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1W25
Asym. Unit
Info
Asym.Unit (154 KB)
Biol.Unit 1 (145 KB)
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(1)
Title
:
RESPONSE REGULATOR PLED IN COMPLEX WITH C-DIGMP
Authors
:
C. Chan, T. Schirmer, U. Jenal
Date
:
28 Jun 04 (Deposition) - 18 Nov 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Two-Component System, Ggdef Domain, Cyclic Dinucleotide, Cyclic-Digmp, Allosteric Product Inhibition, Phosphorylation, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Chan, R. Paul, D. Samoray, N. Amiot, B. Giese, U. Jenal, T. Schirmer
Structural Basis Of Activity And Allosteric Control Of Diguanylate Cyclase
Proc. Natl. Acad. Sci. Usa V. 101 17084 2004
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Hetero Components
(3, 8)
Info
All Hetero Components
1a: 9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10A... (C2Ea)
1b: 9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10A... (C2Eb)
1c: 9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10A... (C2Ec)
1d: 9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10A... (C2Ed)
1e: 9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10A... (C2Ee)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
C2E
5
Ligand/Ion
9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)
2
MG
2
Ligand/Ion
MAGNESIUM ION
3
ZN
1
Ligand/Ion
ZINC ION
[
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:9 , ASP A:10 , ASP A:53 , MET A:55
BINDING SITE FOR RESIDUE MG A 500
2
AC2
SOFTWARE
ASP B:9 , ASP B:10 , ASP B:53 , MET B:55
BINDING SITE FOR RESIDUE MG B 500
3
AC3
SOFTWARE
LYS A:332 , ASN A:335 , HIS A:340 , GLY A:343 , ASP A:344 , GLY A:369 , GLU A:370 , PHE B:331 , LYS B:332 , ASN B:335 , HIS B:340 , ASP B:344 , GLY B:369 , GLU B:370
BINDING SITE FOR RESIDUE C2E A 501
4
AC4
SOFTWARE
ARG A:178 , ARG A:359 , ASP A:362 , THR A:379 , ASP A:383 , ILE A:387 , ARG A:390 , C2E A:505 , ARG B:164
BINDING SITE FOR RESIDUE C2E A 503
5
AC5
SOFTWARE
ARG A:148 , GLY A:153 , GLY A:174 , VAL A:175 , HIS A:177 , ARG A:178 , SER A:356 , ASN A:357 , VAL A:358 , ARG A:359 , ALA A:360 , ARG A:390 , C2E A:503
BINDING SITE FOR RESIDUE C2E A 505
6
AC6
SOFTWARE
ARG A:164 , PRO A:255 , ARG B:178 , ARG B:359 , ASP B:362 , THR B:379 , ASP B:383 , ILE B:387 , ARG B:390 , C2E B:505
BINDING SITE FOR RESIDUE C2E B 503
7
AC7
SOFTWARE
ARG B:148 , GLY B:153 , GLY B:174 , VAL B:175 , HIS B:177 , ARG B:178 , SER B:356 , ASN B:357 , VAL B:358 , ARG B:359 , ALA B:360 , ARG B:390 , C2E B:503
BINDING SITE FOR RESIDUE C2E B 505
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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
(2, 6)
Info
All PROSITE Patterns/Profiles
1: RESPONSE_REGULATORY (A:4-120,B:4-120|A:155-269,B:155-26...)
2: GGDEF (A:319-454,B:319-454,A:319-454,B:31...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RESPONSE_REGULATORY
PS50110
Response regulatory domain profile.
PLED_CAUCN
4-120
155-269
4
A:4-120
B:4-120
A:155-269
B:155-269
PLED_CAUCR
4-120
155-269
4
A:4-120
B:4-120
A:155-269
B:155-269
2
GGDEF
PS50887
GGDEF domain profile.
PLED_CAUCN
319-454
2
A:319-454
B:319-454
PLED_CAUCR
319-454
2
A:319-454
B:319-454
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1w25a3 (A:294-455)
1b: SCOP_d1w25b3 (B:294-455)
2a: SCOP_d1w25a1 (A:2-140)
2b: SCOP_d1w25a2 (A:141-293)
2c: SCOP_d1w25b1 (B:2-140)
2d: SCOP_d1w25b2 (B:141-293)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Nucleotide cyclase
(51)
Family
:
GGDEF domain
(2)
Protein domain
:
Response regulator PleD, C-terminal domain
(2)
Caulobacter crescentus [TaxId: 155892]
(2)
1a
d1w25a3
A:294-455
1b
d1w25b3
B:294-455
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
CheY-like
(258)
Family
:
CheY-related
(166)
Protein domain
:
Response regulator PleD, receiver domain
(2)
Caulobacter crescentus [TaxId: 155892]
(2)
2a
d1w25a1
A:2-140
2b
d1w25a2
A:141-293
2c
d1w25b1
B:2-140
2d
d1w25b2
B:141-293
[
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1w25B03 (B:283-455)
1b: CATH_1w25A03 (A:280-455)
2a: CATH_1w25A01 (A:2-142)
2b: CATH_1w25B01 (B:2-139)
2c: CATH_1w25B02 (B:140-282)
2d: CATH_1w25A02 (A:143-279)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.270, no name defined]
(278)
Caulobacter vibrioides. Organism_taxid: 190650. Strain: cb15.
(1)
1a
1w25B03
B:283-455
1b
1w25A03
A:280-455
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.2300, no name defined]
(308)
Caulobacter vibrioides. Organism_taxid: 190650. Strain: cb15.
(1)
2a
1w25A01
A:2-142
2b
1w25B01
B:2-139
2c
1w25B02
B:140-282
2d
1w25A02
A:143-279
[
close CATH info
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Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Response_reg_1w25B01 (B:156-266)
1b: PFAM_Response_reg_1w25B02 (B:156-266)
1c: PFAM_Response_reg_1w25B03 (B:156-266)
1d: PFAM_Response_reg_1w25B04 (B:156-266)
2a: PFAM_GGDEF_1w25B05 (B:289-448)
2b: PFAM_GGDEF_1w25B06 (B:289-448)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CheY
(97)
Family
:
Response_reg
(94)
Caulobacter crescentus (Caulobacter vibrioides)
(8)
1a
Response_reg-1w25B01
B:156-266
1b
Response_reg-1w25B02
B:156-266
1c
Response_reg-1w25B03
B:156-266
1d
Response_reg-1w25B04
B:156-266
Clan
:
Nucleot_cyclase
(14)
Family
:
GGDEF
(5)
Caulobacter crescentus (Caulobacter vibrioides)
(3)
2a
GGDEF-1w25B05
B:289-448
2b
GGDEF-1w25B06
B:289-448
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Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
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