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3GCL
Asym. Unit
Info
Asym.Unit (115 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, A. Bhushan, P. Kaur, S. Sharma, T. P. Sing
Date
:
22 Feb 09 (Deposition) - 31 Mar 09 (Release) - 17 Feb 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Peroxidase, Oxidoreductase, Antibiotic, Antimicrobial, Cleavage On Pair Of Basic Residues, Glycoprotein, Heme, Hydrogen Peroxide, Iron, Metal-Binding, Secreted
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. K. Singh, N. Singh, M. Sinha, A. Bhushan, P. Kaur, A. Srinivasan, S. Sharma, T. P. Singh
Binding Modes Of Aromatic Ligands To Mammalian Heme Peroxidases With Associated Functional Implications: Crysta Structures Of Lactoperoxidase Complexes With Acetylsalicyli Acid, Salicylhydroxamic Acid, And Benzylhydroxamic Acid
J. Biol. Chem. V. 284 20311 2009
[
close entry info
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Hetero Components
(8, 23)
Info
All Hetero Components
1a: 2-(ACETYLOXY)BENZOIC ACID (AINa)
2a: CALCIUM ION (CAa)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
4a: IODIDE ION (IODa)
4b: IODIDE ION (IODb)
4c: IODIDE ION (IODc)
4d: IODIDE ION (IODd)
4e: IODIDE ION (IODe)
4f: IODIDE ION (IODf)
4g: IODIDE ION (IODg)
4h: IODIDE ION (IODh)
5a: ALPHA-D-MANNOSE (MANa)
5b: ALPHA-D-MANNOSE (MANb)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6g: N-ACETYL-D-GLUCOSAMINE (NAGg)
6h: N-ACETYL-D-GLUCOSAMINE (NAGh)
7a: THIOCYANATE ION (SCNa)
8a: PHOSPHOSERINE (SEPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AIN
1
Ligand/Ion
2-(ACETYLOXY)BENZOIC ACID
2
CA
1
Ligand/Ion
CALCIUM ION
3
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
IOD
8
Ligand/Ion
IODIDE ION
5
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
SCN
1
Ligand/Ion
THIOCYANATE ION
8
SEP
1
Mod. Amino Acid
PHOSPHOSERINE
[
close Hetero Component info
]
Sites
(22, 22)
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)
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 , GLY A:350 , HIS A:351 , VAL A:354 , PHE A:380 , LEU A:417 , LEU A:433 , ILE A:436 , ARG A:440 , AIN A:609 , HOH A:618 , HOH A:632
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
ASN A:95 , ILE A:315 , ARG A:504 , NAG A:597
BINDING SITE FOR RESIDUE NAG A 596
04
AC4
SOFTWARE
NAG A:596 , MAN A:598
BINDING SITE FOR RESIDUE NAG A 597
05
AC5
SOFTWARE
NAG A:597 , HOH A:859
BINDING SITE FOR RESIDUE MAN A 598
06
AC6
SOFTWARE
ASN A:205 , SER A:208 , LEU A:210 , VAL A:215 , GLN A:217 , NAG A:600 , HOH A:876
BINDING SITE FOR RESIDUE NAG A 599
07
AC7
SOFTWARE
NAG A:599 , HOH A:770
BINDING SITE FOR RESIDUE NAG A 600
08
AC8
SOFTWARE
ASN A:241 , ALA A:244 , TRP A:384 , LYS A:388 , NAG A:602 , HOH A:868
BINDING SITE FOR RESIDUE NAG A 601
09
AC9
SOFTWARE
NAG A:601 , MAN A:603
BINDING SITE FOR RESIDUE NAG A 602
10
BC1
SOFTWARE
NAG A:602 , HOH A:893
BINDING SITE FOR RESIDUE MAN A 603
11
BC2
SOFTWARE
ASN A:332 , VAL A:335 , NAG A:607 , HOH A:763 , HOH A:837 , HOH A:933
BINDING SITE FOR RESIDUE NAG A 604
12
BC3
SOFTWARE
NAG A:604 , HOH A:708 , HOH A:837 , HOH A:920
BINDING SITE FOR RESIDUE NAG A 607
13
BC4
SOFTWARE
ARG A:202 , LYS A:474
BINDING SITE FOR RESIDUE SCN A 608
14
BC5
SOFTWARE
HIS A:109 , ARG A:255 , GLU A:258 , PHE A:381 , PHE A:422 , GLN A:423 , PRO A:424 , HEM A:605 , HOH A:618 , HOH A:794 , HOH A:936
BINDING SITE FOR RESIDUE AIN A 609
15
BC6
SOFTWARE
TRP A:46 , VAL A:342
BINDING SITE FOR RESIDUE IOD A 610
16
BC7
SOFTWARE
ASN A:80 , PRO A:145
BINDING SITE FOR RESIDUE IOD A 611
17
BC8
SOFTWARE
ARG A:504
BINDING SITE FOR RESIDUE IOD A 612
18
BC9
SOFTWARE
PHE A:229
BINDING SITE FOR RESIDUE IOD A 613
19
CC1
SOFTWARE
TRP A:530
BINDING SITE FOR RESIDUE IOD A 614
20
CC2
SOFTWARE
GLU A:363 , ARG A:397
BINDING SITE FOR RESIDUE IOD A 615
21
CC3
SOFTWARE
LYS A:462 , THR A:463
BINDING SITE FOR RESIDUE IOD A 616
22
CC4
SOFTWARE
HIS A:565
BINDING SITE FOR RESIDUE IOD 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
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Atom Selection
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Protein
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Sidechain
Hetero
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Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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