PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
5EJ7
Asym. Unit
Info
Asym.Unit (1.7 MB)
Biol.Unit 1 (432 KB)
Biol.Unit 2 (429 KB)
Biol.Unit 3 (429 KB)
Biol.Unit 4 (428 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ECMEND-THDP-MN2+ COMPLEX SOAKED WITH 2-KETOGLUTARATE FOR 21 S
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
:
1.56
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
(3, 31)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
1l: GLYCEROL (GOLl)
1m: GLYCEROL (GOLm)
1n: GLYCEROL (GOLn)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
2e: MANGANESE (II) ION (MNe)
2f: MANGANESE (II) ION (MNf)
2g: MANGANESE (II) ION (MNg)
2h: MANGANESE (II) ION (MNh)
2i: MANGANESE (II) ION (MNi)
3a: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6a)
3b: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6b)
3c: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6c)
3d: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6d)
3e: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6e)
3f: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6f)
3g: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6g)
3h: (4S)-4-{3-[(4-AMINO-2-METHYLPYRIMI... (TD6h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
14
Ligand/Ion
GLYCEROL
2
MN
9
Ligand/Ion
MANGANESE (II) ION
3
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
(31, 31)
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)
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:803 , HOH A:820 , HOH A:945 , PRO B:30 , GLU B:55 , THR B:81 , ALA B:82 , ASN B:117 , GLN B:118
binding site for residue TD6 A 601
02
AC2
SOFTWARE
ASP A:442 , ASN A:469 , GLY A:471 , TD6 A:601 , HOH A:803
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:744 , HOH A:763 , HOH A:1056
binding site for residue GOL A 603
04
AC4
SOFTWARE
ARG A:364 , HIS A:374 , ASP A:378 , HOH A:1115
binding site for residue GOL A 604
05
AC5
SOFTWARE
PRO A:30 , GLU A:55 , THR A:81 , ALA A:82 , ASN A:117 , GLN A:118 , 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 , ASN B:469 , GLY B:471 , GLY B:472 , GLN B:473 , ILE B:474 , MN B:602 , HOH B:884 , HOH B:887 , HOH B:890
binding site for residue TD6 B 601
06
AC6
SOFTWARE
ASP B:442 , ASN B:469 , GLY B:471 , TD6 B:601 , HOH B:887
binding site for residue MN B 602
07
AC7
SOFTWARE
HIS B:49 , HIS B:50 , THR B:51 , ARG B:430 , LEU B:454 , HOH B:728 , HOH B:732 , HOH B:956
binding site for residue GOL B 603
08
AC8
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:6128 , HOH C:6206 , HOH C:6263 , HOH C:6304 , PRO D:30 , GLU D:55 , THR D:81 , ALA D:82 , ASN D:117 , GLN D:118
binding site for residue TD6 C 601
09
AC9
SOFTWARE
ASP C:442 , ASN C:469 , GLY C:471 , TD6 C:601 , HOH C:6206
binding site for residue MN C 602
10
AD1
SOFTWARE
HIS C:49 , HIS C:50 , THR C:51 , ARG C:430 , LEU C:454 , HOH C:6116 , HOH C:6135 , HOH C:6496
binding site for residue GOL C 603
11
AD2
SOFTWARE
HOH B:1406 , ARG C:364 , HIS C:374 , ASP C:378 , HOH C:6376
binding site for residue GOL C 604
12
AD3
SOFTWARE
PRO C:30 , GLU C:55 , THR C:81 , ALA C:82 , ASN C:117 , GLN C:118 , HOH C:6356 , 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:602 , HOH D:792 , HOH D:860 , HOH D:864
binding site for residue TD6 D 601
13
AD4
SOFTWARE
ASP D:442 , ASN D:469 , GLY D:471 , TD6 D:601 , HOH D:864
binding site for residue MN D 602
14
AD5
SOFTWARE
HIS D:50 , THR D:51 , ARG D:430 , LEU D:454 , HOH D:724 , HOH D:760 , HOH D:1022
binding site for residue GOL D 603
15
AD6
SOFTWARE
ARG D:364 , HIS D:374 , ASP D:378 , HOH D:803
binding site for residue GOL D 604
16
AD7
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:787 , HOH E:843 , HOH E:906 , PRO F:30 , GLU F:55 , THR F:81 , ALA F:82 , ASN F:117 , GLN F:118
binding site for residue TD6 E 601
17
AD8
SOFTWARE
ASP E:442 , ASN E:469 , GLY E:471 , TD6 E:601 , HOH E:843
binding site for residue MN E 602
18
AD9
SOFTWARE
HIS E:49 , HIS E:50 , THR E:51 , ARG E:430 , LEU E:454 , GLN E:457 , HOH E:728 , HOH E:784 , HOH E:934
binding site for residue GOL E 603
19
AE1
SOFTWARE
ARG E:364 , HIS E:374 , ARG E:375 , ASP E:378
binding site for residue GOL E 604
20
AE2
SOFTWARE
PRO E:30 , GLU E:55 , THR E:81 , ALA E:82 , ASN E:117 , GLN E:118 , 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:602 , HOH F:744 , HOH F:830 , HOH F:963
binding site for residue TD6 F 601
21
AE3
SOFTWARE
ASP F:442 , ASN F:469 , GLY F:471 , TD6 F:601 , HOH F:744
binding site for residue MN F 602
22
AE4
SOFTWARE
HIS F:50 , THR F:51 , ARG F:430 , LEU F:454 , HOH F:718 , HOH F:724 , HOH F:996
binding site for residue GOL F 603
23
AE5
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 , HOH G:789 , HOH G:832 , HOH G:847 , HOH G:1090 , PRO H:30 , GLU H:55 , THR H:81 , ASN H:117 , GLN H:118
binding site for residue TD6 G 601
24
AE6
SOFTWARE
ASP G:442 , ASN G:469 , GLY G:471 , TD6 G:601 , HOH G:832
binding site for residue MN G 602
25
AE7
SOFTWARE
HIS G:49 , HIS G:50 , THR G:51 , ARG G:430 , LEU G:454 , GLN G:457 , HOH G:746 , HOH G:1021
binding site for residue GOL G 603
26
AE8
SOFTWARE
ARG G:364 , HIS G:374 , ARG G:375 , ASP G:378 , HOH G:964
binding site for residue GOL G 604
27
AE9
SOFTWARE
GLU F:16 , HOH F:841 , HOH F:896 , HOH F:999 , HOH F:1203 , GLU G:354
binding site for residue MN G 605
28
AF1
SOFTWARE
PRO G:30 , GLU G:55 , THR G:81 , ALA G:82 , ASN G:117 , GLN G:118 , 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:602 , HOH H:815 , HOH H:826 , HOH H:963
binding site for residue TD6 H 601
29
AF2
SOFTWARE
ASP H:442 , ASN H:469 , GLY H:471 , TD6 H:601 , HOH H:815
binding site for residue MN H 602
30
AF3
SOFTWARE
HIS H:49 , HIS H:50 , THR H:51 , ARG H:430 , LEU H:454 , GLN H:457 , HOH H:715 , HOH H:794 , HOH H:845
binding site for residue GOL H 603
31
AF4
SOFTWARE
ARG H:364 , HIS H:374 , ARG H:375 , ASP H:378 , HOH H:925
binding site for residue GOL H 604
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
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
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (1.7 MB)
Header - Asym.Unit
Biol.Unit 1 (432 KB)
Header - Biol.Unit 1
Biol.Unit 2 (429 KB)
Header - Biol.Unit 2
Biol.Unit 3 (429 KB)
Header - Biol.Unit 3
Biol.Unit 4 (428 KB)
Header - Biol.Unit 4
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
5EJ7
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help