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5EJ8
Biol. Unit 4
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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(1)
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, 22)
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
4
Ligand/Ion
1,2-ETHANEDIOL
2
FMT
12
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
(28, 28)
Info
All Sites
01: AL4 (SOFTWARE)
02: AL5 (SOFTWARE)
03: AL6 (SOFTWARE)
04: AL7 (SOFTWARE)
05: AL8 (SOFTWARE)
06: AL9 (SOFTWARE)
07: AM1 (SOFTWARE)
08: AM2 (SOFTWARE)
09: AM3 (SOFTWARE)
10: AM4 (SOFTWARE)
11: AM5 (SOFTWARE)
12: AM6 (SOFTWARE)
13: AM7 (SOFTWARE)
14: AM8 (SOFTWARE)
15: AM9 (SOFTWARE)
16: AN1 (SOFTWARE)
17: AN2 (SOFTWARE)
18: AN3 (SOFTWARE)
19: AN4 (SOFTWARE)
20: AN5 (SOFTWARE)
21: AN6 (SOFTWARE)
22: AN7 (SOFTWARE)
23: AN8 (SOFTWARE)
24: AN9 (SOFTWARE)
25: AO1 (SOFTWARE)
26: AO2 (SOFTWARE)
27: AO3 (SOFTWARE)
28: AO4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AL4
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 , ASN G:469 , GLY G:471 , GLY G:472 , GLN G:473 , ILE G:474 , MN G:602 , MG G:603 , HOH G:817 , HOH G:818 , HOH G:941 , 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
02
AL5
SOFTWARE
ASP G:442 , ASN G:469 , GLY G:471 , TD6 G:601 , HOH G:818
binding site for residue MN G 602
03
AL6
SOFTWARE
ASP G:442 , ASN G:469 , GLY G:471 , TD6 G:601 , HOH G:818
binding site for residue MG G 603
04
AL7
SOFTWARE
HIS G:49 , HIS G:50 , THR G:51 , ARG G:430 , LEU G:454 , HOH G:711 , HOH G:739 , HOH G:775
binding site for residue GOL G 604
05
AL8
SOFTWARE
ASP G:311 , HOH G:805 , HOH G:1003 , HOH G:1092 , HOH G:1246
binding site for residue MG G 605
06
AL9
SOFTWARE
ARG G:24 , HIS G:25 , SER G:69 , GLN G:71 , HOH G:788 , HOH G:1029 , HOH G:1031
binding site for residue FMT G 606
07
AM1
SOFTWARE
PRO G:173 , LEU G:174 , TYR G:175 , HOH G:725 , HOH G:863
binding site for residue FMT G 607
08
AM2
SOFTWARE
ARG G:430 , GLN G:457 , HOH G:838 , HOH G:857
binding site for residue FMT G 608
09
AM3
SOFTWARE
GLN G:186 , TRP G:193 , HOH G:702
binding site for residue FMT G 609
10
AM4
SOFTWARE
ARG G:364 , HIS G:374 , ASP G:378 , FMT G:611
binding site for residue EDO G 610
11
AM5
SOFTWARE
HOH D:1226 , ARG G:364 , EDO G:610 , HOH G:1026 , HOH G:1111
binding site for residue FMT G 611
12
AM6
SOFTWARE
HIS G:374 , CYS G:377 , SER G:401 , GLN G:402 , HOH G:707
binding site for residue FMT G 612
13
AM7
SOFTWARE
LEU G:295 , HOH G:905 , HOH G:1141
binding site for residue EDO G 613
14
AM8
SOFTWARE
SER G:288 , LEU G:289 , LEU G:295 , HOH G:703 , HOH G:726 , HOH G:773 , GLY H:115
binding site for residue FMT G 614
15
AM9
SOFTWARE
GLY G:31 , SER G:32 , ARG G:33 , THR G:78 , ARG G:107 , GLN G:118 , HOH G:950 , TD6 H:602
binding site for residue FMT G 615
16
AN1
SOFTWARE
TD6 G:601 , GLY H:31 , SER H:32 , ARG H:33 , THR H:78 , ARG H:107 , GLN H:118 , HOH H:1051
binding site for residue FMT H 601
17
AN2
SOFTWARE
PRO G:30 , GLU G:55 , THR G:81 , ALA G:82 , ASN G:117 , GLN G:118 , FMT G:615 , 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 , ASN H:469 , GLY H:471 , GLY H:472 , GLN H:473 , ILE H:474 , MN H:603 , MG H:604 , HOH H:802 , HOH H:830 , HOH H:941
binding site for residue TD6 H 602
18
AN3
SOFTWARE
ASP H:442 , ASN H:469 , GLY H:471 , TD6 H:602 , HOH H:830
binding site for residue MN H 603
19
AN4
SOFTWARE
ASP H:442 , ASN H:469 , GLY H:471 , TD6 H:602 , HOH H:830
binding site for residue MG H 604
20
AN5
SOFTWARE
HIS H:49 , HIS H:50 , THR H:51 , ARG H:430 , LEU H:454 , GLN H:457 , HOH H:764 , HOH H:768 , HOH H:848
binding site for residue GOL H 605
21
AN6
SOFTWARE
ARG G:487 , ILE H:48 , HIS H:49 , HOH H:1105
binding site for residue FMT H 606
22
AN7
SOFTWARE
THR H:96 , ARG H:228 , ASP H:310 , ASP H:311 , ILE H:312 , MG H:608 , HOH H:703 , HOH H:780 , HOH H:813 , HOH H:1035 , HOH H:1098 , HOH H:1150
binding site for residue GOL H 607
23
AN8
SOFTWARE
ASP H:311 , GOL H:607 , HOH H:813 , HOH H:1018 , HOH H:1098 , HOH H:1150
binding site for residue MG H 608
24
AN9
SOFTWARE
GLY G:115 , ASN G:117 , HOH G:715 , SER H:288 , LEU H:289 , LEU H:295 , HOH H:738 , HOH H:757 , HOH H:843
binding site for residue EDO H 609
25
AO1
SOFTWARE
LYS H:292 , ARG H:395 , HOH H:719 , HOH H:883
binding site for residue FMT H 610
26
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
27
AO3
SOFTWARE
ARG H:364 , HIS H:374 , ASP H:378 , HOH H:1095
binding site for residue EDO H 612
28
AO4
SOFTWARE
HOH H:790 , HOH H:958 , HOH H:1023 , HOH H:1080 , HOH H:1129
binding site for residue FMT H 613
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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Exons
(0, 0)
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SCOP Domains
(0, 0)
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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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