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5EJ8
Biol. Unit 2
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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
(5, 23)
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
7
Ligand/Ion
1,2-ETHANEDIOL
2
FMT
9
Ligand/Ion
FORMIC ACID
3
GOL
4
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
(30, 30)
Info
All Sites
01: AF5 (SOFTWARE)
02: AF6 (SOFTWARE)
03: AF7 (SOFTWARE)
04: AF8 (SOFTWARE)
05: AF9 (SOFTWARE)
06: AG1 (SOFTWARE)
07: AG2 (SOFTWARE)
08: AG3 (SOFTWARE)
09: AG4 (SOFTWARE)
10: AG5 (SOFTWARE)
11: AG6 (SOFTWARE)
12: AG7 (SOFTWARE)
13: AG8 (SOFTWARE)
14: AG9 (SOFTWARE)
15: AH1 (SOFTWARE)
16: AH2 (SOFTWARE)
17: AH3 (SOFTWARE)
18: AH4 (SOFTWARE)
19: AH5 (SOFTWARE)
20: AH6 (SOFTWARE)
21: AH7 (SOFTWARE)
22: AH8 (SOFTWARE)
23: AH9 (SOFTWARE)
24: AI1 (SOFTWARE)
25: AI2 (SOFTWARE)
26: AI3 (SOFTWARE)
27: AI4 (SOFTWARE)
28: AI5 (SOFTWARE)
29: AI6 (SOFTWARE)
30: AM5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AF5
SOFTWARE
PRO B:137 , ARG B:138 , HOH B:917 , PRO C:137 , ARG C:138 , HOH C:704 , HOH C:834 , HOH C:1026
binding site for residue EDO C 601
02
AF6
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:603 , MG C:604 , HOH C:800 , HOH C:859 , HOH C:973 , PRO D:30 , GLU D:55 , THR D:81 , ASN D:117 , GLN D:118 , FMT D:610
binding site for residue TD6 C 602
03
AF7
SOFTWARE
ASP C:442 , ASN C:469 , GLY C:471 , TD6 C:602 , HOH C:859
binding site for residue MN C 603
04
AF8
SOFTWARE
ASP C:442 , ASN C:469 , GLY C:471 , TD6 C:602 , HOH C:859
binding site for residue MG C 604
05
AF9
SOFTWARE
HIS C:49 , HIS C:50 , THR C:51 , ARG C:430 , GLN C:457 , HOH C:733 , HOH C:788 , HOH C:791
binding site for residue GOL C 605
06
AG1
SOFTWARE
GLU C:16 , ASN C:44 , SER C:45 , ALA C:46 , HOH C:757 , HOH C:760
binding site for residue TRS C 606
07
AG2
SOFTWARE
THR C:96 , ARG C:228 , ASP C:311 , MG C:608 , HOH C:761 , HOH C:790 , HOH C:889 , HOH C:995 , HOH C:1087 , HOH C:1104
binding site for residue EDO C 607
08
AG3
SOFTWARE
ASP C:311 , EDO C:607 , HOH C:790 , HOH C:1087 , HOH C:1104
binding site for residue MG C 608
09
AG4
SOFTWARE
ALA C:241 , GLN C:242 , TRP C:246 , EDO C:610 , HOH C:795 , HOH C:941 , HOH C:1072
binding site for residue FMT C 609
10
AG5
SOFTWARE
ALA C:238 , GLN C:242 , LEU C:248 , PRO C:259 , FMT C:609 , HOH C:711 , HOH C:773 , HOH C:1080
binding site for residue EDO C 610
11
AG6
SOFTWARE
MET C:229 , SER C:230 , ALA C:231 , GLN C:255 , VAL C:409 , TYR C:410 , HOH C:778 , HOH C:950
binding site for residue EDO C 611
12
AG7
SOFTWARE
GLU C:505 , LEU C:506 , LYS C:507 , THR C:529 , THR C:530 , HOH C:989
binding site for residue FMT C 612
13
AG8
SOFTWARE
HIS C:21 , LYS C:70 , GLN C:71 , LYS C:99 , HOH C:1038
binding site for residue GOL C 613
14
AG9
SOFTWARE
LYS C:210 , GLN C:211 , ARG C:212 , ASP C:213 , HOH C:793
binding site for residue FMT C 614
15
AH1
SOFTWARE
LEU C:289 , THR C:290 , ARG C:395 , ARG C:413 , EDO C:616 , HOH C:715 , HOH C:721 , ASN D:117 , HOH D:740
binding site for residue EDO C 615
16
AH2
SOFTWARE
SER C:288 , LEU C:289 , LEU C:295 , EDO C:615 , HOH C:738 , HOH C:748 , HOH C:806 , GLY D:115 , ALA D:116 , ASN D:117 , HOH D:740
binding site for residue EDO C 616
17
AH3
SOFTWARE
GLY C:31 , SER C:32 , ARG C:33 , THR C:78 , ARG C:107 , GLN C:118 , HOH C:1023 , TD6 D:602
binding site for residue FMT C 617
18
AH4
SOFTWARE
HIS C:49 , HOH C:1050 , ARG D:487 , HOH D:1081
binding site for residue FMT D 601
19
AH5
SOFTWARE
PRO C:30 , GLU C:55 , THR C:81 , ALA C:82 , ASN C:117 , GLN C:118 , FMT C:617 , 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 , MG D:604 , HOH D:825 , HOH D:870 , HOH D:958
binding site for residue TD6 D 602
20
AH6
SOFTWARE
ASP D:442 , ASN D:469 , GLY D:471 , TD6 D:602 , HOH D:870
binding site for residue MN D 603
21
AH7
SOFTWARE
ASP D:442 , ASN D:469 , GLY D:471 , TD6 D:602 , HOH D:870
binding site for residue MG D 604
22
AH8
SOFTWARE
HIS D:49 , HIS D:50 , THR D:51 , ARG D:430 , LEU D:454 , HOH D:730 , HOH D:746 , HOH D:801
binding site for residue GOL D 605
23
AH9
SOFTWARE
GLU D:16 , HOH D:759 , HOH D:933 , HOH D:1060
binding site for residue GOL D 606
24
AI1
SOFTWARE
PRO D:173 , LEU D:174 , TYR D:175 , HOH D:717 , HOH D:750
binding site for residue FMT D 607
25
AI2
SOFTWARE
ASP D:311 , HOH D:727 , HOH D:846 , HOH D:981 , HOH D:989 , HOH D:1215
binding site for residue MG D 608
26
AI3
SOFTWARE
PRO D:123 , GLY D:124 , ILE D:134 , SER D:135 , HIS D:165 , ASN D:167
binding site for residue FMT D 609
27
AI4
SOFTWARE
TD6 C:602 , GLY D:31 , SER D:32 , ARG D:33 , THR D:78 , ARG D:107 , GLN D:118 , HOH D:962
binding site for residue FMT D 610
28
AI5
SOFTWARE
ASN C:117 , LEU D:289 , THR D:290 , LEU D:295 , ARG D:395 , ARG D:413 , FMT D:612 , HOH D:729 , HOH D:745 , HOH D:876 , HOH D:983
binding site for residue EDO D 611
29
AI6
SOFTWARE
GLY C:115 , ASN C:117 , SER D:288 , LEU D:289 , LEU D:295 , EDO D:611 , HOH D:706 , HOH D:709
binding site for residue FMT D 612
30
AM5
SOFTWARE
HOH D:1226 , ARG G:364 , EDO G:610 , HOH G:1026 , HOH G:1111
binding site for residue FMT G 611
[
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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Pfam Domains
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Asym.Unit (2.3 MB)
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Biol.Unit 1 (609 KB)
Header - Biol.Unit 1
Biol.Unit 2 (600 KB)
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Biol.Unit 3 (610 KB)
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