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(-) Description

Title :  CRYSTAL STRUCTURE OF NEC3PO IN COMPLEX WITH SSDNA.
 
Authors :  J. Gan, J. Zhang
Date :  06 May 16  (Deposition) - 28 Sep 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  C3Po, Complex, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Zhang, H. Liu, Q. Yao, X. Yu, Y. Chen, R. Cui, B. Wu, L. Zheng, J. Zuo, Z. Huang, J. Ma, J. Gan
Structural Basis For Single-Stranded Rna Recognition And Cleavage By C3Po
Nucleic Acids Res. V. 44 9494 2016
PubMed-ID: 27596600  |  Reference-DOI: 10.1093/NAR/GKW776

(-) Compounds

Molecule 1 - NEQ131
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NEQ131
    Organism Scientific: NANOARCHAEUM EQUITANS (STRAIN KIN4-M)
    Organism Taxid: 228908
    Strain: KIN4-M
 
Molecule 2 - SSDNA
    Chains: I, J
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1ADE5Ligand/IonADENINE
2ADZ3Ligand/Ion9-METHYL-9H-PURIN-6-AMINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:74 , PHE A:77 , TRP A:109 , PHE A:113 , MET B:71binding site for residue ADE A 1001
02AC2SOFTWAREMET A:71 , PHE B:77 , TRP B:109binding site for residue ADE B 1001
03AC3SOFTWARESER C:74 , TRP C:109 , PHE C:113 , MET D:71binding site for residue ADZ C 1001
04AC4SOFTWARELEU D:123 , LYS D:175 , ASN G:171 , HOH G:1119binding site for residue ADE D 1001
05AC5SOFTWAREMET E:71 , HOH E:1125 , SER F:74 , TRP F:109binding site for residue ADZ E 1001
06AC6SOFTWARESER E:74 , PHE E:77 , TRP E:109 , PHE E:113 , MET F:71binding site for residue ADZ E 1002
07AC7SOFTWARESER G:74 , PHE G:77 , TRP G:109 , PHE G:113 , MET H:71binding site for residue ADE G 1001
08AC8SOFTWAREASN C:171 , HOH C:1131 , GLY H:120 , LEU H:123 , SER H:127 , LYS H:175binding site for residue ADE H 1001
09AC9SOFTWAREGLN D:20 , VAL D:23 , ASP D:24 , ILE D:27 , GLN H:20 , VAL H:23 , ASP H:24 , ILE H:27 , DA I:3 , DA I:4 , HOH I:101 , HOH I:102 , DA J:3binding site for Di-nucleotide DA I 2 and DA J 2
10AD1SOFTWAREGLN D:20 , VAL D:23 , ASP D:24 , ILE D:27 , GLN H:20 , VAL H:23 , ASP H:24 , ILE H:27 , DA I:3 , DA I:4 , HOH I:101 , HOH I:102 , DA J:3binding site for Di-nucleotide DA I 2 and DA J 2
11AD2SOFTWAREGLN D:20 , VAL D:23 , ASP D:24 , ILE D:27 , GLN H:20 , VAL H:23 , ASP H:24 , ILE H:27 , DA I:3 , DA I:4 , HOH I:101 , HOH I:102 , DA J:3binding site for Di-nucleotide DA I 2 and DA J 2
12AD3SOFTWAREGLN D:20 , VAL D:23 , ASP D:24 , ILE D:27 , GLN H:20 , VAL H:23 , ASP H:24 , ILE H:27 , DA I:3 , DA I:4 , HOH I:101 , HOH I:102 , DA J:3binding site for Di-nucleotide DA I 2 and DA J 2
13AD4SOFTWAREGLN D:20 , VAL D:23 , ASP D:24 , ILE D:27 , GLN H:20 , VAL H:23 , ASP H:24 , ILE H:27 , DA I:3 , DA I:4 , HOH I:101 , HOH I:102 , DA J:3binding site for Di-nucleotide DA I 2 and DA J 2
14AD5SOFTWAREGLN D:20 , VAL D:23 , ASP D:24 , ILE D:27 , GLN H:20 , VAL H:23 , ASP H:24 , ILE H:27 , DA I:3 , DA I:4 , HOH I:101 , HOH I:102 , DA J:3binding site for Di-nucleotide DA I 2 and DA J 2

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JRE)

(-) 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:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jre A  -1 GSMLPNLDNLKEEYQKLEEKKQEIVDRSIRMSKLSKSLIYSMIREDYKSADKYKEELTNLAKTQIEELKKYPMFYSNGFIGLQEYVEALALYYYIKENRIPSKEELGVDTWVYLFGIGDIAGEILRKSSEELIKGNIEYAKKAKQDLESLYLDLLYIELKNFDLRRKLDYVSNIINKLIEFIIWKS 184
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178      


Chain B from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jre B   0 SMLPNLDNLKEEYQKLEEKKQEIVDRSIRMSKLSKSLIYSMIREDYKSADKYKEELTNLAKTQIEELKKYPMFYSNGFIGLQEYVEALALYYYIKENRIPSKEELGVDTWVYLFGIGDIAGEILRKSSEELIKGNIEYAKKAKQDLESLYLDLLYIELKNFDLRRKLDYVSNIINKLIEFIIWK 183
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    


Chain C from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jre C   0 SMLPNLDNLKEEYQKLEEKKQEIVDRSIRMSKLSKSLIYSMIREDYKSADKYKEELTNLAKTQIEELKKYPMFYSNGFIGLQEYVEALALYYYIKENRIPSKEELGVDTWVYLFGIGDIAGEILRKSSEELIKGNIEYAKKAKQDLESLYLDLLYIELKNFDLRRKLDYVSNIINKLIEFIIWKSK 185
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179      


Chain D from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jre D   0 SMLPNLDNLKEEYQKLEEKKQEIVDRSIRMSKLSKSLIYSMIREDYKSADKYKEELTNLAKTQIEELKKYPMFYSNGFIGLQEYVEALALYYYIKENRIPSKEELGVDTWVYLFGIGDIAGEILRKSSEELIKGNIEYAKKAKQDLESLYLDLLYIELKNFDLRRKLDYVSNIINKLIEFIIWKS 184
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179     


Chain E from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jre E  -1 GSMLPNLDNLKEEYQKLEEKKQEIVDRSIRMSKLSKSLIYSMIREDYKSADKYKEELTNLAKTQIEELKKYPMFYSNGFIGLQEYVEALALYYYIKENRIPSKEELGVDTWVYLFGIGDIAGEILRKSSEELIKGNIEYAKKAKQDLESLYLDLLYIELKNFDLRRKLDYVSNIINKLIEFIIWKS 184
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178      


Chain F from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jre F   0 SMLPNLDNLKEEYQKLEEKKQEIVDRSIRMSKLSKSLIYSMIREDYKSADKYKEELTNLAKTQIEELKKYPMFYSNGFIGLQEYVEALALYYYIKENRIPSKEELGVDTWVYLFGIGDIAGEILRKSSEELIKGNIEYAKKAKQDLESLYLDLLYIELKNFDLRRKLDYVSNIINKLIEFIIWK 183
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    


Chain G from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jre G   0 SMLPNLDNLKEEYQKLEEKKQEIVDRSIRMSKLSKSLIYSMIREDYKSADKYKEELTNLAKTQIEELKKYPMFYSNGFIGLQEYVEALALYYYIKENRIPSKEELGVDTWVYLFGIGDIAGEILRKSSEELIKGNIEYAKKAKQDLESLYLDLLYIELKNFDLRRKLDYVSNIINKLIEFIIWKSK 185
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179      


Chain H from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jre H   0 SMLPNLDNLKEEYQKLEEKKQEIVDRSIRMSKLSKSLIYSMIREDYKSADKYKEELTNLAKTQIEELKKYPMFYSNGFIGLQEYVEALALYYYIKENRIPSKEELGVDTWVYLFGIGDIAGEILRKSSEELIKGNIEYAKKAKQDLESLYLDLLYIELKNFDLRRKLDYVSNIINKLIEFIIWKS 184
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179     


Chain I from PDB  Type:DNA  Length:4
                                    
                 5jre I   2 AAAA   5


Chain J from PDB  Type:DNA  Length:4
                                    
                 5jre J   2 AAAA   5
   Legend:   → Mismatch (orange background)
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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 5JRE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        Q74ML9_NANEQ | Q74ML9: 5jr9 5jrc

(-) Related Entries Specified in the PDB File

5jr9 5jrc