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1NY6
Biol. Unit 2
Info
Asym.Unit (582 KB)
Biol.Unit 1 (288 KB)
Biol.Unit 2 (286 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SIGM54 ACTIVATOR (AAA+ ATPASE) IN THE ACTIVE STATE
Authors
:
S. Y. Lee, A. De La Torre, S. Kustu, B. T. Nixon, D. E. Wemmer
Date
:
11 Feb 03 (Deposition) - 11 Nov 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N
Biol. Unit 1: A,B,C,D,E,F,G (1x)
Biol. Unit 2: H,I,J,K,L,M,N (1x)
Keywords
:
Aaa+ Atpase, Sigma54 Activator, Bacterial Transcription, Heptamer
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Y. Lee, A. De La Torre, D. Yan, S. Kustu, B. T. Nixon, D. E. Wemmer
Regulation Of The Transcriptional Activator Ntrc1: Structural Studies Of The Regulatory And Aaa+ Atpase Domains
Genes Dev. V. 17 2552 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 7)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
1e: ADENOSINE-5'-DIPHOSPHATE (ADPe)
1f: ADENOSINE-5'-DIPHOSPHATE (ADPf)
1g: ADENOSINE-5'-DIPHOSPHATE (ADPg)
1h: ADENOSINE-5'-DIPHOSPHATE (ADPh)
1i: ADENOSINE-5'-DIPHOSPHATE (ADPi)
1j: ADENOSINE-5'-DIPHOSPHATE (ADPj)
1k: ADENOSINE-5'-DIPHOSPHATE (ADPk)
1l: ADENOSINE-5'-DIPHOSPHATE (ADPl)
1m: ADENOSINE-5'-DIPHOSPHATE (ADPm)
1n: ADENOSINE-5'-DIPHOSPHATE (ADPn)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
7
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
[
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Sites
(7, 7)
Info
All Sites
1: AC8 (SOFTWARE)
2: AC9 (SOFTWARE)
3: BC1 (SOFTWARE)
4: BC2 (SOFTWARE)
5: BC3 (SOFTWARE)
6: BC4 (SOFTWARE)
7: BC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC8
SOFTWARE
TYR I:139 , VAL I:140 , PHE I:141 , MET I:146 , GLU I:168 , GLY I:170 , VAL I:171 , GLY I:172 , LYS I:173 , GLU I:174 , VAL I:175 , VAL I:356 , ARG I:357 , LYS I:360
BINDING SITE FOR RESIDUE ADP I 8
2
AC9
SOFTWARE
VAL J:140 , GLY J:170 , VAL J:171 , GLY J:172 , LYS J:173 , GLU J:174 , VAL J:175 , VAL J:356 , ARG J:357 , LYS J:360
BINDING SITE FOR RESIDUE ADP J 9
3
BC1
SOFTWARE
VAL K:140 , SER K:169 , GLY K:170 , VAL K:171 , GLY K:172 , LYS K:173 , GLU K:174 , VAL K:175 , VAL K:356 , ARG K:357 , LYS K:360
BINDING SITE FOR RESIDUE ADP K 10
4
BC2
SOFTWARE
VAL L:140 , PHE L:141 , GLY L:170 , VAL L:171 , GLY L:172 , LYS L:173 , GLU L:174 , VAL L:175 , VAL L:356 , ARG L:357 , LYS L:360
BINDING SITE FOR RESIDUE ADP L 11
5
BC3
SOFTWARE
TYR M:139 , VAL M:140 , PHE M:141 , GLY M:170 , VAL M:171 , GLY M:172 , LYS M:173 , GLU M:174 , VAL M:175 , VAL M:356 , ARG M:357 , LYS M:360
BINDING SITE FOR RESIDUE ADP M 12
6
BC4
SOFTWARE
VAL N:140 , GLU N:168 , GLY N:170 , VAL N:171 , GLY N:172 , LYS N:173 , GLU N:174 , VAL N:175 , VAL N:356
BINDING SITE FOR RESIDUE ADP N 13
7
BC5
SOFTWARE
PHE H:141 , GLU H:168 , GLY H:170 , VAL H:171 , GLY H:172 , LYS H:173 , GLU H:174 , VAL H:175 , VAL H:356 , ARG H:357 , LYS H:360 , GLU N:256
BINDING SITE FOR RESIDUE ADP H 14
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 14)
Info
All SCOP Domains
1a: SCOP_d1ny6a_ (A:)
1b: SCOP_d1ny6i_ (I:)
1c: SCOP_d1ny6j_ (J:)
1d: SCOP_d1ny6k_ (K:)
1e: SCOP_d1ny6l_ (L:)
1f: SCOP_d1ny6m_ (M:)
1g: SCOP_d1ny6n_ (N:)
1h: SCOP_d1ny6b_ (B:)
1i: SCOP_d1ny6c_ (C:)
1j: SCOP_d1ny6d_ (D:)
1k: SCOP_d1ny6e_ (E:)
1l: SCOP_d1ny6f_ (F:)
1m: SCOP_d1ny6g_ (G:)
1n: SCOP_d1ny6h_ (H:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
Extended AAA-ATPase domain
(92)
Protein domain
:
Transcriptional activator sigm54 (NtrC1), C-terminal domain
(2)
Aquifex aeolicus [TaxId: 63363]
(2)
1a
d1ny6a_
A:
1b
d1ny6i_
I:
1c
d1ny6j_
J:
1d
d1ny6k_
K:
1e
d1ny6l_
L:
1f
d1ny6m_
M:
1g
d1ny6n_
N:
1h
d1ny6b_
B:
1i
d1ny6c_
C:
1j
d1ny6d_
D:
1k
d1ny6e_
E:
1l
d1ny6f_
F:
1m
d1ny6g_
G:
1n
d1ny6h_
H:
[
close SCOP info
]
CATH Domains
(2, 28)
Info
all CATH domains
1a: CATH_1ny6C01 (C:137-310)
1b: CATH_1ny6K01 (K:137-310)
1c: CATH_1ny6A01 (A:138-310)
1d: CATH_1ny6D01 (D:138-310)
1e: CATH_1ny6H01 (H:138-310)
1f: CATH_1ny6I01 (I:138-310)
1g: CATH_1ny6J01 (J:138-310)
1h: CATH_1ny6L01 (L:138-310)
1i: CATH_1ny6M01 (M:138-310)
1j: CATH_1ny6N01 (N:138-310)
1k: CATH_1ny6B01 (B:142-310)
1l: CATH_1ny6E01 (E:137-310)
1m: CATH_1ny6F01 (F:137-310)
1n: CATH_1ny6G01 (G:137-310)
2a: CATH_1ny6A02 (A:311-384)
2b: CATH_1ny6J02 (J:311-384)
2c: CATH_1ny6K02 (K:311-384)
2d: CATH_1ny6M02 (M:311-384)
2e: CATH_1ny6N02 (N:311-384)
2f: CATH_1ny6L02 (L:311-383)
2g: CATH_1ny6H02 (H:311-382)
2h: CATH_1ny6B02 (B:311-384)
2i: CATH_1ny6C02 (C:311-384)
2j: CATH_1ny6D02 (D:311-384)
2k: CATH_1ny6E02 (E:311-384)
2l: CATH_1ny6F02 (F:311-384)
2m: CATH_1ny6G02 (G:311-384)
2n: CATH_1ny6I02 (I:311-384)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Aquifex aeolicus. Organism_taxid: 63363.
(7)
1a
1ny6C01
C:137-310
1b
1ny6K01
K:137-310
1c
1ny6A01
A:138-310
1d
1ny6D01
D:138-310
1e
1ny6H01
H:138-310
1f
1ny6I01
I:138-310
1g
1ny6J01
J:138-310
1h
1ny6L01
L:138-310
1i
1ny6M01
M:138-310
1j
1ny6N01
N:138-310
1k
1ny6B01
B:142-310
1l
1ny6E01
E:137-310
1m
1ny6F01
F:137-310
1n
1ny6G01
G:137-310
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helicase, Ruva Protein; domain 3
(218)
Homologous Superfamily
:
[code=1.10.8.60, no name defined]
(73)
Aquifex aeolicus. Organism_taxid: 63363.
(5)
2a
1ny6A02
A:311-384
2b
1ny6J02
J:311-384
2c
1ny6K02
K:311-384
2d
1ny6M02
M:311-384
2e
1ny6N02
N:311-384
2f
1ny6L02
L:311-383
2g
1ny6H02
H:311-382
2h
1ny6B02
B:311-384
2i
1ny6C02
C:311-384
2j
1ny6D02
D:311-384
2k
1ny6E02
E:311-384
2l
1ny6F02
F:311-384
2m
1ny6G02
G:311-384
2n
1ny6I02
I:311-384
[
close CATH info
]
Pfam Domains
(1, 14)
Info
all PFAM domains
1a: PFAM_Sigma54_activat_1ny6N01 (N:139-306)
1b: PFAM_Sigma54_activat_1ny6N02 (N:139-306)
1c: PFAM_Sigma54_activat_1ny6N03 (N:139-306)
1d: PFAM_Sigma54_activat_1ny6N04 (N:139-306)
1e: PFAM_Sigma54_activat_1ny6N05 (N:139-306)
1f: PFAM_Sigma54_activat_1ny6N06 (N:139-306)
1g: PFAM_Sigma54_activat_1ny6N07 (N:139-306)
1h: PFAM_Sigma54_activat_1ny6N08 (N:139-306)
1i: PFAM_Sigma54_activat_1ny6N09 (N:139-306)
1j: PFAM_Sigma54_activat_1ny6N10 (N:139-306)
1k: PFAM_Sigma54_activat_1ny6N11 (N:139-306)
1l: PFAM_Sigma54_activat_1ny6N12 (N:139-306)
1m: PFAM_Sigma54_activat_1ny6N13 (N:139-306)
1n: PFAM_Sigma54_activat_1ny6N14 (N:139-306)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
Sigma54_activat
(5)
Aquifex aeolicus
(3)
1a
Sigma54_activat-1ny6N01
N:139-306
1b
Sigma54_activat-1ny6N02
N:139-306
1c
Sigma54_activat-1ny6N03
N:139-306
1d
Sigma54_activat-1ny6N04
N:139-306
1e
Sigma54_activat-1ny6N05
N:139-306
1f
Sigma54_activat-1ny6N06
N:139-306
1g
Sigma54_activat-1ny6N07
N:139-306
1h
Sigma54_activat-1ny6N08
N:139-306
1i
Sigma54_activat-1ny6N09
N:139-306
1j
Sigma54_activat-1ny6N10
N:139-306
1k
Sigma54_activat-1ny6N11
N:139-306
1l
Sigma54_activat-1ny6N12
N:139-306
1m
Sigma54_activat-1ny6N13
N:139-306
1n
Sigma54_activat-1ny6N14
N:139-306
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