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Asym. Unit
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Asym.Unit (116 KB)
Biol.Unit 1 (109 KB)
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(1)
Title
:
MODE OF LIGAND BINDING AND ASSIGNMENT OF SUBSITES IN MAMMALIAN PEROXIDASES: CRYSTAL STRUCTURE OF LACTOPEROXIDASE COMPLEXES WITH ACETYL SALYCYLIC ACID, SALICYLHYDROXAMIC ACID AND BENZYLHYDROXAMIC ACID
Authors
:
A. K. Singh, N. Singh, M. Sinha, P. Kaur, A. Srinivasan, S. Sharma, T. P. S
Date
:
22 Feb 09 (Deposition) - 31 Mar 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.34
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Peroxidase, Heme, Oxidation, 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, N. Singh, M. Sinha, P. Kaur, A. Srinivasan, S. Sharma, T. P. Singh
Mode Of Ligand Binding And Assignment Of Subsites In Mammalian Peroxidases: Crystal Structure Of Lactoperoxidase Complexes With Acetyl Salycylic Acid, Salicylhydroxamic Aci And Benzylhydroxamic Acid
To Be Published
[
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Hetero Components
(8, 23)
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)
3h: IODIDE ION (IODh)
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)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
6a: THIOCYANATE ION (SCNa)
7a: PHOSPHOSERINE (SEPa)
8a: SALICYLHYDROXAMIC ACID (SHAa)
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
8
Ligand/Ion
IODIDE ION
4
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
5
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
SCN
1
Ligand/Ion
THIOCYANATE ION
7
SEP
1
Mod. Amino Acid
PHOSPHOSERINE
8
SHA
1
Ligand/Ion
SALICYLHYDROXAMIC ACID
[
close Hetero Component info
]
Sites
(21, 21)
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)
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 , GLU A:258 , THR A:344 , PHE A:347 , ARG A:348 , HIS A:351 , VAL A:354 , PHE A:380 , LEU A:417 , LEU A:433 , ILE A:436 , ARG A:440 , SHA A:617 , HOH A:646 , HOH A:733 , HOH A:740
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
TRP A:46 , VAL A:342
BINDING SITE FOR RESIDUE IOD A 607
04
AC4
SOFTWARE
ASN A:80 , HOH A:944
BINDING SITE FOR RESIDUE IOD A 608
05
AC5
SOFTWARE
ARG A:96 , ARG A:504
BINDING SITE FOR RESIDUE IOD A 609
06
AC6
SOFTWARE
PHE A:229
BINDING SITE FOR RESIDUE IOD A 610
07
AC7
SOFTWARE
GLU A:363 , ARG A:397
BINDING SITE FOR RESIDUE IOD A 612
08
AC8
SOFTWARE
LYS A:462 , THR A:463
BINDING SITE FOR RESIDUE IOD A 613
09
AC9
SOFTWARE
HIS A:565 , PHE A:567
BINDING SITE FOR RESIDUE IOD A 614
10
BC1
SOFTWARE
ARG A:202 , LYS A:474
BINDING SITE FOR RESIDUE SCN A 615
11
BC2
SOFTWARE
ASN A:95 , ILE A:315 , ARG A:504 , GLN A:568 , NAG A:597
BINDING SITE FOR RESIDUE NAG A 596
12
BC3
SOFTWARE
NAG A:596 , MAN A:598
BINDING SITE FOR RESIDUE NAG A 597
13
BC4
SOFTWARE
NAG A:597 , HOH A:919 , HOH A:934
BINDING SITE FOR RESIDUE MAN A 598
14
BC5
SOFTWARE
ASN A:205 , ALA A:214 , VAL A:215 , GLN A:217 , NAG A:600 , HOH A:809 , HOH A:927
BINDING SITE FOR RESIDUE NAG A 599
15
BC6
SOFTWARE
NAG A:599 , HOH A:909 , HOH A:941
BINDING SITE FOR RESIDUE NAG A 600
16
BC7
SOFTWARE
ASN A:241 , ALA A:244 , TRP A:384 , LYS A:388 , NAG A:602 , HOH A:911
BINDING SITE FOR RESIDUE NAG A 601
17
BC8
SOFTWARE
NAG A:601 , MAN A:603 , HOH A:911
BINDING SITE FOR RESIDUE NAG A 602
18
BC9
SOFTWARE
NAG A:602 , HOH A:917
BINDING SITE FOR RESIDUE MAN A 603
19
CC1
SOFTWARE
ASN A:332 , VAL A:335 , NAG A:616
BINDING SITE FOR RESIDUE NAG A 604
20
CC2
SOFTWARE
NAG A:604
BINDING SITE FOR RESIDUE NAG A 616
21
CC3
SOFTWARE
GLN A:105 , HIS A:109 , ARG A:255 , GLU A:258 , HEM A:605 , HOH A:646 , HOH A:821
BINDING SITE FOR RESIDUE SHA A 617
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
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
[
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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
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
[
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]
Atom Selection
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Protein
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Sidechain
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Solvent
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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