Domain ID e4bbrA5

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  • A: beta barrels
  • X: cradle loop barrel
  • H: RIFT-related
  • T: double psi
  • F: RNA_pol_Rpb1_2
UID: 001307442
Type: Automatic domain
Parent: e1twfA1
Range: A:337-374,A:436-519
Ligands: MG
PDB: 4bbr
PDB Description: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
UniProt: P04050
Hsap BLAST neighbor: P24928
Species: Saccharomyces cerevisiae

Structure of domain e4bbrA5

Domains in the same chain:

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e4bbrA6 A:3-336 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
e4bbrA5 A:337-374,A:436-519 cradle loop barrel RIFT-related double psi
e4bbrA1 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
e4bbrA9 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
e4bbrA7 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
e4bbrA2 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
e4bbrA3 A:1060-1102,A:1301-1455 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
e4bbrA4 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
e4bbrA8 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

Domains in the same PDB:

e4bbrA6 A:3-336 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
e4bbrA5 A:337-374,A:436-519 cradle loop barrel RIFT-related double psi
e4bbrA1 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
e4bbrA9 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
e4bbrA7 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
e4bbrA2 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
e4bbrA3 A:1060-1102,A:1301-1455 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
e4bbrA4 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
e4bbrA8 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
e4bbrB6 B:20-218,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
e4bbrB3 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
e4bbrB1 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
e4bbrB7 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
e4bbrB5 B:814-850,B:975-1097 cradle loop barrel RIFT-related double psi
e4bbrB4 B:851-974 alpha/beta-Hammerhead/Barrel-sandwich hybrid alpha/beta-Hammerhead/Barrel-sandwich hybrid Single hybrid motif
e4bbrB2 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
e4bbrC2 C:3-41,C:173-268 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e4bbrC3 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
e4bbrD1 D:3-76,D:118-221 HhH/H2TH SAM/DNA-glycosylase SAM domain-like
e4bbrE2 E:2-142 Restriction endonuclease-like Eukaryotic RPB5 N-terminal domain Eukaryotic RPB5 N-terminal domain
e4bbrE1 E:143-215 RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit
e4bbrF1 F:69-155 RPB6/omega subunit-like RPB6/omega subunit-like RPB6
e4bbrG4 G:1-68 Dodecin subunit-like Flavin-binding protein dodecin-like Flavin-binding protein dodecin-like
e4bbrG3 G:69-171 OB-fold Nucleic acid-binding proteins Nucleic acid-binding proteins
e4bbrH1 H:2-146 OB-fold Nucleic acid-binding proteins Nucleic acid-binding proteins
e4bbrI3 I:2-49 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e4bbrI4 I:50-120 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e4bbrJ1 J:1-65 HTH RPB10 RPB10
e4bbrK1 K:1-114 DCoH-like RBP11-like subunits of RNA polymerase RBP11-like subunits of RNA polymerase
e4bbrL1 L:27-70 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e4bbrM2 M:22-79 Rubredoxin-like Rubredoxin-related Rubredoxin-related
e4bbrM1 M:80-214 HTH HTH Cyclin-like

Structural contacts of domain e4bbrA5 of H-group "RIFT-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
e4bbrB5 A:X,Y,Z->B:x,y,z RIFT-related Interaction Interface Pymol
e4bbrB2 A:X,Y,Z->B:x,y,z C-terminal domain in beta subunit of DNA dependent RNA-polymerase Interaction Interface Pymol
e4bbrF1 A:X,Y,Z->F:x,y,z RPB6/omega subunit-like Interaction Interface Pymol
e4bbrK1 A:X,Y,Z->K:x,y,z RBP11-like subunits of RNA polymerase Interaction Interface Pymol
e4bbrG4 A:X,Y,Z->G:x,y,z Flavin-binding protein dodecin-like Interaction Interface Pymol