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3KGD
Asym. Unit
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)
]
)
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
[
close entry info
]
Hetero Components
(4, 27)
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:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AMP
4
Ligand/Ion
ADENOSINE MONOPHOSPHATE
2
GOL
10
Ligand/Ion
GLYCEROL
3
NA
5
Ligand/Ion
SODIUM ION
4
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(27, 27)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:18 , ARG A:21 , GLN A:104 , SER A:129 , ALA A:130 , PRO A:131 , PHE A:251 , TYR A:284 , ASP A:287 , GLN A:288 , HIS A:309 , HOH A:367 , HOH A:374 , HOH A:386 , HOH A:397 , HOH A:439 , HOH A:710 , HOH A:1423 , HOH A:1432
BINDING SITE FOR RESIDUE AMP A 501
02
AC2
SOFTWARE
GLY A:16 , GLY A:17 , ARG A:21 , GLN A:51 , ALA A:55 , ILE A:93 , VAL A:102 , HOH A:457 , HOH A:677
BINDING SITE FOR RESIDUE GOL A 340
03
AC3
SOFTWARE
ASP A:88 , PRO A:116 , SER A:117 , GLU A:171 , HOH A:396 , ARG C:4
BINDING SITE FOR RESIDUE GOL A 341
04
AC4
SOFTWARE
GLY A:17 , SO4 A:344 , HOH A:471
BINDING SITE FOR RESIDUE NA A 342
05
AC5
SOFTWARE
GLU A:14 , ARG A:43 , HOH A:429 , HOH A:471 , HOH A:542 , HOH A:918
BINDING SITE FOR RESIDUE SO4 A 343
06
AC6
SOFTWARE
GLN A:51 , HIS A:52 , NA A:342 , HOH A:399 , HOH A:429 , HOH A:677 , HOH A:832
BINDING SITE FOR RESIDUE SO4 A 344
07
AC7
SOFTWARE
SER A:218 , HIS A:220 , HOH A:972 , HOH A:1412 , PRO B:228 , ARG B:229 , HOH B:1074
BINDING SITE FOR RESIDUE SO4 A 345
08
AC8
SOFTWARE
GLN B:18 , ARG B:21 , GLN B:104 , SER B:129 , ALA B:130 , PRO B:131 , PHE B:251 , TYR B:284 , ASP B:287 , GLN B:288 , HIS B:309 , HOH B:367 , HOH B:409 , HOH B:422 , HOH B:446 , HOH B:949 , HOH B:1327
BINDING SITE FOR RESIDUE AMP B 501
09
AC9
SOFTWARE
PHE B:112 , LEU B:295 , HOH B:1311 , HOH B:1438 , HOH B:1491
BINDING SITE FOR RESIDUE GOL B 340
10
BC1
SOFTWARE
HIS B:-12 , ARG B:85 , HOH B:1266
BINDING SITE FOR RESIDUE GOL B 341
11
BC2
SOFTWARE
ARG B:40 , SO4 B:343 , HOH B:473
BINDING SITE FOR RESIDUE NA B 342
12
BC3
SOFTWARE
GLU B:14 , ARG B:40 , ARG B:43 , NA B:342 , HOH B:475 , HOH B:835 , HOH B:871 , HOH B:1256
BINDING SITE FOR RESIDUE SO4 B 343
13
BC4
SOFTWARE
ARG B:208 , SER B:259 , ALA B:260 , HOH B:1140
BINDING SITE FOR RESIDUE SO4 B 344
14
BC5
SOFTWARE
GLN C:18 , ARG C:21 , GLN C:104 , SER C:129 , ALA C:130 , PRO C:131 , PHE C:251 , TYR C:284 , ASP C:287 , GLN C:288 , HIS C:309 , HOH C:384 , HOH C:394 , HOH C:401 , HOH C:402 , HOH C:481 , HOH C:621 , HOH C:920 , HOH C:1428
BINDING SITE FOR RESIDUE AMP C 501
15
BC6
SOFTWARE
ASP A:114 , GLU C:318 , ARG C:324 , PHE C:325 , GLY D:200
BINDING SITE FOR RESIDUE GOL C 340
16
BC7
SOFTWARE
HOH B:990 , MET C:5 , LEU C:78 , ARG C:80 , HOH C:1273
BINDING SITE FOR RESIDUE GOL C 341
17
BC8
SOFTWARE
GLY C:16 , ARG C:21 , GLN C:51 , HIS C:52 , ALA C:55 , ILE C:93 , LEU C:101 , VAL C:102 , SO4 C:346 , HOH C:784 , HOH C:1171 , HOH C:1507
BINDING SITE FOR RESIDUE GOL C 342
18
BC9
SOFTWARE
LEU C:275 , ALA C:276 , SER C:277 , HOH C:442
BINDING SITE FOR RESIDUE NA C 343
19
CC1
SOFTWARE
ARG C:40 , SO4 C:345 , HOH C:367 , HOH C:1026
BINDING SITE FOR RESIDUE NA C 344
20
CC2
SOFTWARE
GLU C:14 , ARG C:40 , ARG C:43 , NA C:344 , HOH C:370 , HOH C:715 , HOH C:1178 , HOH C:1211
BINDING SITE FOR RESIDUE SO4 C 345
21
CC3
SOFTWARE
GLN C:51 , HIS C:52 , GOL C:342 , HOH C:819 , HOH C:1178 , HOH C:1268 , HOH C:1405 , HOH C:1507
BINDING SITE FOR RESIDUE SO4 C 346
22
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
23
CC5
SOFTWARE
LYS D:3 , ARG D:4 , MET D:5
BINDING SITE FOR RESIDUE GOL D 340
24
CC6
SOFTWARE
HIS D:204 , VAL D:205 , ARG D:208 , GLU D:261
BINDING SITE FOR RESIDUE GOL D 341
25
CC7
SOFTWARE
GLY D:64 , ALA D:65 , THR D:66 , ARG D:80 , PRO D:81
BINDING SITE FOR RESIDUE GOL D 342
26
CC8
SOFTWARE
ARG D:40 , SO4 D:344 , HOH D:1378
BINDING SITE FOR RESIDUE NA D 343
27
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
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: RTC (A:158-168,B:158-168,C:158-168,D:15...)
;
View:
Select:
Label:
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
4
A:158-168
B:158-168
C:158-168
D:158-168
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
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)
View:
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(
)
(
)
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)
(
)
Topologies
(
)
(
)
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
[
close CATH info
]
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)
View:
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Clans
(
)
(
)
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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