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3KGD
Biol. Unit 4
Info
Asym.Unit (492 KB)
Biol.Unit 1 (121 KB)
Biol.Unit 2 (123 KB)
Biol.Unit 3 (121 KB)
Biol.Unit 4 (122 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF E. COLI RNA 3' CYCLASE
Authors
:
S. Shuman, N. Tanaka, P. Smith
Date
:
28 Oct 09 (Deposition) - 21 Apr 10 (Release) - 21 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.68
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Cyclase, Rna Processing, 3' Modifying Enzymes, Adenylate, Phosphoramidate, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
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Reference
:
N. Tanaka, P. Smith, S. Shuman
Structure Of The Rna 3'-Phosphate Cyclase-Adenylate Intermediate Illuminates Nucleotide Specificity And Covalen Nucleotidyl Transfer.
Structure V. 18 449 2010
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Hetero Components
(3, 5)
Info
All Hetero Components
1a: ADENOSINE MONOPHOSPHATE (AMPa)
1b: ADENOSINE MONOPHOSPHATE (AMPb)
1c: ADENOSINE MONOPHOSPHATE (AMPc)
1d: ADENOSINE MONOPHOSPHATE (AMPd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
3e: SODIUM ION (NAe)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
View:
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Label:
No.
Name
Count
Type
Full Name
1
AMP
1
Ligand/Ion
ADENOSINE MONOPHOSPHATE
2
GOL
3
Ligand/Ion
GLYCEROL
3
NA
-1
Ligand/Ion
SODIUM ION
4
SO4
1
Ligand/Ion
SULFATE ION
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Sites
(7, 7)
Info
All Sites
1: BC6 (SOFTWARE)
2: CC4 (SOFTWARE)
3: CC5 (SOFTWARE)
4: CC6 (SOFTWARE)
5: CC7 (SOFTWARE)
6: CC8 (SOFTWARE)
7: CC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
BC6
SOFTWARE
ASP A:114 , GLU C:318 , ARG C:324 , PHE C:325 , GLY D:200
BINDING SITE FOR RESIDUE GOL C 340
2
CC4
SOFTWARE
ARG D:21 , GLN D:104 , SER D:129 , ALA D:130 , PRO D:131 , PHE D:251 , TYR D:284 , ASP D:287 , GLN D:288 , HIS D:309 , HOH D:363 , HOH D:413 , HOH D:431 , HOH D:528
BINDING SITE FOR RESIDUE AMP D 501
3
CC5
SOFTWARE
LYS D:3 , ARG D:4 , MET D:5
BINDING SITE FOR RESIDUE GOL D 340
4
CC6
SOFTWARE
HIS D:204 , VAL D:205 , ARG D:208 , GLU D:261
BINDING SITE FOR RESIDUE GOL D 341
5
CC7
SOFTWARE
GLY D:64 , ALA D:65 , THR D:66 , ARG D:80 , PRO D:81
BINDING SITE FOR RESIDUE GOL D 342
6
CC8
SOFTWARE
ARG D:40 , SO4 D:344 , HOH D:1378
BINDING SITE FOR RESIDUE NA D 343
7
CC9
SOFTWARE
GLU D:14 , ARG D:40 , ARG D:43 , NA D:343 , HOH D:358 , HOH D:981 , HOH D:1126
BINDING SITE FOR RESIDUE SO4 D 344
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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: RTC (D:158-168)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RTC
PS01287
RNA 3'-terminal phosphate cyclase signature.
RTCA_ECOLI
157-167
1
-
-
-
D:158-168
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Exons
(0, 0)
Info
All Exons
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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
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_3kgdA02 (A:186-276)
1b: CATH_3kgdB02 (B:186-276)
1c: CATH_3kgdC02 (C:186-276)
1d: CATH_3kgdD02 (D:186-276)
2a: CATH_3kgdA01 (A:4-182,A:277-337)
2b: CATH_3kgdC01 (C:2-182,C:277-337)
2c: CATH_3kgdD01 (D:0-182,D:277-337)
2d: CATH_3kgdB01 (B:-13-182,B:277-337)
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)
(
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(
)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dihydrodipicolinate Reductase; domain 2
(182)
Homologous Superfamily
:
[code=3.30.360.20, no name defined]
(3)
K-12 substr (Escherichia coli str)
(1)
1a
3kgdA02
A:186-276
1b
3kgdB02
B:186-276
1c
3kgdC02
C:186-276
1d
3kgdD02
D:186-276
Architecture
:
Alpha-beta prism
(50)
Topology
:
UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain
(50)
Homologous Superfamily
:
[code=3.65.10.20, no name defined]
(3)
K-12 substr (Escherichia coli str)
(1)
2a
3kgdA01
A:4-182,A:277-337
2b
3kgdC01
C:2-182,C:277-337
2c
3kgdD01
D:0-182,D:277-337
2d
3kgdB01
B:-13-182,B:277-337
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_RTC_3kgdD01 (D:8-329)
1b: PFAM_RTC_3kgdD02 (D:8-329)
1c: PFAM_RTC_3kgdD03 (D:8-329)
1d: PFAM_RTC_3kgdD04 (D:8-329)
2a: PFAM_RTC_insert_3kgdD05 (D:184-278)
2b: PFAM_RTC_insert_3kgdD06 (D:184-278)
2c: PFAM_RTC_insert_3kgdD07 (D:184-278)
2d: PFAM_RTC_insert_3kgdD08 (D:184-278)
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Clans
(
)
(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
EPT_RTPC
(43)
Family
:
RTC
(3)
Escherichia coli (strain K12)
(2)
1a
RTC-3kgdD01
D:8-329
1b
RTC-3kgdD02
D:8-329
1c
RTC-3kgdD03
D:8-329
1d
RTC-3kgdD04
D:8-329
Clan
:
no clan defined [family: RTC_insert]
(3)
Family
:
RTC_insert
(3)
Escherichia coli (strain K12)
(2)
2a
RTC_insert-3kgdD05
D:184-278
2b
RTC_insert-3kgdD06
D:184-278
2c
RTC_insert-3kgdD07
D:184-278
2d
RTC_insert-3kgdD08
D:184-278
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Chain D
Asymmetric Unit 1
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Asym.Unit (492 KB)
Header - Asym.Unit
Biol.Unit 1 (121 KB)
Header - Biol.Unit 1
Biol.Unit 2 (123 KB)
Header - Biol.Unit 2
Biol.Unit 3 (121 KB)
Header - Biol.Unit 3
Biol.Unit 4 (122 KB)
Header - Biol.Unit 4
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