Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AN INTERMEDIATE COMPLEX OF T7 RNAP AND 8NT OF RNA
 
Authors :  K. J. Durniak, S. Bailey, T. A. Steitz
Date :  07 Aug 08  (Deposition) - 04 Nov 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  6.70
Chains :  Asym. Unit :  B,C,N,R,T,X,Y,Z
Biol. Unit 1:  B,X,Y,Z  (1x)
Biol. Unit 2:  C,N,R,T  (1x)
Keywords :  T7 Rna Polymerase, Dna-Directed Rna Polymerase, Transcription, Nucleotidyltransferase, Transferase, Transferase/Rna/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Durniak, S. Bailey, T. A. Steitz
The Structure Of A Transcribing T7 Rna Polymerase In Transition From Initiation To Elongation
Science V. 322 553 2008
PubMed-ID: 18948533  |  Reference-DOI: 10.1126/SCIENCE.1163433
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA-DIRECTED RNA POLYMERASE
    Chains: C, B
    EC Number: 2.7.7.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBH161
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 1
    Mutation: YES
    Organism Scientific: BACTERIOPHAGE T7
 
Molecule 2 - RNA (5'-R(*GP*GP*GP*AP*GP*UP*AP*A)-3')
    Chains: R, Z
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (28-MER)
    Chains: T, X
    Engineered: YES
    Other Details: TEMPLATE DNA
    Synthetic: YES
 
Molecule 4 - DNA (5'- D(*DTP*DAP*DAP*DTP*DAP*DCP*DGP*DAP*DCP*DTP*DCP*DAP*DCP*DTP* DAP*DTP*DAP*DTP*DTP*DTP*DCP*DTP*DGP*DCP*DCP*DAP*DAP*DAP*DCP *DGP*DGP*DC)-3')
    Chains: N, Y
    Engineered: YES
    Other Details: NON-TEMPLATE DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : BCNRTXYZ
Biological Unit 1 (1x): B    XYZ
Biological Unit 2 (1x):  CNRT   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3E3J)

(-) Sites  (0, 0)

(no "Site" information available for 3E3J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E3J)

(-) Cis Peptide Bonds  (53, 53)

Asymmetric Unit
No.Residues
1Lys C:53 -Met C:54
2Asn C:131 -Thr C:132
3Asn C:165 -Val C:166
4Lys C:180 -Ala C:181
5Glu C:222 -Ser C:223
6Ser C:223 -Thr C:224
7Thr C:224 -Gly C:225
8Gly C:263 -Ile C:264
9Ile C:264 -Ser C:265
10Ala C:354 -Ile C:355
11Pro C:361 -Met C:362
12Ile C:367 -Asp C:368
13Asp C:368 -Met C:369
14Met C:369 -Asn C:370
15Thr C:375 -Ala C:376
16Ala C:376 -Trp C:377
17Pro C:451 -Ile C:452
18Glu C:553 -Val C:554
19Val C:554 -Gly C:555
20Gly C:556 -Arg C:557
21Ile C:605 -Ser C:606
22Tyr C:836 -Glu C:837
23Ala C:850 -Asp C:851
24Pro C:862 -Ala C:863
25Ala C:863 -Leu C:864
26Ser B:43 -Tyr B:44
27Lys B:53 -Met B:54
28Asn B:131 -Thr B:132
29Asp B:147 -Glu B:148
30Ala B:149 -Arg B:150
31Asn B:165 -Val B:166
32Lys B:180 -Ala B:181
33Glu B:222 -Ser B:223
34Ser B:223 -Thr B:224
35Thr B:224 -Gly B:225
36Gly B:263 -Ile B:264
37Ile B:264 -Ser B:265
38Ala B:354 -Ile B:355
39Pro B:361 -Met B:362
40Ile B:367 -Asp B:368
41Asp B:368 -Met B:369
42Met B:369 -Asn B:370
43Thr B:375 -Ala B:376
44Ala B:376 -Trp B:377
45Pro B:451 -Ile B:452
46Glu B:553 -Val B:554
47Val B:554 -Gly B:555
48Gly B:556 -Arg B:557
49Ile B:605 -Ser B:606
50Tyr B:836 -Glu B:837
51Ala B:850 -Asp B:851
52Pro B:862 -Ala B:863
53Ala B:863 -Leu B:864

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E3J)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNA_POL_PHAGE_1PS00900 Bacteriophage-type RNA polymerase family active site signature 1.RPOL_BPT7533-544
 		  2B:533-544
C:533-544
2RNA_POL_PHAGE_2PS00489 Bacteriophage-type RNA polymerase family active site signature 2.RPOL_BPT7625-639
 		  2B:625-639
C:625-639
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNA_POL_PHAGE_1PS00900 Bacteriophage-type RNA polymerase family active site signature 1.RPOL_BPT7533-544
 		  1B:533-544
-
2RNA_POL_PHAGE_2PS00489 Bacteriophage-type RNA polymerase family active site signature 2.RPOL_BPT7625-639
 		  1B:625-639
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNA_POL_PHAGE_1PS00900 Bacteriophage-type RNA polymerase family active site signature 1.RPOL_BPT7533-544
 		  1-
C:533-544
2RNA_POL_PHAGE_2PS00489 Bacteriophage-type RNA polymerase family active site signature 2.RPOL_BPT7625-639
 		  1-
C:625-639

(-) Exons   (0, 0)

(no "Exon" information available for 3E3J)

(-) 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 B from PDB  Type:PROTEIN  Length:833
 aligned with RPOL_BPT7 | P00573 from UniProtKB/Swiss-Prot  Length:883

    Alignment length:876
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877      
            RPOL_BPT7     8 KNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 883
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhh...-----------------hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.....hhhhhhhhhhhhh...-------------.......hhhhh.............hhhhhhhhhhhhhhhhh.....eeeeee........eeeeeehhhhhh...-------..................................ee..hhhhhhh.....hhhhhhhhhhhhh.eeeehhhhhhhhhhhh..................................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eeee....eee........hhhhhhheee.......hhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhh..........ee....hhhhhhhhh..................hhhhhhhhhhhhhhhhhhhh....ee....------....ee.hhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.................eeee.....eeee......eee..eeehhheee..eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee...eee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.......hhhhh.........hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNA_POL_PHAG--------------------------------------------------------------------------------RNA_POL_PHAGE_2---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3e3j B   8 KNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMF-----------------LITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNV-------------KAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYAEAIA-------GISLMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVT------ISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 883
                                    17        27        37        47       | -         -     |  77        87        97       107       117       127       137       147       157        |-         -  |    187       197       207       217       227       237       247       | -     | 267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597|      607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877      
                                                                          55                73                                                                                          166           180                                                                        255     263                                                                                                                                                                                                                                                                                                                                            598    605                                                                                                                                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:833
 aligned with RPOL_BPT7 | P00573 from UniProtKB/Swiss-Prot  Length:883

    Alignment length:876
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877      
            RPOL_BPT7     8 KNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 883
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...-----------------hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhh...-------------..........................hhhhhhhhhhhhhhhh.....eeeeee........eeeeeehhhhhh...-------..................................ee..hhhhhhh.....hhhhhhhhhhhhh..eeehhhhhhhhhhhh..................................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeee....eee........hhhhhhheee.......hhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhh..........ee....hhhhhhhhh..................hhhhhhhhhhhhhhhhhhhh....ee....------....ee.hhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.................eeee.....eeee......eee..eeehhheee..eee..................hhhhhhhhhhhhhhhhhhhhh......ee...eee.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.......hhhhh...........hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNA_POL_PHAG--------------------------------------------------------------------------------RNA_POL_PHAGE_2---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3e3j C   8 KNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMF-----------------LITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNV-------------KAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYAEAIA-------GISLMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVT------ISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 883
                                    17        27        37        47       | -         -     |  77        87        97       107       117       127       137       147       157        |-         -  |    187       197       207       217       227       237       247       | -     | 267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597|      607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877      
                                                                          55                73                                                                                          166           180                                                                        255     263                                                                                                                                                                                                                                                                                                                                            598    605                                                                                                                                                                                                                                                                                      


Chain N from PDB  Type:DNA  Length:20
                                                    
                 3e3j N 101 TAATACGACTCACAAACGGC 132
                                   110  ||   132
                                      113|      
                                       126      


Chain R from PDB  Type:RNA  Length:8
                                        
                 3e3j R   1 GGGAGUAA   8


Chain T from PDB  Type:DNA  Length:28
                                                            
                 3e3j T   1 GCCGTTTTTACTCCCGTGAGTCGTATTA  32
                                    10    ||  24        
                                         15|            
                                          20            


Chain X from PDB  Type:DNA  Length:28
                                                            
                 3e3j X   1 GCCGTTTTTACTCCCGTGAGTCGTATTA  32
                                    10    ||  24        
                                         15|            
                                          20            


Chain Y from PDB  Type:DNA  Length:20
                                                    
                 3e3j Y 101 TAATACGACTCACAAACGGC 132
                                   110  ||   132
                                      113|      
                                       126      


Chain Z from PDB  Type:RNA  Length:8
                                        
                 3e3j Z   1 GGGAGUAA   8
   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 3E3J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E3J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E3J)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain B,C   (RPOL_BPT7 | P00573)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003899    DNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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.
biological process
    GO:0039695    DNA-templated viral transcription    A transcription process that uses a viral DNA as a template.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3e3j)
 
  Sites
(no "Sites" information available for 3e3j)
 
  Cis Peptide Bonds
    Ala B:149 - Arg B:150   [ RasMol ]  
    Ala B:354 - Ile B:355   [ RasMol ]  
    Ala B:376 - Trp B:377   [ RasMol ]  
    Ala B:850 - Asp B:851   [ RasMol ]  
    Ala B:863 - Leu B:864   [ RasMol ]  
    Ala C:354 - Ile C:355   [ RasMol ]  
    Ala C:376 - Trp C:377   [ RasMol ]  
    Ala C:850 - Asp C:851   [ RasMol ]  
    Ala C:863 - Leu C:864   [ RasMol ]  
    Asn B:131 - Thr B:132   [ RasMol ]  
    Asn B:165 - Val B:166   [ RasMol ]  
    Asn C:131 - Thr C:132   [ RasMol ]  
    Asn C:165 - Val C:166   [ RasMol ]  
    Asp B:147 - Glu B:148   [ RasMol ]  
    Asp B:368 - Met B:369   [ RasMol ]  
    Asp C:368 - Met C:369   [ RasMol ]  
    Glu B:222 - Ser B:223   [ RasMol ]  
    Glu B:553 - Val B:554   [ RasMol ]  
    Glu C:222 - Ser C:223   [ RasMol ]  
    Glu C:553 - Val C:554   [ RasMol ]  
    Gly B:263 - Ile B:264   [ RasMol ]  
    Gly B:556 - Arg B:557   [ RasMol ]  
    Gly C:263 - Ile C:264   [ RasMol ]  
    Gly C:556 - Arg C:557   [ RasMol ]  
    Ile B:264 - Ser B:265   [ RasMol ]  
    Ile B:367 - Asp B:368   [ RasMol ]  
    Ile B:605 - Ser B:606   [ RasMol ]  
    Ile C:264 - Ser C:265   [ RasMol ]  
    Ile C:367 - Asp C:368   [ RasMol ]  
    Ile C:605 - Ser C:606   [ RasMol ]  
    Lys B:180 - Ala B:181   [ RasMol ]  
    Lys B:53 - Met B:54   [ RasMol ]  
    Lys C:180 - Ala C:181   [ RasMol ]  
    Lys C:53 - Met C:54   [ RasMol ]  
    Met B:369 - Asn B:370   [ RasMol ]  
    Met C:369 - Asn C:370   [ RasMol ]  
    Pro B:361 - Met B:362   [ RasMol ]  
    Pro B:451 - Ile B:452   [ RasMol ]  
    Pro B:862 - Ala B:863   [ RasMol ]  
    Pro C:361 - Met C:362   [ RasMol ]  
    Pro C:451 - Ile C:452   [ RasMol ]  
    Pro C:862 - Ala C:863   [ RasMol ]  
    Ser B:223 - Thr B:224   [ RasMol ]  
    Ser B:43 - Tyr B:44   [ RasMol ]  
    Ser C:223 - Thr C:224   [ RasMol ]  
    Thr B:224 - Gly B:225   [ RasMol ]  
    Thr B:375 - Ala B:376   [ RasMol ]  
    Thr C:224 - Gly C:225   [ RasMol ]  
    Thr C:375 - Ala C:376   [ RasMol ]  
    Tyr B:836 - Glu B:837   [ RasMol ]  
    Tyr C:836 - Glu C:837   [ RasMol ]  
    Val B:554 - Gly B:555   [ RasMol ]  
    Val C:554 - Gly C:555   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3e3j
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RPOL_BPT7 | P00573
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.7.6
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  RPOL_BPT7 | P00573
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RPOL_BPT7 | P00573: 1aro 1cez 1h38 1msw 1qln 1s0v 1s76 1s77 2pi4 2pi5 3e2e 4rnp

(-) Related Entries Specified in the PDB File

3e2e CRYSTAL STRUCTURE OF AN INTERMEDIATE COMPLEX OF T7 RNA POLYMERASE AND 7NT OF RNA