Domain ID e1nikI1

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  • A: few secondary structure elements
  • X: Rubredoxin-like
  • H: Rubredoxin-related
  • T: Rubredoxin-related
  • F: RNA_POL_M_15KD
UID: 000483152
Type: Automatic domain
Parent: e1twfI1
Range: I:2-49
Ligands: ZN
PDB: 1nik
PDB Description: DNA-directed RNA polymerase II, chain RPB9
UniProt: P27999
Hsap BLAST neighbor: P36954
Species: Saccharomyces cerevisiae

Structure of domain e1nikI1

Domains in the same chain:

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e1nikI1 I:2-49 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e1nikI2 I:50-120 Rubredoxin-like Rubredoxin-related Rubredoxin-related

Domains in the same PDB:

e1nikA4 A:2-336 N-terminal domain in RNA-polymerase beta-prime subunit N-terminal domain in RNA-polymerase beta-prime subunit N-terminal domain in RNA-polymerase beta-prime subunit
e1nikA5 A:337-374,A:436-519 cradle loop barrel RIFT-related double psi
e1nikA2 A:375-435 MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase
e1nikA9 A:520-662 first helical domain in RNA-polymerase beta-prime subunit first helical domain in RNA-polymerase beta-prime subunit first helical domain in RNA-polymerase beta-prime subunit
e1nikA3 A:663-871 second helical domain in RNA-polymerase beta-prime subunit second helical domain in RNA-polymerase beta-prime subunit second helical domain in RNA-polymerase beta-prime subunit
e1nikA7 A:872-1059 helical domain in yeast RNA-polymerases third helical domain in yeast RNA-polymerase II beta-prime subunit third helical domain in yeast RNA-polymerase II beta-prime subunit
e1nikA1 A:1060-1102,A:1301-1452 central helical domain in RNA-polymerase beta-prime subunit central helical domain in RNA-polymerase beta-prime subunit central helical domain in RNA-polymerase beta-prime subunit
e1nikA6 A:1103-1131,A:1243-1300 ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit
e1nikA8 A:1132-1242 permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit
e1nikB6 B:20-70,B:90-134,B:164-218,B:405-541 N-terminal domain in beta subunit of DNA dependent RNA-polymerase N-terminal domain in beta subunit of DNA dependent RNA-polymerase N-terminal domain in beta subunit of DNA dependent RNA-polymerase
e1nikB2 B:219-404 insertion domain in beta subunit of DNA dependent RNA-polymerase insertion domain in beta subunit of DNA dependent RNA-polymerase insertion domain in beta subunit of DNA dependent RNA-polymerase
e1nikB5 B:542-630 inserted a+b domain in yeast RNA polymerase beta subunit inserted a+b domain in yeast RNA polymerase beta subunit inserted a+b domain in yeast RNA polymerase beta subunit
e1nikB7 B:631-813 barrel domain in beta subunit of DNA dependent RNA-polymerase barrel domain in beta subunit of DNA dependent RNA-polymerase barrel domain in beta subunit of DNA dependent RNA-polymerase
e1nikB1 B:814-850,B:975-1097 cradle loop barrel RIFT-related double psi
e1nikB4 B:851-974 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e1nikB3 B:1098-1224 C-terminal domain in beta subunit of DNA dependent RNA-polymerase C-terminal domain in beta subunit of DNA dependent RNA-polymerase C-terminal domain in beta subunit of DNA dependent RNA-polymerase
e1nikC3 C:3-41,C:173-268 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e1nikC4 C:42-172 Ribosomal protein TL5/L25 C-terminal domain-like Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit
e1nikE2 E:2-142 Restriction endonuclease-like Eukaryotic RPB5 N-terminal domain Eukaryotic RPB5 N-terminal domain
e1nikE1 E:143-215 RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit
e1nikF1 F:72-155 RPB6/omega subunit-like RPB6/omega subunit-like RPB6
e1nikH1 H:2-146 OB-fold Nucleic acid-binding proteins Nucleic acid-binding proteins
e1nikI1 I:2-49 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e1nikI2 I:50-120 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e1nikJ1 J:1-65 HTH RPB10 RPB10
e1nikK1 K:1-114 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e1nikL1 L:25-70 Rubredoxin-like Rubredoxin-related Rubredoxin-related

Structural contacts of domain e1nikI1 of H-group "Rubredoxin-related":

The domain and its neighboring domains (both within the asymmetric unit and to crystallographic symmetry mates) are represented by spheres and linked by lines. Distances between the center of the domain and interfaces are shown for each contact.

Domain IDSymmetry operatorH-groupVisualization
e1nikA8 I:x,y,z->A:X,Y,Z permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit Interaction Interface Pymol
e1nikA6 I:x,y,z->A:X,Y,Z ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit Interaction Interface Pymol
e1nikB2 I:x,y,z->B:X,Y,Z insertion domain in beta subunit of DNA dependent RNA-polymerase Interaction Interface Pymol
e1nikA7 I:X-1/2,-Y-1/2,-Z->A:x,y,z third helical domain in yeast RNA-polymerase II beta-prime subunit Interaction Interface Pymol