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2R5N
Asym. Unit
Info
Asym.Unit (246 KB)
Biol.Unit 1 (239 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF TRANSKETOLASE FROM ESCHERICHIA COLI IN NONCOVALENT COMPLEX WITH ACCEPTOR ALDOSE RIBOSE 5-PHOSPHATE
Authors
:
C. Parthier, P. Asztalos, G. Wille, K Tittmann
Date
:
04 Sep 07 (Deposition) - 06 Nov 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Thiamin Catalysis, Sugar Phosphates, Acceptor, Near Attack Conformation, Cyclic, Acyclic, Ribose-5-Phospate, Pyranose, Metal- Binding, Thiamine Pyrophosphate, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Asztalos, C. Parthier, R. Golbik, M. Kleinschmidt, G. Hubner, M. S. Weiss, R. Friedemann, G. Wille, K. Tittmann
Strain And Near Attack Conformers In Enzymic Thiamin Catalysis: X-Ray Crystallographic Snapshots Of Bacterial Transketolase In Covalent Complex With Donor Ketoses Xylulose 5-Phosphate And Fructose 6-Phosphate, And In Noncovalent Complex With Acceptor Aldose Ribose 5-Phosphate
Biochemistry V. 46 12037 2007
[
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Hetero Components
(5, 23)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
3a: RIBOSE-5-PHOSPHATE (R5Pa)
4a: 5-O-PHOSPHONO-BETA-D-RIBOFURANOSE (RP5a)
4b: 5-O-PHOSPHONO-BETA-D-RIBOFURANOSE (RP5b)
5a: THIAMINE DIPHOSPHATE (TPPa)
5b: THIAMINE DIPHOSPHATE (TPPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
EDO
16
Ligand/Ion
1,2-ETHANEDIOL
3
R5P
1
Ligand/Ion
RIBOSE-5-PHOSPHATE
4
RP5
2
Ligand/Ion
5-O-PHOSPHONO-BETA-D-RIBOFURANOSE
5
TPP
2
Ligand/Ion
THIAMINE DIPHOSPHATE
[
close Hetero Component info
]
Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:358 , SER A:385 , PHE A:434 , HIS A:461 , ASP A:469 , HIS A:473 , ARG A:520 , HOH A:918 , HOH A:1371 , HOH A:1372 , HOH A:1377 , HIS B:26 , ILE B:189 , HIS B:261 , TPP B:672 , HOH B:1192 , HOH B:1196
BINDING SITE FOR RESIDUE R5P A 670
02
AC2
SOFTWARE
ASP A:155 , ASN A:185 , ILE A:187 , TPP A:672 , HOH A:706
BINDING SITE FOR RESIDUE CA A 2000
03
AC3
SOFTWARE
ASP B:155 , ASN B:185 , ILE B:187 , TPP B:672 , HOH B:1032
BINDING SITE FOR RESIDUE CA B 2000
04
AC4
SOFTWARE
ALA A:29 , HIS A:66 , GLY A:114 , LEU A:116 , ASP A:155 , GLY A:156 , GLU A:160 , ASN A:185 , ILE A:187 , ILE A:189 , ILE A:247 , HIS A:261 , HOH A:726 , HOH A:752 , HOH A:764 , HOH A:870 , CA A:2000 , ASP B:381 , GLU B:411 , PHE B:437 , TYR B:440 , HIS B:473
BINDING SITE FOR RESIDUE TPP A 672
05
AC5
SOFTWARE
GLU A:275 , ARG A:509 , ASP A:511 , LYS A:591 , HOH A:1284
BINDING SITE FOR RESIDUE EDO A 673
06
AC6
SOFTWARE
ALA A:271 , TYR A:505 , GLU A:508 , ARG A:509 , HOH A:960 , HOH A:1154
BINDING SITE FOR RESIDUE EDO A 674
07
AC7
SOFTWARE
PRO A:52 , GLY A:108 , VAL A:109 , HOH A:899
BINDING SITE FOR RESIDUE EDO A 675
08
AC8
SOFTWARE
ARG A:274 , GLU A:275 , TRP A:279 , GLN A:592 , HOH A:856 , HOH A:1283
BINDING SITE FOR RESIDUE EDO A 676
09
AC9
SOFTWARE
GLU A:6 , GLY A:278 , TRP A:279 , LYS A:280 , TYR A:281 , HOH A:861 , HOH A:1347
BINDING SITE FOR RESIDUE EDO A 677
10
BC1
SOFTWARE
LYS A:131 , THR A:172 , LYS A:174 , ASN A:397 , HOH A:987 , HOH A:1077 , HOH A:1103
BINDING SITE FOR RESIDUE EDO A 678
11
BC2
SOFTWARE
PHE A:375 , TRP A:390 , SER A:393 , ASN A:403 , TYR A:404 , TYR A:430
BINDING SITE FOR RESIDUE EDO A 679
12
BC3
SOFTWARE
SER A:559 , GLU A:560 , PHE A:645 , PHE A:650 , HOH A:828 , HOH A:1257
BINDING SITE FOR RESIDUE EDO A 680
13
BC4
SOFTWARE
ARG A:358 , SER A:385 , HIS A:461 , ASP A:469 , ARG A:520 , HOH A:1371 , HOH A:1372 , HOH A:1377 , HIS B:26 , ILE B:189 , HIS B:261 , GLY B:262 , HOH B:1196 , HOH B:1515 , HOH B:1719
BINDING SITE FOR RESIDUE RP5 B 671
14
BC5
SOFTWARE
ASP A:381 , GLU A:411 , PHE A:437 , TYR A:440 , HIS A:473 , R5P A:670 , ALA B:29 , HIS B:66 , GLY B:114 , LEU B:116 , GLY B:154 , ASP B:155 , GLY B:156 , GLU B:160 , ASN B:185 , ILE B:187 , ILE B:189 , ILE B:247 , HIS B:261 , HOH B:1066 , HOH B:1093 , HOH B:1123 , HOH B:1192 , CA B:2000
BINDING SITE FOR RESIDUE TPP B 672
15
BC6
SOFTWARE
ARG A:483 , HOH A:894 , ILE B:615 , ASP B:617 , THR B:633 , HOH B:1558
BINDING SITE FOR RESIDUE EDO B 673
16
BC7
SOFTWARE
PRO B:52 , GLY B:108 , VAL B:109 , HOH B:1102
BINDING SITE FOR RESIDUE EDO B 674
17
BC8
SOFTWARE
ILE B:345 , VAL B:501 , LEU B:533 , ALA B:534 , ILE B:536 , ALA B:537 , HOH B:1225 , HOH B:1480 , HOH B:1598
BINDING SITE FOR RESIDUE EDO B 675
18
BC9
SOFTWARE
SER A:305 , ASN A:308 , GLU A:309 , HOH A:1193 , LYS B:354 , HOH B:1486
BINDING SITE FOR RESIDUE EDO B 676
19
CC1
SOFTWARE
SER B:559 , GLU B:560 , PHE B:645 , PHE B:650 , HOH B:1124
BINDING SITE FOR RESIDUE EDO B 677
20
CC2
SOFTWARE
GLY A:392 , LYS A:394 , ARG B:4 , ARG B:42 , HOH B:1549 , HOH B:1697 , HOH B:1767
BINDING SITE FOR RESIDUE EDO B 678
21
CC3
SOFTWARE
PHE A:635 , HOH A:946 , ALA B:449 , LEU B:450 , LYS B:452 , HOH B:1726
BINDING SITE FOR RESIDUE EDO B 679
22
CC4
SOFTWARE
GLY B:186 , HIS B:192 , VAL B:193 , GLU B:194 , HOH B:1292 , HOH B:1432 , HOH B:1775
BINDING SITE FOR RESIDUE EDO B 680
23
CC5
SOFTWARE
HIS A:26 , ILE A:189 , HIS A:261 , GLY A:262 , ARG B:358 , SER B:385 , HIS B:461 , ASP B:469 , ARG B:520 , HOH B:1174 , HOH B:1383 , HOH B:1571 , HOH B:1647 , HOH B:1782
BINDING SITE FOR RESIDUE RP5 B 681
[
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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, 4)
Info
All PROSITE Patterns/Profiles
1: TRANSKETOLASE_1 (A:12-32,B:12-32)
2: TRANSKETOLASE_2 (A:467-483,B:467-483)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRANSKETOLASE_1
PS00801
Transketolase signature 1.
TKT1_ECOLI
12-32
2
A:12-32
B:12-32
2
TRANSKETOLASE_2
PS00802
Transketolase signature 2.
TKT1_ECOLI
467-483
2
A:467-483
B:467-483
[
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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2r5na1 (A:333-527)
1b: SCOP_d2r5nb1 (B:333-527)
2a: SCOP_d2r5na2 (A:2-332)
2b: SCOP_d2r5nb2 (B:2-332)
3a: SCOP_d2r5na3 (A:528-667)
3b: SCOP_d2r5nb3 (B:528-664)
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Classes
(
)
(
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Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
automated matches
(65)
Protein domain
:
automated matches
(65)
Escherichia coli [TaxId: 562]
(3)
1a
d2r5na1
A:333-527
1b
d2r5nb1
B:333-527
Family
:
TK-like PP module
(24)
Protein domain
:
Transketolase (TK), PP module
(13)
Escherichia coli [TaxId: 562]
(4)
2a
d2r5na2
A:2-332
2b
d2r5nb2
B:2-332
Fold
:
TK C-terminal domain-like
(79)
Superfamily
:
TK C-terminal domain-like
(79)
Family
:
Transketolase C-terminal domain-like
(21)
Protein domain
:
Transketolase (TK), C-domain
(13)
Escherichia coli [TaxId: 562]
(4)
3a
d2r5na3
A:528-667
3b
d2r5nb3
B:528-664
[
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]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_2r5nA03 (A:538-667)
1b: CATH_2r5nB03 (B:538-664)
2a: CATH_2r5nA02 (A:327-537)
2b: CATH_2r5nB02 (B:327-537)
2c: CATH_2r5nA01 (A:2-326)
2d: CATH_2r5nB01 (B:2-326)
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.920, no name defined]
(73)
Escherichia coli. Organism_taxid: 562.
(2)
1a
2r5nA03
A:538-667
1b
2r5nB03
B:538-664
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Escherichia coli. Organism_taxid: 562.
(2)
2a
2r5nA02
A:327-537
2b
2r5nB02
B:327-537
2c
2r5nA01
A:2-326
2d
2r5nB01
B:2-326
[
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]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Transket_pyr_2r5nB01 (B:353-526)
1b: PFAM_Transket_pyr_2r5nB02 (B:353-526)
2a: PFAM_Transketolase_N_2r5nB03 (B:3-334)
2b: PFAM_Transketolase_N_2r5nB04 (B:3-334)
3a: PFAM_Transketolase_C_2r5nB05 (B:540-655)
3b: PFAM_Transketolase_C_2r5nB06 (B:540-655)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
THDP-binding
(106)
Family
:
Transket_pyr
(45)
Escherichia coli (strain K12)
(5)
1a
Transket_pyr-2r5nB01
B:353-526
1b
Transket_pyr-2r5nB02
B:353-526
Family
:
Transketolase_N
(22)
Escherichia coli (strain K12)
(6)
2a
Transketolase_N-2r5nB03
B:3-334
2b
Transketolase_N-2r5nB04
B:3-334
Clan
:
no clan defined [family: Transketolase_C]
(40)
Family
:
Transketolase_C
(40)
Escherichia coli (strain K12)
(4)
3a
Transketolase_C-2r5nB05
B:540-655
3b
Transketolase_C-2r5nB06
B:540-655
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