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.
5HPW
Asym. Unit
Info
Asym.Unit (419 KB)
Biol.Unit 1 (108 KB)
Biol.Unit 2 (107 KB)
Biol.Unit 3 (108 KB)
Biol.Unit 4 (108 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MODE OF BINDING OF ANTITHYROID DRUG, PROPYLTHIOURACIL TO LACTOPEROXIDASE: BINDING STUDIES AND STRUCTURE DETERMINATION
Authors
:
R. P. Singh, A. Singh, P. Sharma, P. Kaur, S. Sharma, T. P. Singh
Date
:
21 Jan 16 (Deposition) - 20 Apr 16 (Release) - 20 Apr 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. P. Singh, A. Singh, P. Sharma, P. Kaur, S. Sharma, T. P. Singh
Mode Of Binding Of Antithyroid Drug, Propylthiouracil To Lactoperoxidase: Binding Studies And Structure Determinatio
To Be Published
[
close entry info
]
Hetero Components
(5, 39)
Info
All Hetero Components
1a: 6-PROPYL-2-THIOXO-2,3-DIHYDROPYRIM... (3CJa)
1b: 6-PROPYL-2-THIOXO-2,3-DIHYDROPYRIM... (3CJb)
1c: 6-PROPYL-2-THIOXO-2,3-DIHYDROPYRIM... (3CJc)
1d: 6-PROPYL-2-THIOXO-2,3-DIHYDROPYRIM... (3CJd)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
3c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
3d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4i: N-ACETYL-D-GLUCOSAMINE (NAGi)
4j: N-ACETYL-D-GLUCOSAMINE (NAGj)
4k: N-ACETYL-D-GLUCOSAMINE (NAGk)
4l: N-ACETYL-D-GLUCOSAMINE (NAGl)
4m: N-ACETYL-D-GLUCOSAMINE (NAGm)
4n: N-ACETYL-D-GLUCOSAMINE (NAGn)
4o: N-ACETYL-D-GLUCOSAMINE (NAGo)
5a: NITRATE ION (NO3a)
5b: NITRATE ION (NO3b)
5c: NITRATE ION (NO3c)
5d: NITRATE ION (NO3d)
5e: NITRATE ION (NO3e)
5f: NITRATE ION (NO3f)
5g: NITRATE ION (NO3g)
5h: NITRATE ION (NO3h)
5i: NITRATE ION (NO3i)
5j: NITRATE ION (NO3j)
5k: NITRATE ION (NO3k)
5l: NITRATE ION (NO3l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3CJ
4
Ligand/Ion
6-PROPYL-2-THIOXO-2,3-DIHYDROPYRIMIDIN-4(1H)-ONE
2
CA
4
Ligand/Ion
CALCIUM ION
3
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
NAG
15
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
NO3
12
Ligand/Ion
NITRATE ION
[
close Hetero Component info
]
Sites
(37, 37)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:110 , THR A:184 , PHE A:186 , ASP A:188 , SER A:190
binding site for residue CA A 605
02
AC2
SOFTWARE
ALA A:44 , ARG A:45 , TRP A:46 , LEU A:47 , ASN A:341 , VAL A:342 , MET A:446 , HOH A:706
binding site for residue NO3 A 606
03
AC3
SOFTWARE
LEU A:92 , LYS A:402 , ASN A:403 , HOH A:724
binding site for residue NO3 A 607
04
AC4
SOFTWARE
GLN A:305 , ILE A:306 , PHE A:309 , TRP A:530 , GLU A:531
binding site for residue NO3 A 608
05
AC5
SOFTWARE
GLN A:105 , HIS A:109 , PHE A:113 , ARG A:255 , HEM A:610
binding site for residue 3CJ A 609
06
AC6
SOFTWARE
MET A:101 , GLY A:104 , GLN A:105 , ASP A:108 , ASP A:112 , PHE A:113 , ALA A:114 , GLU A:258 , THR A:344 , PHE A:347 , ARG A:348 , GLY A:350 , HIS A:351 , VAL A:354 , ILE A:436 , ARG A:440 , 3CJ A:609
binding site for residue HEM A 610
07
AC7
SOFTWARE
ASP B:110 , THR B:184 , PHE B:186 , ASP B:188 , SER B:190
binding site for residue CA B 604
08
AC8
SOFTWARE
ARG B:45 , TRP B:46 , LEU B:47 , ASN B:341 , VAL B:342 , MET B:446 , PRO B:447 , TRP B:452
binding site for residue NO3 B 605
09
AC9
SOFTWARE
LEU B:92 , LYS B:402 , ASN B:403
binding site for residue NO3 B 606
10
AD1
SOFTWARE
GLN B:305 , ILE B:306 , PHE B:309 , ARG B:310
binding site for residue NO3 B 607
11
AD2
SOFTWARE
GLN B:105 , HIS B:109 , PHE B:113 , ARG B:255 , HEM B:608
binding site for residue 3CJ B 609
12
AD3
SOFTWARE
ASP C:110 , THR C:184 , PHE C:186 , ASP C:188 , SER C:190
binding site for residue CA C 605
13
AD4
SOFTWARE
PHE C:309 , ARG C:310 , TRP C:529 , TRP C:530 , GLU C:531
binding site for residue NO3 C 606
14
AD5
SOFTWARE
LEU C:92 , LYS C:402 , ASN C:403
binding site for residue NO3 C 607
15
AD6
SOFTWARE
ALA C:44 , ARG C:45 , TRP C:46 , LEU C:47 , ASN C:341 , VAL C:342 , TRP C:452
binding site for residue NO3 C 608
16
AD7
SOFTWARE
GLN C:105 , ASP C:108 , HIS C:109 , PHE C:113 , ALA C:114 , ARG C:255 , GLU C:258 , HEM C:610
binding site for residue 3CJ C 609
17
AD8
SOFTWARE
ASP D:110 , THR D:184 , PHE D:186 , ASP D:188 , SER D:190
binding site for residue CA D 605
18
AD9
SOFTWARE
ALA D:44 , ARG D:45 , TRP D:46 , LEU D:47 , SER D:340 , ASN D:341 , VAL D:342 , MET D:446
binding site for residue NO3 D 606
19
AE1
SOFTWARE
LEU D:92 , LYS D:402 , ASN D:403
binding site for residue NO3 D 607
20
AE2
SOFTWARE
PHE D:309 , ARG D:310 , TRP D:529 , TRP D:530 , GLU D:531
binding site for residue NO3 D 608
21
AE3
SOFTWARE
GLN D:105 , HIS D:109 , PHE D:113 , ALA D:114 , ARG D:255 , GLU D:258 , HEM D:610
binding site for residue 3CJ D 609
22
AE4
SOFTWARE
ASN A:95 , GLN A:568 , HOH A:709 , HOH A:782 , HOH A:783 , HOH A:787
binding site for Mono-Saccharide NAG A 601 bound to ASN A 95
23
AE5
SOFTWARE
ASN A:205 , SER A:208 , ALA A:214 , VAL A:215 , GLN A:217 , HOH A:701 , HOH A:764 , HOH A:779
binding site for Mono-Saccharide NAG A 602 bound to ASN A 205
24
AE6
SOFTWARE
ASN A:241 , ALA A:244 , PHE D:70
binding site for Poly-Saccharide residues NAG A 603 through NAG A 604 bound to ASN A 241
25
AE7
SOFTWARE
ASN B:205 , SER B:208 , ALA B:214 , VAL B:215 , GLN B:217 , HOH B:759
binding site for Mono-Saccharide NAG B 601 bound to ASN B 205
26
AE8
SOFTWARE
ASN B:241 , ALA B:244 , TRP B:384 , PHE C:70 , LYS C:485
binding site for Poly-Saccharide residues NAG B 602 through NAG B 603 bound to ASN B 241
27
AE9
SOFTWARE
ASN C:95 , ILE C:315 , GLN C:568 , GLY D:5 , CYS D:6
binding site for Mono-Saccharide NAG C 601 bound to ASN C 95
28
AF1
SOFTWARE
ASN C:205 , LEU C:210 , ALA C:214 , VAL C:215 , GLN C:217 , HOH C:757 , HOH C:782
binding site for Mono-Saccharide NAG C 604 bound to ASN C 205
29
AF2
SOFTWARE
PHE B:70 , LYS B:485 , ASN C:241 , THR C:243 , ALA C:244 , TRP C:384 , HOH C:714 , HOH C:731 , HOH C:746 , HOH C:807
binding site for Poly-Saccharide residues NAG C 602 through NAG C 603 bound to ASN C 241
30
AF3
SOFTWARE
CYS C:6 , GLY C:7 , ASN D:95 , ILE D:315 , HOH D:776 , HOH D:784 , HOH D:800
binding site for Mono-Saccharide NAG D 601 bound to ASN D 95
31
AF4
SOFTWARE
SER B:201 , LEU B:206 , ASN D:205 , LEU D:212 , ALA D:214 , VAL D:215 , GLN D:217 , ARG D:278 , HOH D:750
binding site for Mono-Saccharide NAG D 602 bound to ASN D 205
32
AF5
SOFTWARE
ASN D:241 , ALA D:244 , TRP D:384 , HOH D:798
binding site for Poly-Saccharide residues NAG D 603 through NAG D 604 bound to ASN D 241
33
AF6
SOFTWARE
MET B:101 , GLY B:104 , GLN B:105 , ILE B:106 , VAL B:107 , HIS B:109 , ASP B:110 , ASP B:112 , PHE B:113 , ALA B:114 , GLU B:258 , GLN B:259 , THR B:344 , PHE B:347 , ARG B:348 , GLY B:350 , HIS B:351 , LEU B:417 , LEU B:433 , ILE B:436 , ARG B:440 , 3CJ B:609
binding site for Di-peptide HEM B 608 and ASP B 108
34
AF7
SOFTWARE
MET B:101 , GLY B:104 , GLN B:105 , ASP B:108 , ASP B:112 , PHE B:113 , ALA B:114 , ARG B:255 , ALA B:256 , SER B:257 , GLN B:259 , THR B:344 , PHE B:347 , ARG B:348 , GLY B:350 , HIS B:351 , PHE B:380 , PHE B:381 , LEU B:417 , LEU B:433 , ILE B:436 , ARG B:440 , 3CJ B:609
binding site for Di-peptide HEM B 608 and GLU B 258
35
AF8
SOFTWARE
MET C:101 , GLY C:104 , GLN C:105 , ASP C:108 , ASP C:112 , PHE C:113 , ALA C:114 , ARG C:255 , ALA C:256 , SER C:257 , GLN C:259 , TYR C:312 , THR C:344 , PHE C:347 , ARG C:348 , GLY C:350 , HIS C:351 , VAL C:354 , PHE C:380 , PHE C:381 , LEU C:433 , ILE C:436 , ARG C:440 , 3CJ C:609
binding site for Di-peptide HEM C 610 and GLU C 258
36
AF9
SOFTWARE
MET C:101 , GLY C:104 , GLN C:105 , ILE C:106 , VAL C:107 , HIS C:109 , ASP C:110 , LEU C:111 , ASP C:112 , PHE C:113 , ALA C:114 , GLU C:258 , TYR C:312 , THR C:344 , PHE C:347 , ARG C:348 , GLY C:350 , HIS C:351 , VAL C:354 , LEU C:433 , ILE C:436 , ARG C:440 , 3CJ C:609
binding site for Di-peptide HEM C 610 and ASP C 108
37
AG1
SOFTWARE
MET D:101 , GLY D:104 , GLN D:105 , ILE D:106 , VAL D:107 , HIS D:109 , ASP D:110 , LEU D:111 , ASP D:112 , PHE D:113 , ALA D:114 , ARG D:255 , GLU D:258 , THR D:344 , PHE D:347 , ARG D:348 , GLY D:350 , HIS D:351 , VAL D:354 , LEU D:433 , ILE D:436 , ASN D:437 , ARG D:440 , 3CJ D:609
binding site for Di-peptide HEM D 610 and ASP D 108
[
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
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 (419 KB)
Header - Asym.Unit
Biol.Unit 1 (108 KB)
Header - Biol.Unit 1
Biol.Unit 2 (107 KB)
Header - Biol.Unit 2
Biol.Unit 3 (108 KB)
Header - Biol.Unit 3
Biol.Unit 4 (108 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
5HPW
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help