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5EJ8
Biol. Unit 3
Info
Asym.Unit (2.3 MB)
Biol.Unit 1 (609 KB)
Biol.Unit 2 (600 KB)
Biol.Unit 3 (610 KB)
Biol.Unit 4 (607 KB)
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Title
:
ECMEND-THDP-MN2+ COMPLEX STRUCTURE SOAKED WITH 2-KETOGLUTARATE FOR 2 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
:
1.34
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
]
Hetero Components
(4, 19)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
1n: 1,2-ETHANEDIOL (EDOn)
1o: 1,2-ETHANEDIOL (EDOo)
1p: 1,2-ETHANEDIOL (EDOp)
1q: 1,2-ETHANEDIOL (EDOq)
1r: 1,2-ETHANEDIOL (EDOr)
1s: 1,2-ETHANEDIOL (EDOs)
1t: 1,2-ETHANEDIOL (EDOt)
1u: 1,2-ETHANEDIOL (EDOu)
2a: FORMIC ACID (FMTa)
2aa: FORMIC ACID (FMTaa)
2ab: FORMIC ACID (FMTab)
2ac: FORMIC ACID (FMTac)
2ad: FORMIC ACID (FMTad)
2ae: FORMIC ACID (FMTae)
2af: FORMIC ACID (FMTaf)
2ag: FORMIC ACID (FMTag)
2ah: FORMIC ACID (FMTah)
2ai: FORMIC ACID (FMTai)
2aj: FORMIC ACID (FMTaj)
2ak: FORMIC ACID (FMTak)
2al: FORMIC ACID (FMTal)
2am: FORMIC ACID (FMTam)
2an: FORMIC ACID (FMTan)
2ao: FORMIC ACID (FMTao)
2ap: FORMIC ACID (FMTap)
2aq: FORMIC ACID (FMTaq)
2ar: FORMIC ACID (FMTar)
2as: FORMIC ACID (FMTas)
2b: FORMIC ACID (FMTb)
2c: FORMIC ACID (FMTc)
2d: FORMIC ACID (FMTd)
2e: FORMIC ACID (FMTe)
2f: FORMIC ACID (FMTf)
2g: FORMIC ACID (FMTg)
2h: FORMIC ACID (FMTh)
2i: FORMIC ACID (FMTi)
2j: FORMIC ACID (FMTj)
2k: FORMIC ACID (FMTk)
2l: FORMIC ACID (FMTl)
2m: FORMIC ACID (FMTm)
2n: FORMIC ACID (FMTn)
2o: FORMIC ACID (FMTo)
2p: FORMIC ACID (FMTp)
2q: FORMIC ACID (FMTq)
2r: FORMIC ACID (FMTr)
2s: FORMIC ACID (FMTs)
2t: FORMIC ACID (FMTt)
2u: FORMIC ACID (FMTu)
2v: FORMIC ACID (FMTv)
2w: FORMIC ACID (FMTw)
2x: FORMIC ACID (FMTx)
2y: FORMIC ACID (FMTy)
2z: FORMIC ACID (FMTz)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
4h: MAGNESIUM ION (MGh)
4i: MAGNESIUM ION (MGi)
4j: MAGNESIUM ION (MGj)
4k: MAGNESIUM ION (MGk)
4l: MAGNESIUM ION (MGl)
4m: MAGNESIUM ION (MGm)
4n: MAGNESIUM ION (MGn)
4o: MAGNESIUM ION (MGo)
5a: MANGANESE (II) ION (MNa)
5b: MANGANESE (II) ION (MNb)
5c: MANGANESE (II) ION (MNc)
5d: MANGANESE (II) ION (MNd)
5e: MANGANESE (II) ION (MNe)
5f: MANGANESE (II) ION (MNf)
5g: MANGANESE (II) ION (MNg)
5h: MANGANESE (II) ION (MNh)
6a: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6a)
6b: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6b)
6c: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6c)
6d: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6d)
6e: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6e)
6f: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6f)
6g: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6g)
6h: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6h)
7a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
2
FMT
11
Ligand/Ion
FORMIC ACID
3
GOL
3
Ligand/Ion
GLYCEROL
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
MN
-1
Ligand/Ion
MANGANESE (II) ION
6
TD6
2
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
7
TRS
-1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(25, 25)
Info
All Sites
01: AI7 (SOFTWARE)
02: AI8 (SOFTWARE)
03: AI9 (SOFTWARE)
04: AJ1 (SOFTWARE)
05: AJ2 (SOFTWARE)
06: AJ3 (SOFTWARE)
07: AJ4 (SOFTWARE)
08: AJ5 (SOFTWARE)
09: AJ6 (SOFTWARE)
10: AJ7 (SOFTWARE)
11: AJ8 (SOFTWARE)
12: AJ9 (SOFTWARE)
13: AK1 (SOFTWARE)
14: AK2 (SOFTWARE)
15: AK3 (SOFTWARE)
16: AK4 (SOFTWARE)
17: AK5 (SOFTWARE)
18: AK6 (SOFTWARE)
19: AK7 (SOFTWARE)
20: AK8 (SOFTWARE)
21: AK9 (SOFTWARE)
22: AL1 (SOFTWARE)
23: AL2 (SOFTWARE)
24: AL3 (SOFTWARE)
25: AO2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AI7
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 , MG E:603 , HOH E:783 , HOH E:876 , HOH E:906 , PRO F:30 , GLU F:55 , THR F:81 , ASN F:117 , GLN F:118 , FMT F:601
binding site for residue TD6 E 601
02
AI8
SOFTWARE
ASP E:442 , ASN E:469 , GLY E:471 , TD6 E:601 , HOH E:783
binding site for residue MN E 602
03
AI9
SOFTWARE
ASP E:442 , ASN E:469 , GLY E:471 , TD6 E:601 , HOH E:783
binding site for residue MG E 603
04
AJ1
SOFTWARE
HIS E:49 , HIS E:50 , THR E:51 , ARG E:430 , LEU E:454 , GLN E:457 , HOH E:744 , HOH E:789 , HOH E:879
binding site for residue GOL E 604
05
AJ2
SOFTWARE
PRO E:123 , GLY E:124 , ILE E:134 , SER E:135 , HIS E:165
binding site for residue FMT E 605
06
AJ3
SOFTWARE
PRO E:173 , LEU E:174 , TYR E:175 , HOH E:853
binding site for residue FMT E 606
07
AJ4
SOFTWARE
ASP E:311 , HOH E:716 , HOH E:742 , HOH E:851 , HOH E:925 , HOH E:933
binding site for residue MG E 607
08
AJ5
SOFTWARE
LYS E:70 , HOH E:716 , HOH E:733 , HOH E:734
binding site for residue FMT E 608
09
AJ6
SOFTWARE
ARG E:121 , PRO E:123 , MET E:125 , HOH E:703 , ALA F:127 , SER F:128 , HIS F:129
binding site for residue FMT E 609
10
AJ7
SOFTWARE
SER E:288 , LEU E:289 , LEU E:295 , HOH E:701 , HOH E:710 , HOH E:844 , GLY F:115 , ASN F:117
binding site for residue FMT E 610
11
AJ8
SOFTWARE
HIS E:25 , ALA E:431 , HOH E:1061
binding site for residue FMT E 611
12
AJ9
SOFTWARE
HOH E:728 , HOH E:878 , HOH E:1070
binding site for residue EDO E 612
13
AK1
SOFTWARE
GLY E:31 , SER E:32 , ARG E:33 , THR E:78 , ARG E:107 , GLN E:118 , HOH E:1054 , TD6 F:602
binding site for residue FMT E 613
14
AK2
SOFTWARE
TD6 E:601 , GLY F:31 , SER F:32 , ARG F:33 , THR F:78 , ARG F:107 , GLN F:118 , HOH F:1045
binding site for residue FMT F 601
15
AK3
SOFTWARE
PRO E:30 , GLU E:55 , THR E:81 , ALA E:82 , ASN E:117 , GLN E:118 , FMT E:613 , 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 , MG F:604 , HOH F:757 , HOH F:820 , HOH F:921
binding site for residue TD6 F 602
16
AK4
SOFTWARE
ASP F:442 , ASN F:469 , GLY F:471 , TD6 F:602 , HOH F:820
binding site for residue MN F 603
17
AK5
SOFTWARE
ASP F:442 , ASN F:469 , GLY F:471 , TD6 F:602 , HOH F:820
binding site for residue MG F 604
18
AK6
SOFTWARE
HIS F:49 , HIS F:50 , THR F:51 , ARG F:430 , LEU F:454 , GLN F:457 , HOH F:748 , HOH F:755 , HOH F:926
binding site for residue GOL F 605
19
AK7
SOFTWARE
ARG F:364 , HIS F:374 , ARG F:375 , ASP F:378 , HOH F:1193
binding site for residue GOL F 606
20
AK8
SOFTWARE
PRO F:198 , ARG F:201 , HOH F:731 , HOH F:913
binding site for residue FMT F 607
21
AK9
SOFTWARE
GLN F:242 , TRP F:246 , HOH F:853 , HOH F:870 , HOH F:875
binding site for residue FMT F 608
22
AL1
SOFTWARE
HOH F:723 , HOH F:1206
binding site for residue EDO F 609
23
AL2
SOFTWARE
ARG E:487 , HIS F:49 , HOH F:743
binding site for residue EDO F 610
24
AL3
SOFTWARE
GLY E:115 , SER F:288 , LEU F:289 , LEU F:295 , HOH F:705 , HOH F:717 , HOH F:720 , HOH F:747 , HOH F:844
binding site for residue FMT F 611
25
AO2
SOFTWARE
GLN E:219 , ARG E:342 , HOH E:1085 , GLY H:433 , SER H:459 , ALA H:460 , HOH H:721
binding site for residue GOL H 611
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Chain E
Chain F
Asymmetric Unit 1
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Asym.Unit (2.3 MB)
Header - Asym.Unit
Biol.Unit 1 (609 KB)
Header - Biol.Unit 1
Biol.Unit 2 (600 KB)
Header - Biol.Unit 2
Biol.Unit 3 (610 KB)
Header - Biol.Unit 3
Biol.Unit 4 (607 KB)
Header - Biol.Unit 4
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