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Asym. Unit
Info
Asym.Unit (186 KB)
Biol.Unit 1 (178 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MENAQUINONE SYNTHESIS PROTEIN MEND FROM E. COLI IN COMPLEX WITH OXOGLUTARATE
Authors
:
A. Priyadarshi, K. Y. Hwang
Date
:
19 Jun 09 (Deposition) - 03 Nov 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,D
Biol. Unit 1: A,D (1x)
Keywords
:
Menaquinone, Thdp, Mg, Vitamin K2, Carboxylase, Magnesium, Manganese, Menaquinone Biosynthesis, Metal-Binding, Thiamine Pyrophosphate, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Priyadarshi, E. E. Kim, K. Y. Hwang
Structural And Functional Analysis Of Vitamin K2 Synthesis Protein Mend.
Biochem. Biophys. Res. Commun. V. 388 748 2009
[
close entry info
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Hetero Components
(5, 49)
Info
All Hetero Components
1a: 2-OXOGLUTARIC ACID (AKGa)
1b: 2-OXOGLUTARIC ACID (AKGb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: SODIUM ION (NAa)
5aa: SODIUM ION (NAaa)
5ab: SODIUM ION (NAab)
5ac: SODIUM ION (NAac)
5ad: SODIUM ION (NAad)
5ae: SODIUM ION (NAae)
5af: SODIUM ION (NAaf)
5ag: SODIUM ION (NAag)
5ah: SODIUM ION (NAah)
5ai: SODIUM ION (NAai)
5aj: SODIUM ION (NAaj)
5ak: SODIUM ION (NAak)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
5d: SODIUM ION (NAd)
5e: SODIUM ION (NAe)
5f: SODIUM ION (NAf)
5g: SODIUM ION (NAg)
5h: SODIUM ION (NAh)
5i: SODIUM ION (NAi)
5j: SODIUM ION (NAj)
5k: SODIUM ION (NAk)
5l: SODIUM ION (NAl)
5m: SODIUM ION (NAm)
5n: SODIUM ION (NAn)
5o: SODIUM ION (NAo)
5p: SODIUM ION (NAp)
5q: SODIUM ION (NAq)
5r: SODIUM ION (NAr)
5s: SODIUM ION (NAs)
5t: SODIUM ION (NAt)
5u: SODIUM ION (NAu)
5v: SODIUM ION (NAv)
5w: SODIUM ION (NAw)
5x: SODIUM ION (NAx)
5y: SODIUM ION (NAy)
5z: SODIUM ION (NAz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AKG
2
Ligand/Ion
2-OXOGLUTARIC ACID
2
CL
2
Ligand/Ion
CHLORIDE ION
3
GOL
6
Ligand/Ion
GLYCEROL
4
MG
2
Ligand/Ion
MAGNESIUM ION
5
NA
37
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(49, 49)
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)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:391 , LEU A:392 , GLY A:441 , ASP A:442 , LEU A:443 , SER A:444 , GLY A:471 , MG A:558 , NA A:576 , HOH A:660 , HOH A:738
BINDING SITE FOR RESIDUE AKG A 557
02
AC2
SOFTWARE
ASP A:442 , VAL A:467 , ASN A:469 , GLY A:471 , AKG A:557 , HOH A:738
BINDING SITE FOR RESIDUE MG A 558
03
AC3
SOFTWARE
HIS A:21 , ASP A:153 , GLY A:157 , LEU A:200 , ARG A:201 , GLU A:202
BINDING SITE FOR RESIDUE NA A 559
04
AC4
SOFTWARE
THR A:19 , VAL A:23
BINDING SITE FOR RESIDUE NA A 560
05
AC5
SOFTWARE
ASP A:54 , ARG A:56 , TYR A:447 , ASP A:448 , ASN A:450 , NA A:562
BINDING SITE FOR RESIDUE NA A 561
06
AC6
SOFTWARE
TYR A:447 , ASP A:448 , LEU A:449 , ASN A:450 , NA A:561 , ASN D:450 , HOH D:705
BINDING SITE FOR RESIDUE NA A 562
07
AC7
SOFTWARE
ALA A:66 , GLN A:71 , LYS A:99
BINDING SITE FOR RESIDUE CL A 563
08
AC8
SOFTWARE
SER A:79 , GLY A:80 , THR A:81 , ALA A:82 , HOH D:706
BINDING SITE FOR RESIDUE NA A 564
09
AC9
SOFTWARE
SER A:135 , LEU A:136 , ASN A:167 , PRO A:169
BINDING SITE FOR RESIDUE NA A 565
10
BC1
SOFTWARE
HIS A:132 , SER A:133 , HOH A:739
BINDING SITE FOR RESIDUE NA A 566
11
BC2
SOFTWARE
ASP A:179 , ASP A:180
BINDING SITE FOR RESIDUE NA A 567
12
BC3
SOFTWARE
ARG A:146 , ARG A:188 , GOL A:579
BINDING SITE FOR RESIDUE NA A 568
13
BC4
SOFTWARE
ARG A:212
BINDING SITE FOR RESIDUE NA A 569
14
BC5
SOFTWARE
ALA A:203 , SER A:208 , GLU A:209
BINDING SITE FOR RESIDUE NA A 570
15
BC6
SOFTWARE
ALA A:203 , SER A:208 , ARG A:325 , LEU A:326
BINDING SITE FOR RESIDUE NA A 571
16
BC7
SOFTWARE
VAL A:252 , GLN A:255 , NA A:573 , HOH A:743
BINDING SITE FOR RESIDUE NA A 572
17
BC8
SOFTWARE
GLN A:255 , LEU A:403 , PRO A:404 , TYR A:407 , NA A:572
BINDING SITE FOR RESIDUE NA A 573
18
BC9
SOFTWARE
ASP A:264 , GLY A:291 , ARG A:395 , ASP A:398 , ALA A:399
BINDING SITE FOR RESIDUE NA A 574
19
CC1
SOFTWARE
ARG A:315 , LEU A:316 , ASP A:317 , ARG A:325 , HOH A:732 , HOH A:755
BINDING SITE FOR RESIDUE NA A 575
20
CC2
SOFTWARE
ASN A:390 , SER A:391 , LEU A:421 , GLY A:441 , SER A:444 , AKG A:557
BINDING SITE FOR RESIDUE NA A 576
21
CC3
SOFTWARE
SER A:416 , GLY A:417 , ILE A:418 , GLU D:55 , ALA D:82 , GLN D:118 , HOH D:679
BINDING SITE FOR RESIDUE GOL A 577
22
CC4
SOFTWARE
SER A:274
BINDING SITE FOR RESIDUE NA A 578
23
CC5
SOFTWARE
GLN A:141 , ASP A:142 , ILE A:143 , PRO A:144 , ALA A:145 , TRP A:185 , ARG A:188 , NA A:568 , HOH A:706
BINDING SITE FOR RESIDUE GOL A 579
24
CC6
SOFTWARE
LYS A:507 , TYR A:508
BINDING SITE FOR RESIDUE GOL A 580
25
CC7
SOFTWARE
GLU D:369 , SER D:391 , LEU D:392 , VAL D:393 , GLY D:441 , ASP D:442 , LEU D:443 , VAL D:467 , ASN D:469 , MG D:558
BINDING SITE FOR RESIDUE AKG D 557
26
CC8
SOFTWARE
ASP D:442 , VAL D:467 , ASN D:469 , AKG D:557
BINDING SITE FOR RESIDUE MG D 558
27
CC9
SOFTWARE
TRP D:10 , LEU D:136 , PRO D:137 , PRO D:169
BINDING SITE FOR RESIDUE NA D 559
28
DC1
SOFTWARE
ALA D:17 , ARG D:20 , VAL D:149 , ASP D:153 , TRP D:192 , PRO D:198 , TRP D:199
BINDING SITE FOR RESIDUE NA D 560
29
DC2
SOFTWARE
ALA D:66 , GLN D:71 , LYS D:99
BINDING SITE FOR RESIDUE NA D 561
30
DC3
SOFTWARE
ALA D:29 , GLU D:55 , VAL D:77 , THR D:78
BINDING SITE FOR RESIDUE NA D 562
31
DC4
SOFTWARE
ARG D:228 , SER D:411 , ARG D:413
BINDING SITE FOR RESIDUE NA D 563
32
DC5
SOFTWARE
LYS D:67 , TYR D:410 , SER D:411 , HOH D:711
BINDING SITE FOR RESIDUE NA D 564
33
DC6
SOFTWARE
GLY D:124 , MET D:125 , PHE D:126 , HIS D:165 , HOH D:714
BINDING SITE FOR RESIDUE NA D 565
34
DC7
SOFTWARE
ARG A:138 , ARG D:138 , CL D:568 , HOH D:715
BINDING SITE FOR RESIDUE NA D 566
35
DC8
SOFTWARE
THR A:140 , CL D:568 , HOH D:700 , HOH D:715 , HOH D:716
BINDING SITE FOR RESIDUE NA D 567
36
DC9
SOFTWARE
PRO A:137 , ARG A:138 , ARG D:138 , NA D:566 , NA D:567
BINDING SITE FOR RESIDUE CL D 568
37
EC1
SOFTWARE
HIS D:132 , SER D:133 , HIS D:154
BINDING SITE FOR RESIDUE GOL D 569
38
EC2
SOFTWARE
SER D:150 , HIS D:320 , HIS D:321 , HOH D:729
BINDING SITE FOR RESIDUE NA D 570
39
EC3
SOFTWARE
GLN D:186 , TRP D:193
BINDING SITE FOR RESIDUE GOL D 571
40
EC4
SOFTWARE
ILE D:308 , ARG D:324 , NA D:575 , HOH D:619
BINDING SITE FOR RESIDUE NA D 572
41
EC5
SOFTWARE
THR D:96 , GLU D:98
BINDING SITE FOR RESIDUE NA D 573
42
EC6
SOFTWARE
ARG A:138 , HOH A:719
BINDING SITE FOR RESIDUE NA D 574
43
EC7
SOFTWARE
ARG D:315 , LEU D:316 , ASP D:317 , ARG D:325 , NA D:572 , HOH D:729
BINDING SITE FOR RESIDUE NA D 575
44
EC8
SOFTWARE
LEU D:248 , GLY D:250 , GLN D:258 , PRO D:259 , LEU D:260 , NA D:577
BINDING SITE FOR RESIDUE NA D 576
45
EC9
SOFTWARE
GLY D:250 , LEU D:260 , NA D:576 , HOH D:674
BINDING SITE FOR RESIDUE NA D 577
46
FC1
SOFTWARE
ASP D:264 , LYS D:292
BINDING SITE FOR RESIDUE NA D 578
47
FC2
SOFTWARE
LYS D:292 , LEU D:295
BINDING SITE FOR RESIDUE NA D 579
48
FC3
SOFTWARE
GLY D:389 , ASN D:390 , SER D:391 , LEU D:421 , GLY D:441 , SER D:444
BINDING SITE FOR RESIDUE NA D 580
49
FC4
SOFTWARE
ASN D:494 , HIS D:496 , ARG D:510
BINDING SITE FOR RESIDUE GOL D 581
[
close Site info
]
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
;
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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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
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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