Macromolecule Annotations for the Entities in PDB 2JA7

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

Chains Domain Info Class Fold Superfamily Family Domain Species
A2-1450 d2ja7a1 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 d2ja7b1 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 d2ja7c1 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 d2ja7c2 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 d2ja7d1 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 d2ja7e1 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 d2ja7e2 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 d2ja7f1 All alpha proteins RPB6/omega subunit-like RPB6/omega subunit-like RPB6 RPB6 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
G81-171 d2ja7g1 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 d2ja7g2 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 d2ja7h1 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 d2ja7i1 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 d2ja7i2 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 d2ja7j1 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 d2ja7k1 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 d2ja7l1 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]
M2-1450 d2ja7m1 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]
N20-1224 d2ja7n1 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]
O3-37,O173-268 d2ja7o1 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]
O42-172 d2ja7o2 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]
P15-75 d2ja7p1 Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
Q2-143 d2ja7q1 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]
Q144-215 d2ja7q2 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]
R72-155 d2ja7r1 All alpha proteins RPB6/omega subunit-like RPB6/omega subunit-like RPB6 RPB6 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
S81-171 d2ja7s1 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]
S1-80 d2ja7s2 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]
T2-146 d2ja7t1 All beta proteins OB-fold Nucleic acid-binding proteins RNA polymerase subunit RBP8 RNA polymerase subunit RBP8 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
U2-49 d2ja7u1 Small proteins Rubredoxin-like Zinc beta-ribbon Transcriptional factor domain RBP9 subunit of RNA polymerase II Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
U50-117 d2ja7u2 Small proteins Rubredoxin-like Zinc beta-ribbon Transcriptional factor domain RBP9 subunit of RNA polymerase II Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
V1-65 d2ja7v1 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]
W1-114 d2ja7w1 Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RBP11/RpoL RPB11 Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
X25-70 d2ja7x1 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 2ja7B04 Alpha Beta Alpha-Beta Complex Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
B6 2ja7B06 Mainly Beta Beta Barrel Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
B7 2ja7B07 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P)
C1 2ja7C01 Alpha Beta 2-Layer Sandwich Gyrase A; domain 2
C2 2ja7C02 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 RNA Polymerase Alpha Subunit; Chain A, domain 2
E1 2ja7E01 Alpha Beta 3-Layer(aba) Sandwich Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1
E2 2ja7E02 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit
F 2ja7F00 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit
G1 2ja7G01 Alpha Beta 2-Layer Sandwich Dna Ligase; domain 1 DNA-directed RNA polymerase ii subunit; domain 1
G2 2ja7G02 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
H 2ja7H00 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
I1 2ja7I01 Mainly Beta Single Sheet N-terminal domain of TfIIb
I2 2ja7I02 Mainly Beta Single Sheet N-terminal domain of TfIIb
J 2ja7J00 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Homeodomain-like
K 2ja7K00 Alpha Beta 2-Layer Sandwich Gyrase A; domain 2
L 2ja7L00 Mainly Beta Single Sheet Rubrerythrin, domain 2 RNA polymerase ii, chain L
N4 2ja7N04 Alpha Beta Alpha-Beta Complex Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
N6 2ja7N06 Mainly Beta Beta Barrel Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
N7 2ja7N07 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P)
O1 2ja7O01 Alpha Beta 2-Layer Sandwich Gyrase A; domain 2
O2 2ja7O02 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 RNA Polymerase Alpha Subunit; Chain A, domain 2
Q1 2ja7Q01 Alpha Beta 3-Layer(aba) Sandwich Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1
Q2 2ja7Q02 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit
R 2ja7R00 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit
S1 2ja7S01 Alpha Beta 2-Layer Sandwich Dna Ligase; domain 1 DNA-directed RNA polymerase ii subunit; domain 1
S2 2ja7S02 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
T 2ja7T00 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
U1 2ja7U01 Mainly Beta Single Sheet N-terminal domain of TfIIb
U2 2ja7U02 Mainly Beta Single Sheet N-terminal domain of TfIIb
V 2ja7V00 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Homeodomain-like
W 2ja7W00 Alpha Beta 2-Layer Sandwich Gyrase A; domain 2
X 2ja7X00 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
1,4 5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)- 3' (2JA7:1,4)
  • none
  • none
  • none
2,5 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TP*TP*TTP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)- 3' (2JA7:2,5)
  • none
  • none
  • none
3,6 5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3' (2JA7:3,6)
  • none
  • none
  • none
A,M DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT (2JA7:A,M)
B,N DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE (2JA7:B,N)
C,O DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE (2JA7:C,O)
D,P DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE (2JA7:D,P)
E,Q DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE (2JA7:E,Q)
F,R DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE (2JA7:F,R)
G,S DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE (2JA7:G,S)
H,T DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE (2JA7:H,T)
I,U DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 (2JA7:I,U)
J,V DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 (2JA7:J,V)
K,W DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE (2JA7:K,W)
L,X DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE (2JA7:L,X)

Protein Modification Annotation

Type PDB Residue Nr. Description