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3IB0
Asym. Unit
Info
Asym.Unit (76 KB)
Biol.Unit 1 (69 KB)
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(1)
Title
:
STRUCTURAL BASIS OF THE PREVENTION OF NSAID-INDUCED DAMAGE OF THE GASTROINTESTINAL TRACT BY C-TERMINAL HALF (C-LOBE) OF BOVINE COLOSTRUM PROTEIN LACTOFERRIN: BINDING AND STRUCTURAL STUDIES OF C-LOBE COMPLEX WITH DICLOFENAC
Authors
:
R. Mir, N. Singh, M. Sinha, S. Sharma, P. Kaur, A. Srinivasan, T. P. Singh
Date
:
15 Jul 09 (Deposition) - 11 Aug 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.40
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
C-Lobe, Drugs, Metal Binding Protein, Antibiotic, Antimicrobial, Disulfide Bond, Glycoprotein, Hydrolase, Ion Transport, Iron, Iron Transport, Metal-Binding, Phosphoprotein, Protease, Secreted, Serine Protease, Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Mir, N. Singh, G. Vikram, R. P. Kumar, M. Sinha, A. Bhushan, P. Kaur, A. Srinivasan, S. Sharma, T. P. Singh
The Structural Basis For The Prevention Of Nonsteroidal Antiinflammatory Drug-Induced Gastrointestinal Tract Damage By The C-Lobe Of Bovine Colostrum Lactoferrin.
Biophys. J. V. 97 3178 2009
[
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]
Hetero Components
(8, 21)
Info
All Hetero Components
1a: CARBONATE ION (CO3a)
2a: 2-[2,6-DICHLOROPHENYL)AMINO]BENZEN... (DIFa)
3a: ETHANOL (EOHa)
4a: FE (III) ION (FEa)
5a: ALPHA-D-MANNOSE (MANa)
5b: ALPHA-D-MANNOSE (MANb)
5c: ALPHA-D-MANNOSE (MANc)
5d: ALPHA-D-MANNOSE (MANd)
5e: ALPHA-D-MANNOSE (MANe)
5f: ALPHA-D-MANNOSE (MANf)
5g: ALPHA-D-MANNOSE (MANg)
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)
7a: SULFATE ION (SO4a)
7b: SULFATE ION (SO4b)
8a: ZINC ION (ZNa)
8b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CO3
1
Ligand/Ion
CARBONATE ION
2
DIF
1
Ligand/Ion
2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID
3
EOH
1
Ligand/Ion
ETHANOL
4
FE
1
Ligand/Ion
FE (III) ION
5
MAN
7
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
SO4
2
Ligand/Ion
SULFATE ION
8
ZN
2
Ligand/Ion
ZINC ION
[
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
ASP A:395 , TYR A:433 , TYR A:526 , HIS A:595 , CO3 A:687
BINDING SITE FOR RESIDUE FE A 999
02
AC2
SOFTWARE
ASP A:395 , TYR A:433 , THR A:459 , ARG A:463 , THR A:464 , ALA A:465 , GLY A:466 , TYR A:526 , HIS A:595 , FE A:999
BINDING SITE FOR RESIDUE CO3 A 687
03
AC3
SOFTWARE
HOH A:213 , HOH A:260 , PRO A:593 , GLU A:659 , TYR A:660 , GLY A:662 , THR A:663 , HOH A:793
BINDING SITE FOR RESIDUE DIF A 701
04
AC4
SOFTWARE
HOH A:55 , HOH A:139 , HOH A:152 , HOH A:265 , ARG A:570 , ARG A:578 , HOH A:723
BINDING SITE FOR RESIDUE SO4 A 1
05
AC5
SOFTWARE
TYR A:342 , THR A:343 , ARG A:603 , HIS A:606
BINDING SITE FOR RESIDUE SO4 A 2
06
AC6
SOFTWARE
GLU A:659 , HOH A:785
BINDING SITE FOR RESIDUE ZN A 688
07
AC7
SOFTWARE
HOH A:88 , HIS A:588 , HOH A:799 , HOH A:800
BINDING SITE FOR RESIDUE ZN A 689
08
AC8
SOFTWARE
HOH A:103 , HOH A:167 , HOH A:269 , HOH A:308 , TYR A:342 , SER A:365 , ASN A:368 , GLN A:614 , LEU A:617 , NAG A:691
BINDING SITE FOR RESIDUE NAG A 690
09
AC9
SOFTWARE
HOH A:103 , NAG A:690
BINDING SITE FOR RESIDUE NAG A 691
10
BC1
SOFTWARE
NAG A:4 , HOH A:134 , HOH A:309 , ASN A:476 , ASN A:671
BINDING SITE FOR RESIDUE NAG A 3
11
BC2
SOFTWARE
NAG A:3 , MAN A:5 , THR A:667 , ASN A:671 , HOH A:710
BINDING SITE FOR RESIDUE NAG A 4
12
BC3
SOFTWARE
NAG A:4 , MAN A:6 , MAN A:7
BINDING SITE FOR RESIDUE MAN A 5
13
BC4
SOFTWARE
MAN A:5 , HOH A:272
BINDING SITE FOR RESIDUE MAN A 6
14
BC5
SOFTWARE
MAN A:5
BINDING SITE FOR RESIDUE MAN A 7
15
BC6
SOFTWARE
NAG A:9 , LEU A:434 , ASN A:545 , ASP A:546 , TRP A:549 , HOH A:770 , HOH A:775 , HOH A:820 , HOH A:824
BINDING SITE FOR RESIDUE NAG A 8
16
BC7
SOFTWARE
NAG A:8 , MAN A:10 , HOH A:268 , SER A:418 , TRP A:549 , HOH A:734
BINDING SITE FOR RESIDUE NAG A 9
17
BC8
SOFTWARE
NAG A:9 , MAN A:11 , HOH A:207 , LYS A:416
BINDING SITE FOR RESIDUE MAN A 10
18
BC9
SOFTWARE
MAN A:10 , MAN A:12 , LYS A:419 , HIS A:420 , HOH A:854
BINDING SITE FOR RESIDUE MAN A 11
19
CC1
SOFTWARE
MAN A:11 , MAN A:13 , HOH A:836
BINDING SITE FOR RESIDUE MAN A 12
20
CC2
SOFTWARE
MAN A:12
BINDING SITE FOR RESIDUE MAN A 13
21
CC3
SOFTWARE
GLY A:479
BINDING SITE FOR RESIDUE EOH A 703
[
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
(4, 4)
Info
All PROSITE Patterns/Profiles
1: TRANSFERRIN_LIKE_4 (-|A:345-674)
2: TRANSFERRIN_LIKE_1 (-|A:433-442)
3: TRANSFERRIN_LIKE_2 (-|A:526-542)
4: TRANSFERRIN_LIKE_3 (-|A:568-598)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRANSFERRIN_LIKE_4
PS51408
Transferrin-like domain profile.
TRFL_BOVIN
25-352
364-693
1
-
A:345-674
2
TRANSFERRIN_LIKE_1
PS00205
Transferrin-like domain signature 1.
TRFL_BOVIN
111-120
452-461
1
-
A:433-442
3
TRANSFERRIN_LIKE_2
PS00206
Transferrin-like domain signature 2.
TRFL_BOVIN
211-227
545-561
1
-
A:526-542
4
TRANSFERRIN_LIKE_3
PS00207
Transferrin-like domain signature 3.
TRFL_BOVIN
245-275
587-617
1
-
A:568-598
[
close PROSITE info
]
Exons
(9, 9)
Info
All Exons
Exon 1.9 (A:342-385)
Exon 1.10 (A:386-416)
Exon 1.11 (A:416-432)
Exon 1.12 (A:432-484)
Exon 1.13 (A:484-531)
Exon 1.14 (A:531-554)
Exon 1.15 (A:554-615)
Exon 1.16 (A:616-676)
Exon 1.17 (A:681-686)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.8/1.9
02: Boundary 1.9/1.10
03: Boundary 1.10/1.11
04: Boundary 1.11/1.12
05: Boundary 1.12/1.13
06: Boundary 1.13/1.14
07: Boundary 1.14/1.15
08: Boundary 1.15/1.16
09: Boundary 1.16/1.17
10: Boundary 1.17/-
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
ENSBTAT00000001704
1
ENSBTAE00000406255
chr22:
54313830-54314011
182
TRFL_BOVIN
1-15
15
0
-
-
1.2
ENSBTAT00000001704
2
ENSBTAE00000391946
chr22:
54317754-54317917
164
TRFL_BOVIN
15-69
55
0
-
-
1.3
ENSBTAT00000001704
3
ENSBTAE00000378931
chr22:
54320894-54321002
109
TRFL_BOVIN
70-106
37
0
-
-
1.4
ENSBTAT00000001704
4
ENSBTAE00000247433
chr22:
54321299-54321481
183
TRFL_BOVIN
106-167
62
0
-
-
1.5
ENSBTAT00000001704
5
ENSBTAE00000013647
chr22:
54322098-54322245
148
TRFL_BOVIN
167-216
50
0
-
-
1.6
ENSBTAT00000001704
6
ENSBTAE00000247432
chr22:
54323189-54323244
56
TRFL_BOVIN
216-235
20
0
-
-
1.7
ENSBTAT00000001704
7
ENSBTAE00000013649
chr22:
54328592-54328770
179
TRFL_BOVIN
235-294
60
0
-
-
1.8
ENSBTAT00000001704
8
ENSBTAE00000013654
chr22:
54329198-54329372
175
TRFL_BOVIN
295-353
59
0
-
-
1.9
ENSBTAT00000001704
9
ENSBTAE00000013658
chr22:
54329898-54330052
155
TRFL_BOVIN
353-404
52
1
A:342-385
44
1.10
ENSBTAT00000001704
10
ENSBTAE00000013661
chr22:
54332009-54332099
91
TRFL_BOVIN
405-435
31
1
A:386-416
31
1.11
ENSBTAT00000001704
11
ENSBTAE00000013664
chr22:
54334326-54334373
48
TRFL_BOVIN
435-451
17
1
A:416-432
17
1.12
ENSBTAT00000001704
12
ENSBTAE00000013668
chr22:
54334997-54335152
156
TRFL_BOVIN
451-503
53
1
A:432-484
53
1.13
ENSBTAT00000001704
13
ENSBTAE00000013670
chr22:
54337061-54337202
142
TRFL_BOVIN
503-550
48
1
A:484-531
48
1.14
ENSBTAT00000001704
14
ENSBTAE00000013674
chr22:
54341961-54342028
68
TRFL_BOVIN
550-573
24
1
A:531-554
24
1.15
ENSBTAT00000001704
15
ENSBTAE00000013678
chr22:
54343949-54344133
185
TRFL_BOVIN
573-634
62
1
A:554-615
62
1.16
ENSBTAT00000001704
16
ENSBTAE00000429733
chr22:
54345264-54345453
190
TRFL_BOVIN
635-698
64
1
A:616-676
61
1.17
ENSBTAT00000001704
17
ENSBTAE00000407091
chr22:
54347010-54347235
226
TRFL_BOVIN
698-708
11
1
A:681-686
6
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3ib0a_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Periplasmic binding protein-like II
(813)
Superfamily
:
Periplasmic binding protein-like II
(813)
Family
:
automated matches
(267)
Protein domain
:
automated matches
(267)
Cow (Bos taurus) [TaxId: 9913]
(50)
1a
d3ib0a_
A:
[
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]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3ib0A01 (A:343-414,A:596-657)
1b: CATH_3ib0A02 (A:415-595,A:658-668)
View:
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Classes
(
)
(
)
Architectures
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
D-Maltodextrin-Binding Protein; domain 2
(600)
Homologous Superfamily
:
Periplasmic binding protein-like II
(486)
Bovine (Bos taurus)
(9)
1a
3ib0A01
A:343-414,A:596-657
1b
3ib0A02
A:415-595,A:658-668
[
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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 & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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Asym.Unit (76 KB)
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