General information
PDB ID 6KF9
Title CRYO-EM STRUCTURE OF THERMOCOCCUS KODAKARENSIS RNA POLYMERASE
PDB header TRANSCRIPTION
Date 2019-07-07
Experimental method ELECTRON MICROSCOPY
Resolution (A) 3.79
Kind dna
Organism THERMOCOCCUS KODAKARENSIS KOD1
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb6kf9.pdb ABCDEFHKLNPG XY 0
Biounits:
6kf9.pdb1.pdb ABCDEFHKLNPG XY 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
RNA_pol_Rpb1_1 Domain Q5JE33_5-319 7.3e-108 1 No_clan A 5 319   
RNA_pol_Rpb1_2 Domain Q5JE33_321-487 9.5e-74 1 No_clan A 321 487 X   
RNA_pol_Rpb1_3 Domain Q5JE33_490-673 4.1e-38 1 No_clan A 490 673   
RNA_pol_Rpb1_4 Domain Q5JE33_698-804 1e-31 1 No_clan A 698 804   
RNA_pol_Rpb1_5 Domain Q5JE33_811-896 4.8e-29 1 No_clan A 811 895 X   
RNA_pol_Rpb2_6 Domain Q5JE32_653-1026 1.1e-131 1 CL0410 B 653 1026 X   
RNA_pol_Rpb2_2 Domain Q5JE32_175-349 8.4e-41 1 No_clan B 175 349   
RNA_pol_Rpb2_7 Domain Q5JE32_1028-1120 9.1e-31 1 No_clan B 1028 1120 X   
RNA_pol_Rpb2_3 Domain Q5JE32_425-489 3.2e-30 1 No_clan B 425 489 Y  L-Mn 
RNA_pol_Rpb2_4 Domain Q5JE32_522-585 8.5e-20 1 No_clan B 522 585   
RNA_pol_Rpb2_5 Domain Q5JE32_606-647 3e-08 1 No_clan B 606 647   
RNA_pol_Rpb1_5 Domain Q5JE34_7-334 6.9e-56 1 No_clan C 8 334 Y  L-Bb 
RNA_pol_A_bac Domain Q5JJF4_45-147 1.7e-27 1 No_clan D 45 147   
RNA_pol_L Domain Q5JJF4_15-247 6e-18 1 CL0509 D 15 247   
SHS2_Rpb7-N Domain Q5JIY4_8-64 1.3e-15 1 CL0319 E 8 64   
S1 Domain Q5JIY4_78-159 1.2e-14 1 CL0021 E 78 159   
RNA_pol_Rpb5_C Domain Q5JE31_7-79 1.3e-32 1 No_clan H 7 79   
RNA_pol_L_2 Domain Q5JE88_12-88 4.2e-21 1 CL0509 L 12 88   
RNA_pol_N Domain Q5JJC9_2-59 1.1e-29 1 No_clan N 2 59   
DNA_RNApol_7kD Domain Q5JDM8_6-39 1.4e-08 1 CL0167 P 6 39   
HypA Domain Q5JDM8_2-34 0.00063 0 No_clan P 6 38   
RNA_pol_Rpb2_1 Family Q5JE32_29-396 8.6e-54 1 No_clan B 29 396   
RNA_pol_Rpb4 Family Q5JI52_11-114 1.3e-07 1 CL0426 F 11 119   
TFIIE_alpha Family Q5JDD5_7-111 1.3e-24 1 CL0123 G 7 111   
RNA_pol_Rpb6 Family Q5JJD0_3-51 8.3e-11 1 No_clan K 3 51   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
C=1-391 F DNA binding
C=1-391 F DNA-directed 5'-3' RNA polymerase activity
C=1-391 P transcription, DNA-templated
D=1-259 F DNA binding
D=1-259 F DNA-directed 5'-3' RNA polymerase activity
D=1-259 F protein dimerization activity
D=1-259 P transcription, DNA-templated
G=1-185 F DNA binding
G=1-185 F RNA polymerase II complex binding
G=1-185 F TFIIH-class transcription factor complex binding
G=1-185 P regulation of transcription by RNA polymerase II
G=1-185 P transcription open complex formation at RNA polymerase II promoter
H=1-82 F DNA binding
H=1-82 F DNA-directed 5'-3' RNA polymerase activity
H=1-82 P transcription, DNA-templated
K=1-57 F DNA binding
K=1-57 F DNA-directed 5'-3' RNA polymerase activity
K=1-57 P transcription, DNA-templated
L=1-94 F DNA binding
L=1-94 F DNA-directed 5'-3' RNA polymerase activity
L=1-94 F protein dimerization activity
L=1-94 P transcription, DNA-templated
N=1-65 F DNA binding
N=1-65 F DNA-directed 5'-3' RNA polymerase activity
N=1-65 F zinc ion binding
N=1-65 P transcription, DNA-templated
P=1-49 F DNA binding
P=1-49 F DNA-directed 5'-3' RNA polymerase activity
P=1-49 F metal ion binding
P=1-49 P transcription, DNA-templated
Sequences
Download file with secondary structure created by Stride  
6kf9.pdb1.pdb:   [ download sequences in FASTA format ]
X (dna): 
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Y (dna): 
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A (protein): 
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B (protein): 
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C (protein): 
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D (protein): 
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E (protein): 
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F (protein): 
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G (protein): 
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H (protein): 
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K (protein): 
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L (protein): 
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N (protein): 
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P (protein): 
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