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.
3GC1
Asym. Unit
Info
Asym.Unit (116 KB)
Biol.Unit 1 (108 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF BOVINE LACTOPEROXIDASE
Authors
:
A. K. Singh, N. Singh, M. Sinha, P. Kaur, A. Srinivasan, S. Sharma, T. P. S
Date
:
21 Feb 09 (Deposition) - 31 Mar 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Peroxidase, Heme, Oxidoreductase, Antibiotic, Antimicrobial, Cleavage On Pair Of Basic Residues, Glycoprotein, Hydrogen Peroxide, Iron, Metal-Binding, Secreted
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. K. Singh, R. P. Kumar, N. Pandey, N. Singh, M. Sinha, A. Bhushan, P. Kaur, S. Sharma, T. P. Singh
Mode Of Binding Of The Tuberculosis Prodrug Isoniazid To Heme Peroxidases: Binding Studies And Crystal Structure Of Bovine Lactoperoxidase With Isoniazid At 2. 7 A Resolution.
J. Biol. Chem. V. 285 1569 2010
[
close entry info
]
Hetero Components
(8, 21)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3a: IODIDE ION (IODa)
3b: IODIDE ION (IODb)
3c: IODIDE ION (IODc)
3d: IODIDE ION (IODd)
3e: IODIDE ION (IODe)
3f: IODIDE ION (IODf)
3g: IODIDE ION (IODg)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
6b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
7a: THIOCYANATE ION (SCNa)
8a: PHOSPHOSERINE (SEPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
IOD
7
Ligand/Ion
IODIDE ION
4
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
NDG
2
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
7
SCN
1
Ligand/Ion
THIOCYANATE ION
8
SEP
1
Mod. Amino Acid
PHOSPHOSERINE
[
close Hetero Component info
]
Sites
(19, 19)
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: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MET A:101 , GLY A:104 , GLN A:105 , ASP A:108 , ASP A:112 , PHE A:113 , ALA A:114 , ARG A:255 , GLU A:258 , GLN A:259 , PHE A:347 , ARG A:348 , HIS A:351 , VAL A:354 , LEU A:417 , GLN A:423 , LEU A:433 , ILE A:436 , ARG A:440 , HOH A:616 , HOH A:855
BINDING SITE FOR RESIDUE HEM A 605
02
AC2
SOFTWARE
ASP A:110 , THR A:184 , PHE A:186 , ASP A:188 , SER A:190
BINDING SITE FOR RESIDUE CA A 606
03
AC3
SOFTWARE
ARG A:202 , LYS A:474
BINDING SITE FOR RESIDUE SCN A 615
04
AC4
SOFTWARE
ASN A:95 , ARG A:504 , GLN A:568 , NAG A:597 , HOH A:895
BINDING SITE FOR RESIDUE NDG A 596
05
AC5
SOFTWARE
ARG A:504 , NDG A:596 , MAN A:598
BINDING SITE FOR RESIDUE NAG A 597
06
AC6
SOFTWARE
NAG A:597
BINDING SITE FOR RESIDUE MAN A 598
07
AC7
SOFTWARE
ASN A:205 , LEU A:212 , ALA A:214 , VAL A:215 , GLN A:217 , NAG A:600
BINDING SITE FOR RESIDUE NAG A 599
08
AC8
SOFTWARE
GLN A:217 , NAG A:599 , HOH A:835
BINDING SITE FOR RESIDUE NAG A 600
09
AC9
SOFTWARE
ASN A:241 , ALA A:244 , TRP A:384 , LYS A:388 , NAG A:602
BINDING SITE FOR RESIDUE NDG A 601
10
BC1
SOFTWARE
NDG A:601 , MAN A:603 , HOH A:755
BINDING SITE FOR RESIDUE NAG A 602
11
BC2
SOFTWARE
NAG A:602 , HOH A:659
BINDING SITE FOR RESIDUE MAN A 603
12
BC3
SOFTWARE
ASN A:332 , NAG A:607 , HOH A:854 , HOH A:893
BINDING SITE FOR RESIDUE NAG A 604
13
BC4
SOFTWARE
NAG A:604 , HOH A:904
BINDING SITE FOR RESIDUE NAG A 607
14
BC5
SOFTWARE
TRP A:46 , VAL A:342 , TRP A:452
BINDING SITE FOR RESIDUE IOD A 608
15
BC6
SOFTWARE
ASN A:80 , PRO A:145
BINDING SITE FOR RESIDUE IOD A 609
16
BC7
SOFTWARE
PRO A:424 , HOH A:717
BINDING SITE FOR RESIDUE IOD A 610
17
BC8
SOFTWARE
THR A:560
BINDING SITE FOR RESIDUE IOD A 612
18
BC9
SOFTWARE
PHE A:229
BINDING SITE FOR RESIDUE IOD A 613
19
CC1
SOFTWARE
HIS A:377
BINDING SITE FOR RESIDUE IOD A 614
[
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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PEROXIDASE_3 (A:12-594)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEROXIDASE_3
PS50292
Animal heme peroxidase superfamily profile.
PERL_BOVIN
129-711
1
A:12-594
[
close PROSITE info
]
Exons
(9, 9)
Info
All Exons
Exon 1.5 (A:1-31)
Exon 1.6 (A:31-74)
Exon 1.7 (A:75-143)
Exon 1.8 (A:144-252)
Exon 1.9 (A:252-305)
Exon 1.10 (A:306-390)
Exon 1.11 (A:390-448)
Exon 1.12 (A:448-527)
Exon 1.13 (A:527-595)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.4/1.5
02: Boundary 1.5/1.6
03: Boundary 1.6/1.7
04: Boundary 1.7/1.8
05: Boundary 1.8/1.9
06: Boundary 1.9/1.10
07: Boundary 1.10/1.11
08: Boundary 1.11/1.12
09: Boundary 1.12/1.13
10: Boundary 1.13/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENSBTAT00000016986
1
ENSBTAE00000279445
chr19:
8430632-8430751
120
PERL_BOVIN
-
0
0
-
-
1.2
ENSBTAT00000016986
2
ENSBTAE00000137885
chr19:
8435757-8435834
78
PERL_BOVIN
1-26
26
0
-
-
1.3
ENSBTAT00000016986
3
ENSBTAE00000137889
chr19:
8437178-8437265
88
PERL_BOVIN
26-55
30
0
-
-
1.4
ENSBTAT00000016986
4
ENSBTAE00000137892
chr19:
8441906-8442066
161
PERL_BOVIN
55-109
55
0
-
-
1.5
ENSBTAT00000016986
5
ENSBTAE00000137896
chr19:
8443636-8443753
118
PERL_BOVIN
109-148
40
1
A:1-31
31
1.6
ENSBTAT00000016986
6
ENSBTAE00000137903
chr19:
8444165-8444294
130
PERL_BOVIN
148-191
44
1
A:31-74
44
1.7
ENSBTAT00000016986
7
ENSBTAE00000137906
chr19:
8445032-8445238
207
PERL_BOVIN
192-260
69
1
A:75-143
69
1.8
ENSBTAT00000016986
8
ENSBTAE00000137912
chr19:
8446677-8447001
325
PERL_BOVIN
261-369
109
1
A:144-252
109
1.9
ENSBTAT00000016986
9
ENSBTAE00000137915
chr19:
8448604-8448764
161
PERL_BOVIN
369-422
54
1
A:252-305
54
1.10
ENSBTAT00000016986
10
ENSBTAE00000137918
chr19:
8457180-8457432
253
PERL_BOVIN
423-507
85
1
A:306-390
85
1.11
ENSBTAT00000016986
11
ENSBTAE00000137921
chr19:
8458505-8458678
174
PERL_BOVIN
507-565
59
1
A:390-448
59
1.12
ENSBTAT00000016986
12
ENSBTAE00000137923
chr19:
8459302-8459539
238
PERL_BOVIN
565-644
80
1
A:448-527
80
1.13
ENSBTAT00000016986
13
ENSBTAE00000279432
chr19:
8459727-8460382
656
PERL_BOVIN
644-712
69
1
A:527-595
69
[
close EXON info
]
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
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 (116 KB)
Header - Asym.Unit
Biol.Unit 1 (108 KB)
Header - Biol.Unit 1
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
3GC1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
