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(-) Description

Title :  STRUCTURE OF THE C. DIFFICILE TCDB CYSTEINE PROTEASE DOMAIN IN COMPLEX WITH A PEPTIDE INHIBITOR
 
Authors :  P. J. Lupardus, K. C. Garcia
Date :  18 Oct 10  (Deposition) - 15 Dec 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Clan Cd Cysteine Protease, Protease, Toxin, Toxin-Peptide Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. W. Puri, P. J. Lupardus, E. Deu, V. E. Albrow, K. C. Garcia, M. Bogyo, A. Shen
Rational Design Of Inhibitors And Activity-Based Probes Targeting Clostridium Difficile Virulence Factor Tcdb.
Chem. Biol. V. 17 1201 2010
PubMed-ID: 21095570  |  Reference-DOI: 10.1016/J.CHEMBIOL.2010.09.011

(-) Compounds

Molecule 1 - TOXIN B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 544-797
    Gene: CD0660, TCDB
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    Organism Taxid: 272563
    Strain: 630

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
16212Ligand/IonN-ACETYLGLYCYL-N-[(3S)-1-HYDROXY-5-METHYL-2-OXOHEXAN-3-YL]-L-SERINAMIDE
2CA1Ligand/IonCALCIUM ION
3IHP2Ligand/IonINOSITOL HEXAKISPHOSPHATE
4NA2Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:71 , ILE B:46 , GLY B:109 , HIS B:110 , GLY B:111 , CYS B:155 , GLU B:200 , VAL B:201 , ARG B:202 , TRP B:218 , HOH B:299 , HOH B:358BINDING SITE FOR RESIDUE 621 B 300
2AC2SOFTWAREGLU A:17 , GLU A:21 , ILE A:46 , GLY A:109 , HIS A:110 , GLY A:111 , CYS A:155 , GLU A:200 , VAL A:201 , ARG A:202 , TRP A:218 , HOH A:303 , HOH A:314 , HOH A:410BINDING SITE FOR RESIDUE 621 A 300
3AC3SOFTWAREIHP A:257 , HOH A:260 , IHP B:256 , HOH B:258BINDING SITE FOR RESIDUE CA A 255
4AC4SOFTWAREARG A:208 , LYS A:221 , IHP A:257 , HOH A:262 , HOH A:274BINDING SITE FOR RESIDUE NA A 256
5AC5SOFTWAREARG B:209 , IHP B:256 , HOH B:259 , HOH B:305 , HOH B:308BINDING SITE FOR RESIDUE NA B 255
6AC6SOFTWARECA A:255 , IHP A:257 , HOH A:260 , ARG B:28 , ARG B:32 , TYR B:34 , LEU B:54 , LYS B:57 , LYS B:104 , ARG B:208 , ARG B:209 , LYS B:221 , LYS B:232 , TYR B:234 , LYS B:249 , NA B:255 , HOH B:258 , HOH B:259 , HOH B:260 , HOH B:265 , HOH B:266 , HOH B:288 , HOH B:305 , HOH B:319 , HOH B:335 , HOH B:349 , HOH B:351 , HOH B:353 , HOH B:356BINDING SITE FOR RESIDUE IHP B 256
7AC7SOFTWAREARG A:28 , ARG A:32 , TYR A:34 , LEU A:54 , LYS A:57 , LYS A:104 , ARG A:208 , ARG A:209 , LYS A:221 , LYS A:232 , TYR A:234 , LYS A:249 , CA A:255 , NA A:256 , HOH A:260 , HOH A:262 , HOH A:270 , HOH A:291 , HOH A:293 , HOH A:295 , HOH A:318 , HOH A:336 , HOH A:345 , HOH A:358 , HOH A:359 , HOH A:412 , HOH A:417 , IHP B:256 , HOH B:258BINDING SITE FOR RESIDUE IHP A 257

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PA8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PA8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PA8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PA8)

(-) Exons   (0, 0)

(no "Exon" information available for 3PA8)

(-) 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:245
 aligned with Q189K3_PEPD6 | Q189K3 from UniProtKB/TrEMBL  Length:2366

    Alignment length:245
                                   559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789     
         Q189K3_PEPD6   550 DFSQNIVVDKEYLLEKISSLARSSERGYIHYIVQLQGDKISYEAACNLFAKTPYDSVLFQKNIEDSEIAYYYNPGDGEIQEIDKYKIPSIISDRPKIKLTFIGHGKDEFNTDIFAGFDVDSLSTEIEAAIDLAKEDISPKSIEINLLGCNMFSYSINVEETYPGKLLLKVKDKISELMPSISQDSIIVSANQYEVRINSEGRRELLDHSGEWINKEESIIKDISSKEYISFNPKENKITVKSKNL 794
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhh...eeeee.......eeeeee....eeeeee............eeeeeee..........ee..eehhhhhhhhhhhhhhhh......eeeeeee.........hhhhhhhhhhhhhhhhhhhhhh...hhh.eeeee....eee.....eeee.....eehhhhhhhh.....eeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pa8 A   7 DFSQNIVVDKEYLLEKISSLARSSERGYIHYIVQLQGDKISYEAACNLFAKTPYDSVLFQKNIEDSEIAYYYNPGDGEIQEIDKYKIPSIISDRPKIKLTFIGHGKDEFNTDIFAGFDVDSLSTEIEAAIDLAKEDISPKSIEINLLGCNMFSYSINVEETYPGKLLLKVKDKISELMPSISQDSIIVSANQYEVRINSEGRRELLDHSGEWINKEESIIKDISSKEYISFNPKENKITVKSKNL 251
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246     


Chain B from PDB  Type:PROTEIN  Length:242
 aligned with Q189K3_PEPD6 | Q189K3 from UniProtKB/TrEMBL  Length:2366

    Alignment length:242
                                   562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792  
         Q189K3_PEPD6   553 QNIVVDKEYLLEKISSLARSSERGYIHYIVQLQGDKISYEAACNLFAKTPYDSVLFQKNIEDSEIAYYYNPGDGEIQEIDKYKIPSIISDRPKIKLTFIGHGKDEFNTDIFAGFDVDSLSTEIEAAIDLAKEDISPKSIEINLLGCNMFSYSINVEETYPGKLLLKVKDKISELMPSISQDSIIVSANQYEVRINSEGRRELLDHSGEWINKEESIIKDISSKEYISFNPKENKITVKSKNL 794
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhh...eeeee.......eeeeee....eeeeee............eeeeeee..........ee..eehhhhhhhhhhhhhhhh......eeeeeee.........hhhhhhhhhhhhhhhhhhhhhh...hhh.eeeee....eee.....eeee.....eehhhhhhhh.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pa8 B  10 QNIVVDKEYLLEKISSLARSSERGYIHYIVQLQGDKISYEAACNLFAKTPYDSVLFQKNIEDSEIAYYYNPGDGEIQEIDKYKIPSIISDRPKIKLTFIGHGKDEFNTDIFAGFDVDSLSTEIEAAIDLAKEDISPKSIEINLLGCNMFSYSINVEETYPGKLLLKVKDKISELMPSISQDSIIVSANQYEVRINSEGRRELLDHSGEWINKEESIIKDISSKEYISFNPKENKITVKSKNL 251
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249
   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 3PA8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PA8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PA8)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q189K3_PEPD6 | Q189K3)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.

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 Related Entries

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UniProtKB/TrEMBL
        Q189K3_PEPD6 | Q189K3: 3pee

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