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5EJ4
Asym. Unit
Info
Asym.Unit (1.5 MB)
Biol.Unit 1 (379 KB)
Biol.Unit 2 (379 KB)
Biol.Unit 3 (379 KB)
Biol.Unit 4 (379 KB)
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Title
:
ECMEND-THDP-MN2+ COMPLEX SOAKED WITH 2-KETOGLUTARATE FOR 15 MIN
Authors
:
H. G. Song, C. Dong, Y. Z. Chen, Y. R. Sun, Z. H. Guo
Date
:
01 Nov 15 (Deposition) - 01 Jun 16 (Release) - 29 Jun 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.77
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Keywords
:
Post-Decarboxylation Intermediate, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. G. Song, C. Dong, M. M. Qin, Y. Z. Chen, Y. R. Sun, J. J. Liu, W. Chan, Z. H. Guo
A Thiamine-Dependent Enzyme Utilizes An Active Tetrahedral Intermediate In Vitamin K Biosynthesis
J. Am. Chem. Soc. V. 138 7244 2016
[
close entry info
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Hetero Components
(4, 40)
Info
All Hetero Components
1a: FORMIC ACID (FMTa)
1b: FORMIC ACID (FMTb)
1c: FORMIC ACID (FMTc)
1d: FORMIC ACID (FMTd)
1e: FORMIC ACID (FMTe)
1f: FORMIC ACID (FMTf)
1g: FORMIC ACID (FMTg)
1h: FORMIC ACID (FMTh)
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)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
3a: MANGANESE (II) ION (MNa)
3b: MANGANESE (II) ION (MNb)
3c: MANGANESE (II) ION (MNc)
3d: MANGANESE (II) ION (MNd)
3e: MANGANESE (II) ION (MNe)
3f: MANGANESE (II) ION (MNf)
3g: MANGANESE (II) ION (MNg)
3h: MANGANESE (II) ION (MNh)
4a: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6a)
4b: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6b)
4c: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6c)
4d: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6d)
4e: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6e)
4f: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6f)
4g: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6g)
4h: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FMT
8
Ligand/Ion
FORMIC ACID
2
GOL
16
Ligand/Ion
GLYCEROL
3
MN
8
Ligand/Ion
MANGANESE (II) ION
4
TD6
8
Ligand/Ion
(4S)-4-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3LAMBDA~5~-THIAZOL-2-YL}-4-HYDROXYBUTANOICACID
[
close Hetero Component info
]
Sites
(40, 40)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
29: AF2 (SOFTWARE)
30: AF3 (SOFTWARE)
31: AF4 (SOFTWARE)
32: AF5 (SOFTWARE)
33: AF6 (SOFTWARE)
34: AF7 (SOFTWARE)
35: AF8 (SOFTWARE)
36: AF9 (SOFTWARE)
37: AG1 (SOFTWARE)
38: AG2 (SOFTWARE)
39: AG3 (SOFTWARE)
40: AG4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:390 , SER A:391 , LEU A:392 , ARG A:395 , ARG A:413 , SER A:416 , GLY A:417 , ILE A:418 , ASP A:419 , GLY A:441 , ASP A:442 , LEU A:443 , SER A:444 , TYR A:447 , ASN A:469 , GLY A:471 , GLY A:472 , GLN A:473 , ILE A:474 , MN A:602 , HOH A:854 , HOH A:877 , HOH A:988 , PRO B:30 , GLU B:55 , THR B:81 , ALA B:82 , ASN B:117 , GLN B:118 , FMT B:601
binding site for residue TD6 A 601
02
AC2
SOFTWARE
ASP A:442 , ASN A:469 , GLY A:471 , TD6 A:601 , HOH A:877
binding site for residue MN A 602
03
AC3
SOFTWARE
HIS A:49 , HIS A:50 , THR A:51 , ARG A:430 , LEU A:454 , GLN A:457 , HOH A:801 , HOH A:807 , HOH A:939
binding site for residue GOL A 603
04
AC4
SOFTWARE
ARG A:364 , HIS A:374 , ARG A:375 , CYS A:377 , ASP A:378
binding site for residue GOL A 604
05
AC5
SOFTWARE
GLY A:31 , SER A:32 , ARG A:33 , THR A:78 , ARG A:107 , GLN A:118 , HOH A:874 , TD6 B:602
binding site for residue FMT A 605
06
AC6
SOFTWARE
TD6 A:601 , GLY B:31 , SER B:32 , ARG B:33 , THR B:78 , ARG B:107 , GLN B:118 , HOH B:710
binding site for residue FMT B 601
07
AC7
SOFTWARE
PRO A:30 , GLU A:55 , THR A:81 , ALA A:82 , ASN A:117 , GLN A:118 , FMT A:605 , ASN B:390 , SER B:391 , LEU B:392 , ARG B:395 , ARG B:413 , 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:603 , HOH B:748 , HOH B:803 , HOH B:946
binding site for residue TD6 B 602
08
AC8
SOFTWARE
ASP B:442 , ASN B:469 , GLY B:471 , TD6 B:602 , HOH B:748
binding site for residue MN B 603
09
AC9
SOFTWARE
HIS B:49 , HIS B:50 , THR B:51 , ARG B:430 , LEU B:454 , GLN B:457 , HOH B:772 , HOH B:861
binding site for residue GOL B 604
10
AD1
SOFTWARE
HOH A:701 , ILE B:361 , ARG B:364 , HIS B:374 , ASP B:378 , HOH B:1004
binding site for residue GOL B 605
11
AD2
SOFTWARE
ASN C:390 , SER C:391 , LEU C:392 , ARG C:395 , ARG C:413 , SER C:416 , GLY C:417 , ILE C:418 , ASP C:419 , GLY C:441 , ASP C:442 , LEU C:443 , SER C:444 , TYR C:447 , ASN C:469 , GLY C:471 , GLY C:472 , GLN C:473 , ILE C:474 , MN C:602 , HOH C:783 , HOH C:864 , HOH C:991 , PRO D:30 , GLU D:55 , THR D:81 , ASN D:117 , GLN D:118 , FMT D:601
binding site for residue TD6 C 601
12
AD3
SOFTWARE
ASP C:442 , ASN C:469 , GLY C:471 , TD6 C:601 , HOH C:783
binding site for residue MN C 602
13
AD4
SOFTWARE
HIS C:49 , HIS C:50 , THR C:51 , ARG C:430 , LEU C:454 , GLN C:457 , HOH C:769 , HOH C:922 , HOH C:926
binding site for residue GOL C 603
14
AD5
SOFTWARE
ARG C:364 , HIS C:374 , ARG C:375 , ASP C:378 , HOH C:867
binding site for residue GOL C 604
15
AD6
SOFTWARE
SER C:32 , ARG C:33 , THR C:78 , ARG C:107 , GLN C:118 , HOH C:880 , TD6 D:602
binding site for residue FMT C 605
16
AD7
SOFTWARE
TD6 C:601 , SER D:32 , ARG D:33 , THR D:78 , ARG D:107 , GLN D:118 , HOH D:974
binding site for residue FMT D 601
17
AD8
SOFTWARE
PRO C:30 , GLU C:55 , THR C:81 , ALA C:82 , ASN C:117 , GLN C:118 , FMT C:605 , ASN D:390 , SER D:391 , LEU D:392 , ARG D:395 , ARG D:413 , 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:603 , HOH D:866 , HOH D:875 , HOH D:988
binding site for residue TD6 D 602
18
AD9
SOFTWARE
ASP D:442 , ASN D:469 , GLY D:471 , TD6 D:602 , HOH D:866
binding site for residue MN D 603
19
AE1
SOFTWARE
HIS D:49 , HIS D:50 , THR D:51 , ARG D:430 , LEU D:454 , GLN D:457 , HOH D:722 , HOH D:908
binding site for residue GOL D 604
20
AE2
SOFTWARE
ARG D:364 , HIS D:374 , CYS D:377 , ASP D:378 , HOH D:718
binding site for residue GOL D 605
21
AE3
SOFTWARE
ASN E:390 , SER E:391 , LEU E:392 , ARG E:395 , ARG E:413 , SER E:416 , GLY E:417 , ILE E:418 , ASP E:419 , GLY E:441 , ASP E:442 , LEU E:443 , SER E:444 , TYR E:447 , ASN E:469 , GLY E:471 , GLY E:472 , GLN E:473 , ILE E:474 , MN E:602 , HOH E:827 , HOH E:919 , HOH E:933 , PRO F:30 , GLU F:55 , THR F:81 , ALA F:82 , ASN F:117 , GLN F:118 , FMT F:601
binding site for residue TD6 E 601
22
AE4
SOFTWARE
ASP E:442 , ASN E:469 , GLY E:471 , TD6 E:601 , HOH E:827
binding site for residue MN E 602
23
AE5
SOFTWARE
HIS E:49 , HIS E:50 , THR E:51 , ARG E:430 , LEU E:454 , GLN E:457 , HOH E:723 , HOH E:805 , HOH E:873
binding site for residue GOL E 603
24
AE6
SOFTWARE
ARG E:364 , HIS E:374 , ASP E:378 , HOH E:1035
binding site for residue GOL E 604
25
AE7
SOFTWARE
GLY E:31 , SER E:32 , ARG E:33 , THR E:78 , ARG E:107 , GLN E:118 , HOH E:817 , HOH E:937 , TD6 F:602
binding site for residue FMT E 605
26
AE8
SOFTWARE
TD6 E:601 , SER F:32 , ARG F:33 , THR F:78 , ARG F:107 , GLN F:118 , HOH F:832 , HOH F:863
binding site for residue FMT F 601
27
AE9
SOFTWARE
PRO E:30 , GLU E:55 , THR E:81 , ALA E:82 , ASN E:117 , GLN E:118 , FMT E:605 , ASN F:390 , SER F:391 , LEU F:392 , ARG F:395 , ARG F:413 , SER F:416 , GLY F:417 , ILE F:418 , ASP F:419 , GLY F:441 , ASP F:442 , LEU F:443 , SER F:444 , TYR F:447 , ASN F:469 , GLY F:471 , GLY F:472 , GLN F:473 , ILE F:474 , MN F:603 , HOH F:779 , HOH F:791 , HOH F:966
binding site for residue TD6 F 602
28
AF1
SOFTWARE
ASP F:442 , ASN F:469 , GLY F:471 , TD6 F:602 , HOH F:791
binding site for residue MN F 603
29
AF2
SOFTWARE
HIS F:49 , HIS F:50 , THR F:51 , ARG F:430 , LEU F:454 , GLN F:457 , HOH F:834 , HOH F:848 , HOH F:976
binding site for residue GOL F 604
30
AF3
SOFTWARE
ARG F:364 , HIS F:374 , ARG F:375 , CYS F:377 , ASP F:378
binding site for residue GOL F 605
31
AF4
SOFTWARE
ASN G:390 , SER G:391 , LEU G:392 , ARG G:395 , ARG G:413 , SER G:416 , GLY G:417 , ILE G:418 , ASP G:419 , GLY G:441 , ASP G:442 , LEU G:443 , SER G:444 , TYR G:447 , ASN G:469 , GLY G:471 , GLY G:472 , GLN G:473 , ILE G:474 , MN G:602 , HOH G:801 , HOH G:919 , HOH G:1029 , HOH G:1031 , PRO H:30 , GLU H:55 , THR H:81 , ALA H:82 , ASN H:117 , GLN H:118 , FMT H:601
binding site for residue TD6 G 601
32
AF5
SOFTWARE
ASP G:442 , ASN G:469 , GLY G:471 , TD6 G:601 , HOH G:919
binding site for residue MN G 602
33
AF6
SOFTWARE
HIS G:49 , HIS G:50 , THR G:51 , ARG G:430 , LEU G:454 , GLN G:457 , HOH G:734 , HOH G:811 , HOH G:912
binding site for residue GOL G 603
34
AF7
SOFTWARE
ARG G:364 , HIS G:374 , ARG G:375 , ASP G:378
binding site for residue GOL G 604
35
AF8
SOFTWARE
GLY G:31 , SER G:32 , ARG G:33 , THR G:78 , ARG G:107 , GLN G:118 , HOH G:755 , HOH G:988 , TD6 H:602
binding site for residue FMT G 605
36
AF9
SOFTWARE
TD6 G:601 , HOH G:1029 , GLY H:31 , SER H:32 , ARG H:33 , THR H:78 , ARG H:107 , GLN H:118 , HOH H:891
binding site for residue FMT H 601
37
AG1
SOFTWARE
PRO G:30 , GLU G:55 , THR G:81 , ALA G:82 , ASN G:117 , GLN G:118 , FMT G:605 , ASN H:390 , SER H:391 , LEU H:392 , ARG H:395 , ARG H:413 , SER H:416 , GLY H:417 , ILE H:418 , ASP H:419 , GLY H:441 , ASP H:442 , LEU H:443 , SER H:444 , TYR H:447 , ASN H:469 , GLY H:471 , GLY H:472 , GLN H:473 , ILE H:474 , MN H:603 , HOH H:816 , HOH H:884 , HOH H:955
binding site for residue TD6 H 602
38
AG2
SOFTWARE
ASP H:442 , ASN H:469 , GLY H:471 , TD6 H:602 , HOH H:816
binding site for residue MN H 603
39
AG3
SOFTWARE
HOH G:928 , HIS H:50 , THR H:51 , ARG H:430 , LEU H:454 , HOH H:741 , HOH H:754
binding site for residue GOL H 604
40
AG4
SOFTWARE
HOH G:1092 , ARG H:364 , HIS H:374 , ASP H:378 , HOH H:807
binding site for residue GOL H 605
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Exons
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Asym.Unit (1.5 MB)
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