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(-) Description

Title :  MONOMERIC PCNA BOUND TO A SMALL PROTEIN INHIBITOR
 
Authors :  J. E. Ladner, A. S. Altieri, Z. Kelman
Date :  19 Aug 15  (Deposition) - 11 May 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  D,E  (1x)
Keywords :  Complex, Inhibitor, Dna Binding Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Altieri, J. E. Ladner, Z. Li, H. Robinson, Z. F. Sallman, J. P. Marino, Z. Kelman
A Small Protein Inhibits Proliferating Cell Nuclear Antigen By Breaking The Dna Clamp.
Nucleic Acids Res. V. 44 6232 2016
PubMed-ID: 27141962  |  Reference-DOI: 10.1093/NAR/GKW351

(-) Compounds

Molecule 1 - DNA POLYMERASE SLIDING CLAMP 1, PROLIFERATING CELL NUCLEAR ANTIGEN
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PCN1, TK0535
    Organism Scientific: THERMOCOCCUS KODAKARENSIS (STRAIN ATCC BAA-918 / JCM 12380 / KOD1)
    Organism Taxid: 69014
    Strain: ATCC BAA-918 / JCM 12380 / KOD1
    Synonym: PROLIFERATING CELL NUCLEAR ANTIGEN HOMOLOG 1,PCNA 1
 
Molecule 2 - THERMOCOCCALES INHIBITOR OF PCNA
    Chains: B, E
    Engineered: YES
    Organism Scientific: THERMOCOCCUS KODAKARENSIS (STRAIN ATCC BAA-918 / JCM 12380 / KOD1)
    Organism Taxid: 69014
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   DE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 18)

Asymmetric Unit (1, 18)
No.NameCountTypeFull Name
1SO418Ligand/IonSULFATE ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:45 , ARG B:47binding site for residue SO4 A 301
02AC2SOFTWAREGLY A:94 , ASP A:95 , GLU A:96 , ARG A:112binding site for residue SO4 A 302
03AC3SOFTWARELYS A:160 , GLU A:194 , LYS A:196binding site for residue SO4 A 303
04AC4SOFTWAREVAL A:46 , GLY A:200 , TYR A:203 , ALA A:244 , PRO A:245 , ARG A:246 , THR B:32binding site for residue SO4 A 304
05AC5SOFTWAREASP A:117 , ASP D:117binding site for residue SO4 A 305
06AC6SOFTWAREGLY A:212 , LYS A:213binding site for residue SO4 A 306
07AC7SOFTWAREASP A:117binding site for residue SO4 A 307
08AC8SOFTWARELYS A:133 , GLU A:192 , GLU A:193 , GLU A:194 , ARG A:220binding site for residue SO4 A 308
09AC9SOFTWARELYS A:30 , GLU A:122 , LEU A:123binding site for residue SO4 A 309
10AD1SOFTWAREASP A:153 , ARG A:246binding site for residue SO4 A 310
11AD2SOFTWAREARG D:45 , ARG E:47binding site for residue SO4 D 301
12AD3SOFTWAREGLY D:94 , ASP D:95 , GLU D:96 , ARG D:112binding site for residue SO4 D 302
13AD4SOFTWARELYS D:160 , GLU D:194 , LYS D:196binding site for residue SO4 D 303
14AD5SOFTWAREVAL D:46 , GLY D:200 , TYR D:203 , ALA D:244 , PRO D:245 , ARG D:246 , PRO E:31 , THR E:32binding site for residue SO4 D 304
15AD6SOFTWARETHR B:32 , SER B:33 , SER B:36binding site for residue SO4 B 101
16AD7SOFTWAREARG B:50 , LYS B:54binding site for residue SO4 B 102
17AD8SOFTWAREPRO D:43 , ARG E:50 , LYS E:54binding site for residue SO4 E 101
18AD9SOFTWARETHR E:32 , SER E:33 , SER E:36binding site for residue SO4 E 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DA7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DA7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DA7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DA7)

(-) Exons   (0, 0)

(no "Exon" information available for 5DA7)

(-) 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:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhhh....eeeeee...eeeeeee.....eeeeeeee.hhh..eee...eeeeeehhhhhhhhh......eeeeee....eeeeeee....eeeeee.................eeeeeehhhhhhhhhhhhh...eeeeee....eeeeee....eeeeee......eeeeee...eeeeeehhhhhhhhh......eeeeee.....eeeeeee...eeeeeee..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5da7 A   2 PFEVVFDGAKEFADLIATASNLIDEAAFKFTEEGISMRAMDPSRVVLIDLNLPESIFSKYEVEEPETIGINMDQFKKILKRGKAKDTLILRKGDENFLEITFEGTAKRTFRLPLIDVEELELELPELPFTAKVVLLGEVLKEGIKDASLVSDAIKFIAKENEFTMKAEGETNEVEIRLTLEDEGLLDLEVEEETKSAYGIRYLSDMVKGIGKADEVILRFGNEMPLQMEYMIRDEGRLTFLLAPRVE 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       


Chain B from PDB  Type:PROTEIN  Length:35
                                                                   
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhh.hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 5da7 B  28 RLKPTSLDSFLPEEHINYFRDLRIGSKKIRNAKIE  62
                                    37        47        57     


Chain D from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhhh....eeeeee...eeeeeee.....eeeeeeee.hhh..eee...eeeeeehhhhhhhhhh.....eeeeee....eeeeeee....eeeeee.................eeeeeehhhhhhhhhhhhh...eeeeee...eeeeeee....eeeeeee.....eeeeee...eeeeeehhhhhhhh.......eeeeee.....eeeeeee...eeeeeee..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5da7 D   2 PFEVVFDGAKEFADLIATASNLIDEAAFKFTEEGISMRAMDPSRVVLIDLNLPESIFSKYEVEEPETIGINMDQFKKILKRGKAKDTLILRKGDENFLEITFEGTAKRTFRLPLIDVEELELELPELPFTAKVVLLGEVLKEGIKDASLVSDAIKFIAKENEFTMKAEGETNEVEIRLTLEDEGLLDLEVEEETKSAYGIRYLSDMVKGIGKADEVILRFGNEMPLQMEYMIRDEGRLTFLLAPRVE 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       


Chain E from PDB  Type:PROTEIN  Length:35
                                                                   
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhh.hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 5da7 E  28 RLKPTSLDSFLPEEHINYFRDLRIGSKKIRNAKIE  62
                                    37        47        57
   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 5DA7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DA7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DA7)

(-) Gene Ontology  (4, 4)

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 Related Entries

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        PCNA1_THEKO | Q5JF32: 3lx1 5dai

(-) Related Entries Specified in the PDB File

3lx1 3LX1 IS THE SAME PROTEIN WITHOUT THE BOUND INHIBITOR PROTEIN
5dai