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1I6V
Asym. Unit
Info
Asym.Unit (455 KB)
Biol.Unit 1 (434 KB)
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(1)
Title
:
THERMUS AQUATICUS CORE RNA POLYMERASE-RIFAMPICIN COMPLEX
Authors
:
E. A. Campbell, N. Korzheva, A. Mustaev, K. Murakami, A. Goldfarb, S. A. Darst
Date
:
05 Mar 01 (Deposition) - 18 Apr 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
Transferase, Transcription, Dna-Directed Rna Polymerase, 3D- Structure
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
E. A. Campbell, N. Korzheva, A. Mustaev, K. Murakami, S. Nair, A. Goldfarb, S. A. Darst
Structural Mechanism For Rifampicin Inhibition Of Bacterial Rna Polymerase.
Cell(Cambridge, Mass. ) V. 104 901 2001
(for further references see the
PDB file header
)
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Hetero Components
(4, 39)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
2a: RIFAMPICIN (RFPa)
3a: (UNKa)
3aa: (UNKaa)
3ab: (UNKab)
3ac: (UNKac)
3ad: (UNKad)
3ae: (UNKae)
3af: (UNKaf)
3ag: (UNKag)
3ah: (UNKah)
3ai: (UNKai)
3aj: (UNKaj)
3b: (UNKb)
3c: (UNKc)
3d: (UNKd)
3e: (UNKe)
3f: (UNKf)
3g: (UNKg)
3h: (UNKh)
3i: (UNKi)
3j: (UNKj)
3k: (UNKk)
3l: (UNKl)
3m: (UNKm)
3n: (UNKn)
3o: (UNKo)
3p: (UNKp)
3q: (UNKq)
3r: (UNKr)
3s: (UNKs)
3t: (UNKt)
3u: (UNKu)
3v: (UNKv)
3w: (UNKw)
3x: (UNKx)
3y: (UNKy)
3z: (UNKz)
4a: ZINC ION (ZNa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MG
1
Ligand/Ion
MAGNESIUM ION
2
RFP
1
Ligand/Ion
RIFAMPICIN
3
UNK
36
Mod. Amino Acid
4
ZN
1
Ligand/Ion
ZINC ION
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP D:741 , ASP D:743
BINDING SITE FOR RESIDUE MG D 1600
2
AC2
SOFTWARE
CYS D:1112 , CYS D:1194 , CYS D:1201 , CYS D:1204
BINDING SITE FOR RESIDUE ZN D 1601
3
AC3
SOFTWARE
ARG C:134 , SER C:389 , GLN C:390 , LEU C:391 , SER C:392 , GLN C:393 , PHE C:394 , ASP C:396 , ARG C:409 , SER C:411 , GLU C:445 , ILE C:452
BINDING SITE FOR RESIDUE RFP C 1640
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RNA_POL_BETA (C:836-848)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RNA_POL_BETA
PS01166
RNA polymerases beta chain signature.
RPOB_THEAQ
836-848
1
C:836-848
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(5, 7)
Info
All SCOP Domains
1a: SCOP_d1i6ve_ (E:)
2a: SCOP_d1i6va1 (A:6-49,A:173-229)
2b: SCOP_d1i6vb1 (B:3-49,B:173-232)
3a: SCOP_d1i6va2 (A:50-172)
3b: SCOP_d1i6vb2 (B:50-172)
4a: SCOP_d1i6vc_ (C:)
5a: SCOP_d1i6vd_ (D:)
View:
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Classes
(
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)
Folds
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(
)
Superfamilies
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(
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Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
RPB6/omega subunit-like
(56)
Superfamily
:
RPB6/omega subunit-like
(56)
Family
:
RNA polymerase omega subunit
(19)
Protein domain
:
RNA polymerase omega subunit
(19)
Thermus aquaticus [TaxId: 271]
(3)
1a
d1i6ve_
E:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
DCoH-like
(107)
Superfamily
:
RBP11-like subunits of RNA polymerase
(76)
Family
:
RNA polymerase alpha subunit dimerisation domain
(43)
Protein domain
:
RNA polymerase alpha
(18)
Thermus aquaticus [TaxId: 271]
(4)
2a
d1i6va1
A:6-49,A:173-229
2b
d1i6vb1
B:3-49,B:173-232
Fold
:
Insert subdomain of RNA polymerase alpha subunit
(43)
Superfamily
:
Insert subdomain of RNA polymerase alpha subunit
(43)
Family
:
Insert subdomain of RNA polymerase alpha subunit
(43)
Protein domain
:
RNA polymerase alpha subunit
(18)
Thermus aquaticus [TaxId: 271]
(4)
3a
d1i6va2
A:50-172
3b
d1i6vb2
B:50-172
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
beta and beta-prime subunits of DNA dependent RNA-polymerase
(103)
Superfamily
:
beta and beta-prime subunits of DNA dependent RNA-polymerase
(103)
Family
:
RNA-polymerase beta
(54)
Protein domain
:
RNA-polymerase beta
(9)
Thermus aquaticus [TaxId: 271]
(4)
4a
d1i6vc_
C:
Family
:
RNA-polymerase beta-prime
(49)
Protein domain
:
RNA-polymerase beta-prime
(16)
Thermus aquaticus [TaxId: 271]
(4)
5a
d1i6vd_
D:
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CATH Domains
(9, 11)
Info
all CATH domains
1a: CATH_1i6vB01 (B:3-49,B:172-225)
1b: CATH_1i6vA01 (A:6-49,A:172-225)
2a: CATH_1i6vC03 (C:144-323)
3a: CATH_1i6vE00 (E:1-98)
4a: CATH_1i6vC02 (C:9-143,C:324-470,C:536-592)
5a: CATH_1i6vC01 (C:2-8,C:668-702,C:831-1004)
6a: CATH_1i6vC05 (C:593-667)
7a: CATH_1i6vC06 (C:703-830)
8a: CATH_1i6vA02 (A:50-171)
8b: CATH_1i6vB02 (B:50-171)
9a: CATH_1i6vC04 (C:471-535)
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Homologous Superfamilies
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)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Gyrase A; domain 2
(166)
Homologous Superfamily
:
[code=3.30.1360.10, no name defined]
(72)
Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271.
(4)
1a
1i6vB01
B:3-49,B:172-225
1b
1i6vA01
A:6-49,A:172-225
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
(48)
Homologous Superfamily
:
[code=3.90.1110.10, no name defined]
(48)
Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271.
(4)
2a
1i6vC03
C:144-323
Topology
:
Eukaryotic RPB6 RNA polymerase subunit
(77)
Homologous Superfamily
:
[code=3.90.940.10, no name defined]
(71)
Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271.
(4)
3a
1i6vE00
E:1-98
Topology
:
Rna Polymerase Beta Subunit; Chain: C,domain 2
(18)
Homologous Superfamily
:
[code=3.90.1100.10, no name defined]
(18)
Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271.
(4)
4a
1i6vC02
C:9-143,C:324-470,C:536-592
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
(18)
Homologous Superfamily
:
[code=2.40.270.10, no name defined]
(18)
Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271.
(4)
5a
1i6vC01
C:2-8,C:668-702,C:831-1004
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
[code=2.40.50.100, no name defined]
(113)
Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271.
(4)
6a
1i6vC05
C:593-667
Homologous Superfamily
:
[code=2.40.50.150, no name defined]
(48)
Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271.
(4)
7a
1i6vC06
C:703-830
Architecture
:
Beta Complex
(381)
Topology
:
RNA Polymerase Alpha Subunit; Chain A, domain 2
(118)
Homologous Superfamily
:
RNA Polymerase Alpha Subunit; Chain A, domain 2
(71)
Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271.
(4)
8a
1i6vA02
A:50-171
8b
1i6vB02
B:50-171
Architecture
:
Roll
(1513)
Topology
:
Rna Polymerase Beta Subunit; Chain: C, domain 4
(18)
Homologous Superfamily
:
[code=2.30.150.10, no name defined]
(18)
Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271. Thermus aquaticus. Organism_taxid: 271.
(4)
9a
1i6vC04
C:471-535
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Pfam Domains
(0, 0)
Info
all PFAM domains
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