AC4SOFTWARESER A:72 , ASN A:76 , SER A:108 , GOL A:411binding site for residue IOD A 405
05AC5SOFTWARELYS A:210 , HOH A:632 , HOH A:844binding site for residue IOD A 406
06AC6SOFTWAREASN A:63 , LYS B:407binding site for residue IOD A 407
07AC7SOFTWAREGLY A:309 , LYS A:312 , K A:401 , GOL A:412 , HOH A:626binding site for residue CL A 408
08AC8SOFTWAREGLU A:102 , ASN A:105 , ALA A:145 , HIS A:149 , SER A:160 , ASP A:223 , HOH A:602binding site for residue GOL A 409
09AC9SOFTWARETHR A:123 , GLN A:174 , LYS A:175 , THR A:176 , ASN A:177 , TYR A:200 , HOH A:513 , HOH A:614binding site for residue GOL A 410
10AD1SOFTWARELYS A:43 , ASP A:44 , SER A:72 , TYR A:107 , LEU A:111 , IOD A:405 , HOH A:577 , HOH A:741 , HOH B:507binding site for residue GOL A 411
11AD2SOFTWARELYS A:307 , GLY A:309 , LYS A:312 , CL A:408 , HOH A:510 , HOH A:546binding site for residue GOL A 412

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:245 -A:246

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5NCU)

(-) 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:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....eeeeeeeeeee.....hhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhh...............eeeeeeeeeeeeee.....hhhhheeeeee.....eeeeeeeeeeeeeeeee...eeeeeee.....eeeeeeee....hhhhhhhh.hhhhhhhhhhhheeeeeeeeee.eeeeeeee...hhhhhhh.hhhhh............eeeeeeeeeeeeee...eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ncu A  40 KIEKDNAFAFDLLQTTRKHVTEANVFISPLSVSMALNMTLNGAAGVTADEMKTALRETGYTMEDINEYSHSLREALLKVDPSTTIGMANSIWYKQGELVKEPFILANRTHYDAEVKAVDFSSPATLPAINGWCAQKTNDKITKILDYIPGNAFMYLINAVYFKGIWVTQFKKSDTKRAPFRKADGTTQEVNMMAQKSTFGYTTDECCQYLEMDYGNKAFSMIVMLPNEGQTTRDVIEQLDNKHWSMIIKGIRPTQVSLRMPRFKTEcKYGLEKKILPEMGMNVPFTETADFPGITDAAIFISRVIHKTFVQVDEEGTEAAAVTAVEMVKT 369
                                    49        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       339       349       359       369
                                                                                                                                                                                                                                                                                                    306-CSX                                                           


Chain B from PDB  Type:PROTEIN  Length:33
                                                                 
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author .eeee....eeeeeee.....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                 5ncu B 376 PINFHINKPFVFAIREKSTGVILFIGEIGEVKE 408
                                   385       395       405
   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 5NCU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        G8UQY8_TANFA | G8UQY8: 5ncs 5nct 5ncw

(-) Related Entries Specified in the PDB File

5ncs 5NCS CONTAINS THE SAME PROTEIN AFTER REACTION WITH SUBTILISIN.