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2JLA
Asym. Unit
Info
Asym.Unit (363 KB)
Biol.Unit 1 (180 KB)
Biol.Unit 2 (181 KB)
Biol.Unit 3 (353 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF E.COLI MEND, 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXADIENE-1-CARBOXYLATE SYNTHASE - SEMET PROTEIN
Authors
:
A. Dawson, P. K. Fyfe, W. N. Hunter
Date
:
05 Sep 08 (Deposition) - 21 Oct 08 (Release) - 14 Apr 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.81
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Manganese, Transferase, Thiamine Diphosphate Cofactor, Thiamine Pyrophosphate, Menaquinone Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Dawson, P. K. Fyfe, W. N. Hunter
Specificity And Reactivity In Menaquinone Biosynthesis: The Structure Of Escherichia Coli Mend (2-Succinyl-5-Enolpyruvyl-6-Hydroxy-3- Cyclohexadiene-1-Carboxylate Synthase).
J. Mol. Biol. V. 384 1353 2008
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Hetero Components
(4, 54)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
1j: CHLORIDE ION (CLj)
1k: CHLORIDE ION (CLk)
1l: CHLORIDE ION (CLl)
1m: CHLORIDE ION (CLm)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
2e: MANGANESE (II) ION (MNe)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
3ab: SELENOMETHIONINE (MSEab)
3ac: SELENOMETHIONINE (MSEac)
3ad: SELENOMETHIONINE (MSEad)
3ae: SELENOMETHIONINE (MSEae)
3af: SELENOMETHIONINE (MSEaf)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
3y: SELENOMETHIONINE (MSEy)
3z: SELENOMETHIONINE (MSEz)
4a: THIAMINE DIPHOSPHATE (TPPa)
4b: THIAMINE DIPHOSPHATE (TPPb)
4c: THIAMINE DIPHOSPHATE (TPPc)
4d: THIAMINE DIPHOSPHATE (TPPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
13
Ligand/Ion
CHLORIDE ION
2
MN
5
Ligand/Ion
MANGANESE (II) ION
3
MSE
32
Mod. Amino Acid
SELENOMETHIONINE
4
TPP
4
Ligand/Ion
THIAMINE DIPHOSPHATE
[
close Hetero Component info
]
Sites
(22, 22)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:391 , LEU A:392 , SER A:416 , GLY A:417 , ILE A:418 , ASP A:419 , GLY A:441 , ASP A:442 , LEU A:443 , SER A:444 , ASN A:469 , GLY A:471 , GLY A:472 , GLN A:473 , ILE A:474 , MN A:1558 , HOH A:2096 , HOH A:2097 , HOH A:2098 , PRO B:30 , GLU B:55 , THR B:81 , ALA B:82
BINDING SITE FOR RESIDUE TPP A 1557
02
AC2
SOFTWARE
ASP A:442 , ASN A:469 , GLY A:471 , TPP A:1557 , HOH A:2098
BINDING SITE FOR RESIDUE MN A 1558
03
AC3
SOFTWARE
PRO A:30 , GLU A:55 , THR A:81 , ALA A:82 , SER B:391 , LEU B:392 , SER B:416 , GLY B:417 , ILE B:418 , ASP B:419 , GLY B:441 , ASP B:442 , LEU B:443 , SER B:444 , TYR B:447 , ASN B:469 , GLY B:471 , GLY B:472 , GLN B:473 , ILE B:474 , MN B:1558 , HOH B:2099
BINDING SITE FOR RESIDUE TPP B 1557
04
AC4
SOFTWARE
ASP B:442 , ASN B:469 , GLY B:471 , TPP B:1557 , HOH B:2099
BINDING SITE FOR RESIDUE MN B 1558
05
AC5
SOFTWARE
SER C:391 , LEU C:392 , SER C:416 , GLY C:417 , ILE C:418 , ASP C:419 , GLY C:441 , ASP C:442 , LEU C:443 , SER C:444 , ASN C:469 , GLY C:471 , GLY C:472 , GLN C:473 , ILE C:474 , MN C:1558 , HOH C:2084 , HOH C:2085 , HOH C:2086 , PRO D:30 , GLU D:55 , THR D:81 , ALA D:82
BINDING SITE FOR RESIDUE TPP C 1557
06
AC6
SOFTWARE
ASP C:442 , ASN C:469 , GLY C:471 , TPP C:1557 , HOH C:2086
BINDING SITE FOR RESIDUE MN C 1558
07
AC7
SOFTWARE
PRO C:30 , GLU C:55 , THR C:81 , ALA C:82 , SER D:391 , LEU D:392 , SER D:416 , GLY D:417 , ILE D:418 , ASP D:419 , GLY D:441 , ASP D:442 , LEU D:443 , SER D:444 , TYR D:447 , ASN D:469 , GLY D:471 , GLY D:472 , GLN D:473 , ILE D:474 , MN D:1558 , HOH D:2111
BINDING SITE FOR RESIDUE TPP D 1557
08
AC8
SOFTWARE
ASP D:442 , ASN D:469 , GLY D:471 , TPP D:1557 , HOH D:2111
BINDING SITE FOR RESIDUE MN D 1558
09
AC9
SOFTWARE
SER A:32 , ARG A:33 , THR A:78 , GLN A:118
BINDING SITE FOR RESIDUE CL A 1559
10
BC1
SOFTWARE
SER B:32 , ARG B:33 , THR B:78 , GLN B:118
BINDING SITE FOR RESIDUE CL B 1559
11
BC2
SOFTWARE
GLY C:31 , SER C:32 , THR C:78 , GLN C:118
BINDING SITE FOR RESIDUE CL C 1559
12
BC3
SOFTWARE
SER D:32 , THR D:78
BINDING SITE FOR RESIDUE CL D 1559
13
BC4
SOFTWARE
PRO A:137 , ARG A:138 , ARG C:138
BINDING SITE FOR RESIDUE CL C 1560
14
BC5
SOFTWARE
ARG B:138 , ARG D:138 , HOH D:2028
BINDING SITE FOR RESIDUE CL B 1560
15
BC6
SOFTWARE
ASN A:390 , SER A:391 , ARG A:395 , ARG A:413
BINDING SITE FOR RESIDUE CL A 1560
16
BC7
SOFTWARE
ASN B:390 , SER B:391 , ARG B:395 , ARG B:413
BINDING SITE FOR RESIDUE CL B 1561
17
BC8
SOFTWARE
SER C:391 , ARG C:395 , ARG C:413
BINDING SITE FOR RESIDUE CL C 1561
18
BC9
SOFTWARE
SER D:391 , ARG D:395 , ARG D:413
BINDING SITE FOR RESIDUE CL D 1560
19
CC1
SOFTWARE
HIS C:509 , ASP C:523 , HOH C:2087
BINDING SITE FOR RESIDUE MN C 1562
20
CC2
SOFTWARE
GLU A:505 , HIS D:496
BINDING SITE FOR RESIDUE CL A 1561
21
CC3
SOFTWARE
LEU B:506 , LYS B:507 , THR B:530 , HOH B:2095
BINDING SITE FOR RESIDUE CL B 1562
22
CC4
SOFTWARE
THR B:243 , THR D:243
BINDING SITE FOR RESIDUE CL D 1561
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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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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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:
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_TPP_enzyme_C_2jlaD01 (D:396-535)
1b: PFAM_TPP_enzyme_C_2jlaD02 (D:396-535)
1c: PFAM_TPP_enzyme_C_2jlaD03 (D:396-535)
1d: PFAM_TPP_enzyme_C_2jlaD04 (D:396-535)
2a: PFAM_TPP_enzyme_N_2jlaD05 (D:8-172)
2b: PFAM_TPP_enzyme_N_2jlaD06 (D:8-172)
2c: PFAM_TPP_enzyme_N_2jlaD07 (D:8-172)
2d: PFAM_TPP_enzyme_N_2jlaD08 (D:8-172)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
THDP-binding
(106)
Family
:
TPP_enzyme_C
(54)
Escherichia coli (strain K12)
(6)
1a
TPP_enzyme_C-2jlaD01
D:396-535
1b
TPP_enzyme_C-2jlaD02
D:396-535
1c
TPP_enzyme_C-2jlaD03
D:396-535
1d
TPP_enzyme_C-2jlaD04
D:396-535
Family
:
TPP_enzyme_N
(54)
Escherichia coli (strain K12)
(6)
2a
TPP_enzyme_N-2jlaD05
D:8-172
2b
TPP_enzyme_N-2jlaD06
D:8-172
2c
TPP_enzyme_N-2jlaD07
D:8-172
2d
TPP_enzyme_N-2jlaD08
D:8-172
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