Macromolecule Annotations for the Entities in PDB 2JA5

Domain Annotation: SCOP Classification SCOP Database (version: 1.75) Homepage

Chains Domain Info Class Fold Superfamily Family Domain Species
A2-1450 d2ja5a1 Multi-domain proteins (alpha and beta) beta and beta-prime subunits of DNA dependent RNA- polymerase beta and beta-prime subunits of DNA dependent RNA- polymerase RNA-polymerase beta-prime RBP1 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
B20-1224 d2ja5b1 Multi-domain proteins (alpha and beta) beta and beta-prime subunits of DNA dependent RNA- polymerase beta and beta-prime subunits of DNA dependent RNA- polymerase RNA-polymerase beta RBP2 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
C3-37,C173-268 d2ja5c1 Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RNA polymerase alpha subunit dimerisation domain RPB3 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
C42-172 d2ja5c2 Alpha and beta proteins (a+b) Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit Insert subdomain of RNA polymerase alpha subunit RPB3 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
D15-75 d2ja5d1 Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
E2-143 d2ja5e1 Alpha and beta proteins (a/b) Restriction endonuclease-like Eukaryotic RPB5 N-terminal domain Eukaryotic RPB5 N-terminal domain Eukaryotic RPB5 N-terminal domain Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
E144-215 d2ja5e2 Alpha and beta proteins (a+b) RPB5-like RNA polymerase subunit RPB5-like RNA polymerase subunit RPB5 Eukaryotic RPB5 C-terminal domain Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
F72-155 d2ja5f1 All alpha proteins RPB6/omega subunit-like RPB6/omega subunit-like RPB6 RPB6 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
G81-171 d2ja5g1 All beta proteins OB-fold Nucleic acid-binding proteins Cold shock DNA-binding domain-like C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
G1-80 d2ja5g2 Alpha and beta proteins (a+b) Dodecin subunit-like N-terminal, heterodimerisation domain of RBP7 (RpoE) N-terminal, heterodimerisation domain of RBP7 (RpoE) N-terminal, heterodimerisation domain of RBP7 (RpoE) Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
H2-146 d2ja5h1 All beta proteins OB-fold Nucleic acid-binding proteins RNA polymerase subunit RBP8 RNA polymerase subunit RBP8 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
I2-49 d2ja5i1 Small proteins Rubredoxin-like Zinc beta-ribbon Transcriptional factor domain RBP9 subunit of RNA polymerase II Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
I50-117 d2ja5i2 Small proteins Rubredoxin-like Zinc beta-ribbon Transcriptional factor domain RBP9 subunit of RNA polymerase II Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
J1-65 d2ja5j1 All alpha proteins DNA/RNA-binding 3-helical bundle RNA polymerase subunit RPB10 RNA polymerase subunit RPB10 RNA polymerase subunit RPB10 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
K1-114 d2ja5k1 Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RBP11/RpoL RPB11 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
L25-70 d2ja5l1 Small proteins Rubredoxin-like RNA polymerase subunits RBP12 subunit of RNA polymerase II RBP12 subunit of RNA polymerase II Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Domain Annotation: CATH CATH Database (version 4.0.0) Homepage

Chains Domain Class Architecture Topology Homology
B4 2ja5B04 Alpha Beta Alpha-Beta Complex Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
B6 2ja5B06 Mainly Beta Beta Barrel Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
B7 2ja5B07 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P)
C1 2ja5C01 Alpha Beta 2-Layer Sandwich Gyrase A; domain 2
C2 2ja5C02 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 RNA Polymerase Alpha Subunit; Chain A, domain 2
E1 2ja5E01 Alpha Beta 3-Layer(aba) Sandwich Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1
E2 2ja5E02 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit
F 2ja5F00 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit
G1 2ja5G01 Alpha Beta 2-Layer Sandwich Dna Ligase; domain 1 DNA-directed RNA polymerase ii subunit; domain 1
G2 2ja5G02 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
H 2ja5H00 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
I1 2ja5I01 Mainly Beta Single Sheet N-terminal domain of TfIIb
I2 2ja5I02 Mainly Beta Single Sheet N-terminal domain of TfIIb
J 2ja5J00 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Homeodomain-like
K 2ja5K00 Alpha Beta 2-Layer Sandwich Gyrase A; domain 2
L 2ja5L00 Mainly Beta Single Sheet Rubrerythrin, domain 2 RNA polymerase ii, chain L

Protein Family Annotation Pfam Database Homepage

Chains Pfam Accession Pfam Identifier Pfam Description Type Source

Gene Product Annotation Gene Ontology Consortium Homepage

Chains Polymer Molecular Function Biological Process Cellular Component
A DNA-directed RNA polymerase II subunit RPB1 (2JA5:A)
B DNA-directed RNA polymerase II subunit RPB2 (2JA5:B)
C DNA-directed RNA polymerase II subunit RPB3 (2JA5:C)
D DNA-directed RNA polymerase II subunit RPB4 (2JA5:D)
E DNA-directed RNA polymerases I, II, and III subunit RPABC1 (2JA5:E)
F DNA-directed RNA polymerases I, II, and III subunit RPABC2 (2JA5:F)
G DNA-directed RNA polymerase II subunit RPB7 (2JA5:G)
H DNA-directed RNA polymerases I, II, and III subunit RPABC3 (2JA5:H)
I DNA-directed RNA polymerase II subunit RPB9 (2JA5:I)
J DNA-directed RNA polymerases I, II, and III subunit RPABC5 (2JA5:J)
K DNA-directed RNA polymerase II subunit RPB11 (2JA5:K)
L DNA-directed RNA polymerases I, II, and III subunit RPABC4 (2JA5:L)
P 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3' (2JA5:P)
  • none
  • none
  • none
T 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TTP*TP*TP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)- 3' (2JA5:T)
  • none
  • none
  • none

Protein Modification Annotation

Type PDB Residue Nr. Description