Domain ID e4aybA3

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  • A: beta barrels
  • X: cradle loop barrel
  • H: RIFT-related
  • T: double psi
  • F: RNA_pol_Rpb1_2
UID: 001710326
Type: Automatic domain
Parent: e1twfA1
Range: A:307-494
Ligands: MG ZN
PDB: 4ayb
PDB Description: DNA-DIRECTED RNA POLYMERASE
UniProt: B8YB53
Hsap BLAST neighbor: P24928
Species: Sulfolobus shibatae

Structure of domain e4aybA3

Domains in the same chain:

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e4aybA1 A:3-306 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
e4aybA3 A:307-494 cradle loop barrel RIFT-related double psi
e4aybA4 A:495-644 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
e4aybA2 A:645-879 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

Domains in the same PDB:

e4aybA1 A:3-306 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
e4aybA3 A:307-494 cradle loop barrel RIFT-related double psi
e4aybA4 A:495-644 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
e4aybA2 A:645-879 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
e4aybB3 B:7-170,B:345-475 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
e4aybB7 B:171-344 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
e4aybB6 B:476-575 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
e4aybB2 B:576-715 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
e4aybB5 B:716-752,B:876-998 cradle loop barrel RIFT-related double psi
e4aybB4 B:753-875 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e4aybB1 B:999-1125 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
e4aybC4 C:6-65 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
e4aybC1 C:66-115,C:276-394 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
e4aybC3 C:116-147,C:233-275 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
e4aybC2 C:148-232 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
e4aybD1 D:2-36,D:159-263 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e4aybD2 D:37-158 Ribosomal protein TL5/L25 C-terminal domain-like Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit
e4aybE2 E:1-78 Dodecin subunit-like Flavin-binding protein dodecin-like Flavin-binding protein dodecin-like
e4aybE1 E:79-178 OB-fold Nucleic acid-binding proteins Nucleic acid-binding proteins
e4aybF1 F:3-110 HhH/H2TH SAM/DNA-glycosylase SAM domain-like
e4aybG1 G:5-117 OB-fold Nucleic acid-binding proteins Nucleic acid-binding proteins
e4aybH1 H:8-83 RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit
e4aybK2 K:11-94 RPB6/omega subunit-like RPB6/omega subunit-like RPB6
e4aybL1 L:1-91 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e4aybN1 N:1-65 HTH RPB10 RPB10
e4aybP2 P:5-48 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e4aybQ1 Q:33-82 YqgQ-like YqgQ-like YqgQ-like

Structural contacts of domain e4aybA3 of H-group "RIFT-related":

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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
e4aybB5 A:X,Y,Z->B:x,y,z RIFT-related Interaction Interface Pymol
e4aybB1 A:X,Y,Z->B:x,y,z C-terminal domain in beta subunit of DNA dependent RNA-polymerase Interaction Interface Pymol
e4aybC1 A:X,Y,Z->C:x,y,z central helical domain in RNA-polymerase beta-prime subunit Interaction Interface Pymol
e4aybK2 A:X,Y,Z->K:x,y,z RPB6/omega subunit-like Interaction Interface Pymol
e4aybL1 A:X,Y,Z->L:x,y,z RBP11-like subunits of RNA polymerase Interaction Interface Pymol
e4aybE2 A:X,Y,Z->E:x,y,z Flavin-binding protein dodecin-like Interaction Interface Pymol