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2X7J
Asym. Unit
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Asym.Unit (395 KB)
Biol.Unit 1 (386 KB)
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(1)
Title
:
STRUCTURE OF THE MENAQUINONE BIOSYNTHESIS PROTEIN MEND FROM BACILLUS SUBTILIS
Authors
:
A. Dawson, M. Chen, P. K. Fyfe, Z. Guo, W. N. Hunter
Date
:
01 Mar 10 (Deposition) - 14 Jul 10 (Release) - 04 Aug 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Transferase, Metal-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Dawson, M. Chen, P. K. Fyfe, Z. Guo, W. N. Hunter
Structure And Reactivity Of Bacillus Subtilis Mend Catalyzing The First Committed Step In Menaquinone Biosynthesis.
J. Mol. Biol. V. 401 253 2010
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close entry info
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Hetero Components
(5, 24)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
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)
5a: THIAMINE DIPHOSPHATE (TPPa)
5b: THIAMINE DIPHOSPHATE (TPPb)
5c: THIAMINE DIPHOSPHATE (TPPc)
5d: THIAMINE DIPHOSPHATE (TPPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
4
Ligand/Ion
1,2-ETHANEDIOL
2
MN
4
Ligand/Ion
MANGANESE (II) ION
3
NA
4
Ligand/Ion
SODIUM ION
4
SO4
8
Ligand/Ion
SULFATE ION
5
TPP
4
Ligand/Ion
THIAMINE DIPHOSPHATE
[
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]
Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:405 , MET A:406 , ASN A:431 , ILE A:433 , ASP A:434 , GLY A:456 , ASP A:457 , LEU A:458 , SER A:459 , ASN A:484 , GLY A:486 , GLY A:487 , GLY A:488 , ILE A:489 , PHE A:490 , MN A:602 , HOH A:2200 , HOH A:2213 , HOH A:2237 , HOH A:2282 , GLU B:54 , GLN B:117 , EDO B:603
BINDING SITE FOR RESIDUE TPP A 601
02
AC2
SOFTWARE
ASP A:457 , ASN A:484 , GLY A:486 , TPP A:601 , HOH A:2237
BINDING SITE FOR RESIDUE MN A 602
03
AC3
SOFTWARE
GLY A:30 , SER A:31 , ARG A:32 , THR A:77 , ARG A:106 , GLN A:117 , PHE B:490 , TPP B:601
BINDING SITE FOR RESIDUE EDO A 603
04
AC4
SOFTWARE
GLU A:54 , GLN A:117 , EDO A:603 , SER B:405 , MET B:406 , ASN B:431 , ILE B:433 , ASP B:434 , GLY B:456 , ASP B:457 , LEU B:458 , SER B:459 , ASN B:484 , GLY B:486 , GLY B:487 , GLY B:488 , ILE B:489 , MN B:602 , HOH B:2155 , HOH B:2238 , HOH B:2239
BINDING SITE FOR RESIDUE TPP B 601
05
AC5
SOFTWARE
ASP B:457 , ASN B:484 , GLY B:486 , TPP B:601 , HOH B:2239
BINDING SITE FOR RESIDUE MN B 602
06
AC6
SOFTWARE
PHE A:490 , TPP A:601 , GLY B:30 , SER B:31 , ARG B:32 , THR B:77 , GLN B:117
BINDING SITE FOR RESIDUE EDO B 603
07
AC7
SOFTWARE
SER C:405 , MET C:406 , PRO C:407 , ASN C:431 , GLY C:432 , ILE C:433 , ASP C:434 , GLY C:456 , ASP C:457 , LEU C:458 , SER C:459 , ASN C:484 , GLY C:486 , GLY C:487 , GLY C:488 , ILE C:489 , PHE C:490 , MN C:602 , HOH C:2251 , HOH C:2252 , HOH C:2253 , PRO D:29 , GLU D:54 , THR D:80 , GLN D:117 , EDO D:603
BINDING SITE FOR RESIDUE TPP C 601
08
AC8
SOFTWARE
ASP C:457 , ASN C:484 , GLY C:486 , TPP C:601 , HOH C:2253
BINDING SITE FOR RESIDUE MN C 602
09
AC9
SOFTWARE
GLY C:30 , SER C:31 , ARG C:32 , THR C:77 , GLN C:117 , PHE D:490 , TPP D:601
BINDING SITE FOR RESIDUE EDO C 603
10
BC1
SOFTWARE
PRO C:29 , GLU C:54 , THR C:80 , GLN C:117 , EDO C:603 , SER D:405 , MET D:406 , ASN D:431 , ILE D:433 , ASP D:434 , GLY D:456 , ASP D:457 , LEU D:458 , SER D:459 , ASN D:484 , GLY D:486 , GLY D:487 , GLY D:488 , ILE D:489 , PHE D:490 , MN D:602 , HOH D:2206 , HOH D:2290 , HOH D:2291 , HOH D:2292
BINDING SITE FOR RESIDUE TPP D 601
11
BC2
SOFTWARE
ASP D:457 , ASN D:484 , GLY D:486 , TPP D:601 , HOH D:2292
BINDING SITE FOR RESIDUE MN D 602
12
BC3
SOFTWARE
PHE C:490 , TPP C:601 , GLY D:30 , SER D:31 , ARG D:32 , THR D:77 , GLN D:117
BINDING SITE FOR RESIDUE EDO D 603
13
BC4
SOFTWARE
CYS D:40 , ALA D:41 , HIS D:43 , ILE D:46
BINDING SITE FOR RESIDUE NA D1581
14
BC5
SOFTWARE
CYS A:40 , ALA A:41 , HIS A:43 , ILE A:46
BINDING SITE FOR RESIDUE NA A1581
15
BC6
SOFTWARE
CYS B:40 , ALA B:41 , HIS B:43 , ILE B:46 , HOH B:2022 , HOH B:2024
BINDING SITE FOR RESIDUE NA B1581
16
BC7
SOFTWARE
CYS C:40 , ALA C:41 , HIS C:43 , ILE C:46 , HOH C:2015
BINDING SITE FOR RESIDUE NA C1579
17
BC8
SOFTWARE
ARG A:32 , PRO A:107 , LEU A:110 , LEU A:173 , ARG A:174 , GLU A:175 , HOH A:2283
BINDING SITE FOR RESIDUE SO4 A1582
18
BC9
SOFTWARE
ARG B:32 , PRO B:107 , LEU B:110 , LEU B:173 , ARG B:174 , GLU B:175
BINDING SITE FOR RESIDUE SO4 B1582
19
CC1
SOFTWARE
ARG D:32 , PRO D:107 , LEU D:110 , ARG D:174 , GLU D:175 , HOH D:2041 , HOH D:2293
BINDING SITE FOR RESIDUE SO4 D1582
20
CC2
SOFTWARE
ARG C:32 , PRO C:107 , GLU C:109 , LEU C:110 , LEU C:173 , ARG C:174 , GLU C:175 , HOH C:2254 , HOH C:2255
BINDING SITE FOR RESIDUE SO4 C1580
21
CC3
SOFTWARE
LYS A:276 , ARG A:564 , HOH A:2284 , HOH A:2285
BINDING SITE FOR RESIDUE SO4 A1583
22
CC4
SOFTWARE
LYS B:276 , ARG B:564 , HOH B:2121
BINDING SITE FOR RESIDUE SO4 B1583
23
CC5
SOFTWARE
LYS C:276 , PHE C:492 , ARG C:564 , HOH C:2256
BINDING SITE FOR RESIDUE SO4 C1581
24
CC6
SOFTWARE
LYS D:276 , PHE D:492 , ARG D:564
BINDING SITE FOR RESIDUE SO4 D1583
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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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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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
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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_2x7jD01 (D:409-552)
1b: PFAM_TPP_enzyme_C_2x7jD02 (D:409-552)
1c: PFAM_TPP_enzyme_C_2x7jD03 (D:409-552)
1d: PFAM_TPP_enzyme_C_2x7jD04 (D:409-552)
2a: PFAM_TPP_enzyme_N_2x7jD05 (D:12-180)
2b: PFAM_TPP_enzyme_N_2x7jD06 (D:12-180)
2c: PFAM_TPP_enzyme_N_2x7jD07 (D:12-180)
2d: PFAM_TPP_enzyme_N_2x7jD08 (D:12-180)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
THDP-binding
(106)
Family
:
TPP_enzyme_C
(54)
Bacillus subtilis
(1)
1a
TPP_enzyme_C-2x7jD01
D:409-552
1b
TPP_enzyme_C-2x7jD02
D:409-552
1c
TPP_enzyme_C-2x7jD03
D:409-552
1d
TPP_enzyme_C-2x7jD04
D:409-552
Family
:
TPP_enzyme_N
(54)
Bacillus subtilis
(1)
2a
TPP_enzyme_N-2x7jD05
D:12-180
2b
TPP_enzyme_N-2x7jD06
D:12-180
2c
TPP_enzyme_N-2x7jD07
D:12-180
2d
TPP_enzyme_N-2x7jD08
D:12-180
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