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.
3Q9K
Asym. Unit
Info
Asym.Unit (122 KB)
Biol.Unit 1 (115 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 COMPLEXED WITH PHENYL ISOTHIOCYANATE AT 1.7 A RESOLUTION
Authors
:
N. Pandey, A. K. Singh, R. P. Singh, M. Sinha, P. Kaur, S. Sharma, T. P. Sin
Date
:
08 Jan 11 (Deposition) - 02 Mar 11 (Release) - 02 Mar 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Bovine Lactoperoxidase, Oxidoreductase, Phenyl Isothiocyanate, Iodide, Peg, Edman Reagent
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Pandey, A. K. Singh, R. P. Singh, M. Sinha, P. Kaur, S. Sharma, T. P. Singh
Crystal Structure Of Bovine Lactoperoxidase Complexed With Phenyl Isothiocyanate At 1. 7 A Resolution
To Be Published
[
close entry info
]
Hetero Components
(12, 29)
Info
All Hetero Components
01a: CALCIUM ION (CAa)
02a: 1,2-ETHANEDIOL (EDOa)
02b: 1,2-ETHANEDIOL (EDOb)
03a: PHENYLISOTHIOCYANATE (FTEa)
04a: GLYCEROL (GOLa)
05a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
06a: IODIDE ION (IODa)
06b: IODIDE ION (IODb)
06c: IODIDE ION (IODc)
06d: IODIDE ION (IODd)
06e: IODIDE ION (IODe)
06f: IODIDE ION (IODf)
06g: IODIDE ION (IODg)
06h: IODIDE ION (IODh)
06i: IODIDE ION (IODi)
06j: IODIDE ION (IODj)
06k: IODIDE ION (IODk)
06l: IODIDE ION (IODl)
07a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
08a: N-ACETYL-D-GLUCOSAMINE (NAGa)
08b: N-ACETYL-D-GLUCOSAMINE (NAGb)
08c: N-ACETYL-D-GLUCOSAMINE (NAGc)
08d: N-ACETYL-D-GLUCOSAMINE (NAGd)
08e: N-ACETYL-D-GLUCOSAMINE (NAGe)
09a: DI(HYDROXYETHYL)ETHER (PEGa)
09b: DI(HYDROXYETHYL)ETHER (PEGb)
10a: THIOCYANATE ION (SCNa)
11a: PHOSPHOSERINE (SEPa)
12a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
3
FTE
1
Ligand/Ion
PHENYLISOTHIOCYANATE
4
GOL
1
Ligand/Ion
GLYCEROL
5
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
6
IOD
12
Ligand/Ion
IODIDE ION
7
MPD
1
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
8
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
9
PEG
2
Ligand/Ion
DI(HYDROXYETHYL)ETHER
10
SCN
1
Ligand/Ion
THIOCYANATE ION
11
SEP
1
Mod. Amino Acid
PHOSPHOSERINE
12
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(28, 28)
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)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (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 606
02
AC2
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 , THR A:344 , PHE A:347 , ARG A:348 , GLY A:350 , HIS A:351 , VAL A:354 , PHE A:380 , LEU A:417 , GLN A:423 , LEU A:433 , ILE A:436 , ARG A:440 , FTE A:598 , HOH A:644 , HOH A:926 , HOH A:1093 , HOH A:1240
BINDING SITE FOR RESIDUE HEM A 605
03
AC3
SOFTWARE
ASN A:95 , ILE A:315 , HOH A:791 , HOH A:805
BINDING SITE FOR RESIDUE NAG A 596
04
AC4
SOFTWARE
ASN A:205 , SER A:208 , LEU A:210 , VAL A:215 , GLN A:217 , HOH A:835 , HOH A:1019
BINDING SITE FOR RESIDUE NAG A 599
05
AC5
SOFTWARE
ASN A:241 , ALA A:244 , TRP A:384 , NAG A:602 , HOH A:874 , HOH A:936 , HOH A:955 , HOH A:1087
BINDING SITE FOR RESIDUE NAG A 601
06
AC6
SOFTWARE
NAG A:601 , HOH A:873 , HOH A:874 , HOH A:924 , HOH A:936 , HOH A:1122 , HOH A:1156
BINDING SITE FOR RESIDUE NAG A 602
07
AC7
SOFTWARE
ASN A:332 , VAL A:335 , HOH A:671 , HOH A:674 , HOH A:1044 , HOH A:1134 , HOH A:1214
BINDING SITE FOR RESIDUE NAG A 604
08
AC8
SOFTWARE
TRP A:46 , VAL A:342
BINDING SITE FOR RESIDUE IOD A 607
09
AC9
SOFTWARE
ASN A:80
BINDING SITE FOR RESIDUE IOD A 608
10
BC1
SOFTWARE
ARG A:96 , HOH A:750
BINDING SITE FOR RESIDUE IOD A 609
11
BC2
SOFTWARE
TRP A:530
BINDING SITE FOR RESIDUE IOD A 611
12
BC3
SOFTWARE
ARG A:397
BINDING SITE FOR RESIDUE IOD A 612
13
BC4
SOFTWARE
PHE A:567 , HOH A:1060
BINDING SITE FOR RESIDUE IOD A 614
14
BC5
SOFTWARE
HOH A:1064
BINDING SITE FOR RESIDUE IOD A 618
15
BC6
SOFTWARE
ALA A:225 , HOH A:655
BINDING SITE FOR RESIDUE IOD A 620
16
BC7
SOFTWARE
SER A:359
BINDING SITE FOR RESIDUE IOD A 621
17
BC8
SOFTWARE
THR A:425
BINDING SITE FOR RESIDUE IOD A 622
18
BC9
SOFTWARE
LYS A:462
BINDING SITE FOR RESIDUE IOD A 623
19
CC1
SOFTWARE
GLU A:218 , PHE A:229
BINDING SITE FOR RESIDUE IOD A 629
20
CC2
SOFTWARE
HIS A:222 , HIS A:558 , HOH A:1307
BINDING SITE FOR RESIDUE ZN A 630
21
CC3
SOFTWARE
LEU A:36 , VAL A:335 , HOH A:1117 , HOH A:1223
BINDING SITE FOR RESIDUE GOL A 597
22
CC4
SOFTWARE
ASN A:230 , CYS A:248 , FTE A:598 , HOH A:930
BINDING SITE FOR RESIDUE SCN A 700
23
CC5
SOFTWARE
PHE A:254 , GLU A:258 , PHE A:381 , HEM A:605 , SCN A:700 , HOH A:1240
BINDING SITE FOR RESIDUE FTE A 598
24
CC6
SOFTWARE
ARG A:76 , ASN A:80 , PRO A:149 , LYS A:150 , ARG A:418 , ASN A:419 , HOH A:1158 , HOH A:1271
BINDING SITE FOR RESIDUE PEG A 610
25
CC7
SOFTWARE
ARG A:45 , TRP A:46 , LEU A:47 , PRO A:48 , HOH A:723 , HOH A:727 , HOH A:929 , HOH A:1285
BINDING SITE FOR RESIDUE PEG A 613
26
CC8
SOFTWARE
SEP A:198 , LEU A:199 , ARG A:202 , ASN A:473 , LYS A:474 , HOH A:767 , HOH A:1099 , HOH A:1281
BINDING SITE FOR RESIDUE MPD A 615
27
CC9
SOFTWARE
HIS A:377 , HIS A:429 , HOH A:642 , HOH A:1004
BINDING SITE FOR RESIDUE EDO A 616
28
DC1
SOFTWARE
SER A:33 , ALA A:35 , ARG A:41 , ARG A:338 , HOH A:841 , HOH A:1219
BINDING SITE FOR RESIDUE EDO A 617
[
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
(1, 1)
Info
all PFAM domains
1a: PFAM_An_peroxidase_3q9kA01 (A:21-567)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: An_peroxidase]
(45)
Family
:
An_peroxidase
(45)
Bos taurus (Bovine)
(11)
1a
An_peroxidase-3q9kA01
A:21-567
[
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 (122 KB)
Header - Asym.Unit
Biol.Unit 1 (115 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
3Q9K
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help