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(-) Description

Title :  STRUCTURE OF PROTEASE
 
Authors :  M. A. Gorman, M. W. Parker
Date :  28 May 14  (Deposition) - 31 Dec 14  (Release) - 08 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  L
Keywords :  Cysteine Protease, Gingivalis, Kgp, Co-Valent Inhibitor, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Gorman, C. A. Seers, B. J. Michell, S. C. Feil, N. L. Huq, K. J. Cross E. C. Reynolds, M. W. Parker
Structure Of The Lysine Specific Protease Kgp From Porphyromonas Gingivalis, A Target For Improved Oral Health
Protein Sci. V. 24 162 2015
PubMed-ID: 25327141  |  Reference-DOI: 10.1002/PRO.2589

(-) Compounds

Molecule 1 - LYS-GINGIPAIN W83
    Chains: L
    EC Number: 3.4.22.47
    Engineered: YES
    Expression System: PORPHYROMONAS GINGIVALIS
    Expression System Taxid: 837
    Fragment: CATALYTIC DOMAIN
    Gene: KGP, PRTK, PRTP
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 837
    Synonym: LYSINE SPECIFIC CYSTEINE PROTEASE,LYSINE-SPECIFIC CYSTEINE PROTEINASE,PORPHYPAIN,PRTK48

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : L

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 20)

Asymmetric/Biological Unit (7, 20)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO10Ligand/Ion1,2-ETHANEDIOL
3K1Ligand/IonPOTASSIUM ION
4NA2Ligand/IonSODIUM ION
5PB1Ligand/IonLEAD (II) ION
6SO44Ligand/IonSULFATE ION
7TCK1Ligand/IonN-[(1S)-5-AMINO-1-(CHLOROACETYL)PENTYL]-4-METHYLBENZENESULFONAMIDE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU L:547 , ARG L:597 , LYS L:601 , ASN L:670 , HOH L:801 , HOH L:839 , HOH L:1234binding site for residue SO4 L 701
02AC2SOFTWAREPRO L:424 , TYR L:425 , THR L:426 , EDO L:716binding site for residue SO4 L 702
03AC3SOFTWAREASP L:229 , VAL L:230 , HIS L:566 , ASN L:569 , HOH L:1266binding site for residue SO4 L 703
04AC4SOFTWAREGLY L:427 , CYS L:428 , TYR L:429 , SER L:430 , EDO L:709 , EDO L:716binding site for residue SO4 L 704
05AC5SOFTWAREALA L:543 , THR L:544 , LEU L:546 , SER L:549 , TYR L:550 , ASN L:551binding site for residue NA L 705
06AC6SOFTWARETYR L:402 , VAL L:521 , THR L:536 , SER L:537 , ASP L:542 , HOH L:963binding site for residue NA L 706
07AC7SOFTWAREASP L:388 , HIS L:444 , HOH L:805binding site for residue K L 707
08AC8SOFTWAREGLU L:279 , SER L:286 , PHE L:290 , HOH L:804 , HOH L:806 , HOH L:822binding site for residue ACT L 708
09AC9SOFTWARETYR L:429 , ASN L:433 , GLN L:459 , SO4 L:704 , HOH L:972binding site for residue EDO L 709
10AD1SOFTWAREGLU L:356 , HOH L:990 , HOH L:1217binding site for residue EDO L 710
11AD2SOFTWAREASN L:524 , VAL L:529 , PRO L:531 , THR L:532 , HOH L:934 , HOH L:1074 , HOH L:1102 , HOH L:1192binding site for residue EDO L 711
12AD3SOFTWAREHIS L:412 , ARG L:597 , MET L:599 , LYS L:601 , ASN L:670 , HOH L:807 , HOH L:837binding site for residue EDO L 712
13AD4SOFTWAREHIS L:412 , THR L:604 , GLN L:621 , ALA L:622 , HOH L:815 , HOH L:851binding site for residue EDO L 713
14AD5SOFTWARESER L:537 , HIS L:566 , HOH L:1004 , HOH L:1273binding site for residue EDO L 714
15AD6SOFTWAREASP L:416 , TYR L:418 , HOH L:1009 , HOH L:1242binding site for residue EDO L 715
16AD7SOFTWARETHR L:426 , CYS L:428 , PRO L:453 , SO4 L:702 , SO4 L:704 , HOH L:1083 , HOH L:1122binding site for residue EDO L 716
17AD8SOFTWAREASP L:236 , LEU L:237 , TYR L:238binding site for residue EDO L 717
18AD9SOFTWAREASP L:362 , MET L:366 , LYS L:466 , ASP L:467 , TYR L:469 , GLU L:498 , HOH L:886binding site for residue EDO L 718
19AE1SOFTWAREASP L:313 , PHE L:482 , GLU L:491 , HOH L:1203 , HOH L:1238 , HOH L:1275binding site for residue PB L 719
20AE2SOFTWARESER L:390 , TRP L:391 , THR L:442 , ALA L:443 , HIS L:444 , GLY L:445 , ASN L:475 , CYS L:477 , ASN L:510 , SER L:511 , TYR L:512 , TRP L:513 , ASP L:516 , HOH L:805 , HOH L:856 , HOH L:949binding site for residue TCK L 720

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Thr L:240 -Pro L:241
2Ala L:423 -Pro L:424
3Asp L:452 -Pro L:453

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TKX)

(-) 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 L from PDB  Type:PROTEIN  Length:452
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.......eeeeeee...hhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhh.....eeeee........ee......eehhhhhh.........eeeee...hhhhhhhhhhhhhhhhhh...hhhhh.eeeeee....hhhhhhhhhhhhhhhhhh.hhhhh..eeeee........hhhhhhh..eeeee..ee..ee....eehhhhhh.......eeeeee............hhhhhhhhh....eeeeeee....hhhhhhhhhhh................hhhhhhhh.....hhhhhhhhhhhhhhhhhhh......hhhhhhhheeeee...............ee..........eeeeee....eeeeee..eeeeeee.....eeeeee.......eeeeeeee......eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tkx L 229 DVYTDHGDLYNTPVRMLVVAGAKFKEALKPWLTWKAQKGFYLDVHYTDEAEVGTTNASIKAFIHKKYNDGLAASAAPVFLALVGDTDVISGEKGKKTKKVTDLYYSAVDGDYFPEMYTFRMSASSPEELTNIIDKVLMYEKATMPDKSYLEKVLLIAGADYSWNSQVGQPTIKYGMQYYYNQEHGYTDVYNYLKAPYTGCYSHLNTGVSFANYTAHGSETAWADPLLTTSQLKALTNKDKYFLAIGNCCITAQFDYVQPCFGEVITRVKEKGAYAYIGSSPNSYWGEDYYWSVGANAVFGVQPTFEGTSMGSYDATFLEDSYNTVNSIMWAGNLAATHAGNIGNITHIGAHYYWEAYHVLGDGSVMPYRAMPKTNTYTLPASLPQNQASYSIQASAGSYVAISKDGVLYGTGVANASGVATVSMTKQITENGNYDVVITRSNYLPVIKQIQV 680
                                   238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678
   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 4TKX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala L:423 - Pro L:424   [ RasMol ]  
    Asp L:452 - Pro L:453   [ RasMol ]  
    Thr L:240 - Pro L:241   [ RasMol ]  
 

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  KGP83_PORGN | Q51817
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UniProtKB/Swiss-Prot
        KGP83_PORGN | Q51817: 3km5 3m1h 4itc 4rbm 5mun

(-) Related Entries Specified in the PDB File

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