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3NYH
Asym. Unit
Info
Asym.Unit (125 KB)
Biol.Unit 1 (118 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF LACTOPEROXIDASE COMPLEXED SIMULTANEOUSLY WITH THIOCYANATE ION, IODIDE ION, BROMIDE ION, CHLORIDE ION THROUGH THE SUBSTRATE DIFFUSION CHANNEL REVEALS A PREFERENTIAL QUEUE OF THE INORGANIC SUBSTRATES TOWARDS THE DISTAL HEME CAVITY
Authors
:
N. Pandey, A. K. Singh, M. Sinha, P. Kaur, S. Sharma, T. P. Singh
Date
:
15 Jul 10 (Deposition) - 20 Oct 10 (Release) - 20 Oct 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.77
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Bovine Lactoperoxidase, Oxidoreductase, Bromide, Chloride, Iodide, Mpd, Thiocyanate Ion
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Pandey, A. K. Singh, M. Sinha, P. Kaur, S. Sharma, T. P. Singh
Crystal Structure Of Lactoperoxidase Complexed Simultaneously With Thiocyanate Ion, Iodide Ion, Bromide Ion, Chloride Ion Through The Substrate Diffusion Channel Reveals A Preferential Queue Of The Inorganic Substrates Towards The Distal Heme Cavity
To Be Published
[
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Hetero Components
(14, 35)
Info
All Hetero Components
01a: BROMIDE ION (BRa)
02a: CALCIUM ION (CAa)
03a: CHLORIDE ION (CLa)
04a: 1,2-ETHANEDIOL (EDOa)
05a: GLYCEROL (GOLa)
05b: GLYCEROL (GOLb)
05c: GLYCEROL (GOLc)
06a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
07a: IODIDE ION (IODa)
07b: IODIDE ION (IODb)
07c: IODIDE ION (IODc)
07d: IODIDE ION (IODd)
07e: IODIDE ION (IODe)
07f: IODIDE ION (IODf)
07g: IODIDE ION (IODg)
07h: IODIDE ION (IODh)
07i: IODIDE ION (IODi)
07j: IODIDE ION (IODj)
07k: IODIDE ION (IODk)
07l: IODIDE ION (IODl)
07m: IODIDE ION (IODm)
07n: IODIDE ION (IODn)
07o: IODIDE ION (IODo)
08a: ALPHA-D-MANNOSE (MANa)
09a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
10a: N-ACETYL-D-GLUCOSAMINE (NAGa)
10b: N-ACETYL-D-GLUCOSAMINE (NAGb)
10c: N-ACETYL-D-GLUCOSAMINE (NAGc)
10d: N-ACETYL-D-GLUCOSAMINE (NAGd)
10e: N-ACETYL-D-GLUCOSAMINE (NAGe)
10f: N-ACETYL-D-GLUCOSAMINE (NAGf)
11a: DI(HYDROXYETHYL)ETHER (PEGa)
12a: THIOCYANATE ION (SCNa)
13a: PHOSPHOSERINE (SEPa)
14a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BR
1
Ligand/Ion
BROMIDE ION
2
CA
1
Ligand/Ion
CALCIUM ION
3
CL
1
Ligand/Ion
CHLORIDE ION
4
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
5
GOL
3
Ligand/Ion
GLYCEROL
6
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
7
IOD
15
Ligand/Ion
IODIDE ION
8
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
9
MPD
1
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
10
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
11
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
12
SCN
1
Ligand/Ion
THIOCYANATE ION
13
SEP
1
Mod. Amino Acid
PHOSPHOSERINE
14
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(32, 32)
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)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (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 , THR A:344 , PHE A:347 , ARG A:348 , GLY A:350 , HIS A:351 , VAL A:354 , LEU A:417 , LEU A:433 , ILE A:436 , ARG A:440 , BR A:597 , HOH A:790 , HOH A:1110 , HOH A:1136
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 , ARG A:96 , PRO A:209 , ILE A:315 , IOD A:609 , HOH A:664 , HOH A:1265
BINDING SITE FOR RESIDUE NAG A 596
04
AC4
SOFTWARE
ASN A:205 , SER A:208 , ALA A:214 , VAL A:215 , GLN A:217 , NAG A:600 , HOH A:1015 , HOH A:1147
BINDING SITE FOR RESIDUE NAG A 599
05
AC5
SOFTWARE
NAG A:599 , HOH A:1188 , HOH A:1198
BINDING SITE FOR RESIDUE NAG A 600
06
AC6
SOFTWARE
ASN A:241 , ALA A:244 , TRP A:384 , NAG A:602 , GOL A:615 , HOH A:648 , HOH A:861 , HOH A:987 , HOH A:1041 , HOH A:1049
BINDING SITE FOR RESIDUE NAG A 601
07
AC7
SOFTWARE
NAG A:601 , MAN A:603 , HOH A:648 , HOH A:948 , HOH A:987 , HOH A:1049 , HOH A:1126
BINDING SITE FOR RESIDUE NAG A 602
08
AC8
SOFTWARE
NAG A:602 , HOH A:1096 , HOH A:1227 , HOH A:1254
BINDING SITE FOR RESIDUE MAN A 603
09
AC9
SOFTWARE
ASN A:332 , VAL A:335 , HOH A:940 , HOH A:1100
BINDING SITE FOR RESIDUE NAG A 604
10
BC1
SOFTWARE
TRP A:46 , VAL A:342
BINDING SITE FOR RESIDUE IOD A 607
11
BC2
SOFTWARE
ASN A:80
BINDING SITE FOR RESIDUE IOD A 608
12
BC3
SOFTWARE
ARG A:96 , NAG A:596
BINDING SITE FOR RESIDUE IOD A 609
13
BC4
SOFTWARE
GLN A:217
BINDING SITE FOR RESIDUE IOD A 610
14
BC5
SOFTWARE
TRP A:530
BINDING SITE FOR RESIDUE IOD A 611
15
BC6
SOFTWARE
ARG A:397 , THR A:560
BINDING SITE FOR RESIDUE IOD A 612
16
BC7
SOFTWARE
HIS A:565 , ALA A:566 , PHE A:567
BINDING SITE FOR RESIDUE IOD A 614
17
BC8
SOFTWARE
GLU A:88 , VAL A:91 , PRO A:355 , SER A:356 , HOH A:888
BINDING SITE FOR RESIDUE IOD A 616
18
BC9
SOFTWARE
ALA A:225 , HOH A:1115 , HOH A:1328
BINDING SITE FOR RESIDUE IOD A 620
19
CC1
SOFTWARE
SER A:359
BINDING SITE FOR RESIDUE IOD A 621
20
CC2
SOFTWARE
THR A:425
BINDING SITE FOR RESIDUE IOD A 622
21
CC3
SOFTWARE
LYS A:462
BINDING SITE FOR RESIDUE IOD A 623
22
CC4
SOFTWARE
HOH A:690
BINDING SITE FOR RESIDUE IOD A 624
23
CC5
SOFTWARE
ARG A:255 , GLU A:258 , HEM A:605 , HOH A:1150
BINDING SITE FOR RESIDUE BR A 597
24
CC6
SOFTWARE
PHE A:254 , PHE A:381
BINDING SITE FOR RESIDUE CL A 598
25
CC7
SOFTWARE
SER A:235 , GLU A:238 , PHE A:239 , THR A:242 , ARG A:245
BINDING SITE FOR RESIDUE GOL A 613
26
CC8
SOFTWARE
ILE A:240 , THR A:242 , THR A:243 , NAG A:601 , HOH A:687
BINDING SITE FOR RESIDUE GOL A 615
27
CC9
SOFTWARE
HIS A:377 , THR A:378 , HIS A:429 , HOH A:689
BINDING SITE FOR RESIDUE GOL A 617
28
DC1
SOFTWARE
ARG A:76 , ASN A:80 , PRO A:149 , ARG A:418 , ASN A:419 , HOH A:694 , HOH A:763 , HOH A:1083 , HOH A:1389
BINDING SITE FOR RESIDUE PEG A 625
29
DC2
SOFTWARE
PRO A:197 , SER A:201 , ARG A:204 , LYS A:472 , HOH A:841 , HOH A:907 , HOH A:1139 , HOH A:1344
BINDING SITE FOR RESIDUE MPD A 626
30
DC3
SOFTWARE
ASP A:362 , GLU A:363
BINDING SITE FOR RESIDUE EDO A 627
31
DC4
SOFTWARE
HIS A:222 , HIS A:558 , HOH A:1016
BINDING SITE FOR RESIDUE ZN A 628
32
DC5
SOFTWARE
ASN A:230 , CYS A:248 , HOH A:1134
BINDING SITE FOR RESIDUE SCN A 629
[
close Site info
]
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
[
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
[
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]
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
(1, 1)
Info
all PFAM domains
1a: PFAM_An_peroxidase_3nyhA01 (A:21-567)
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Clans
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)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: An_peroxidase]
(45)
Family
:
An_peroxidase
(45)
Bos taurus (Bovine)
(11)
1a
An_peroxidase-3nyhA01
A:21-567
[
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Asymmetric Unit 1
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