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.
2DQV
Asym. Unit
Info
Asym.Unit (67 KB)
Biol.Unit 1 (61 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE C-TERMINAL LOBE OF BOVINE LACTOFERRIN IN COMPLEX WITH GALACTOSE AT 2.7 A RESOLUTION
Authors
:
R. Mir, N. Singh, M. Sinha, S. Sharma, A. Bhushan, T. P. Singh
Date
:
31 May 06 (Deposition) - 13 Jun 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Iron Transport Protein, Metal Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Mir, N. Singh, M. Sinha, S. Sharma, A. Bhushan, T. P. Singh
Structure Of The C-Terminal Lobe Of Bovine Lactoferrin In Complex With Galactose At 2. 7 A Resolution
To Be Published
[
close entry info
]
Hetero Components
(8, 17)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: CARBONATE ION (CO3a)
3a: FE (III) ION (FEa)
4a: BETA-D-GALACTOSE (GALa)
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)
7a: SULFATE ION (SO4a)
8a: ZINC ION (ZNa)
8b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
3
Ligand/Ion
BETA-D-MANNOSE
2
CO3
1
Ligand/Ion
CARBONATE ION
3
FE
1
Ligand/Ion
FE (III) ION
4
GAL
1
Ligand/Ion
BETA-D-GALACTOSE
5
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
7
SO4
1
Ligand/Ion
SULFATE ION
8
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:655 , GLU A:659
BINDING SITE FOR RESIDUE GAL A 3015
02
AC2
SOFTWARE
NAG A:2 , SER A:365 , ASN A:368 , HIS A:613 , GLN A:614 , LEU A:617
BINDING SITE FOR RESIDUE NAG A 1
03
AC3
SOFTWARE
NAG A:1
BINDING SITE FOR RESIDUE NAG A 2
04
AC4
SOFTWARE
NAG A:4 , ASN A:476 , ASN A:671 , HOH A:3048
BINDING SITE FOR RESIDUE NAG A 3
05
AC5
SOFTWARE
NAG A:3 , MAN A:5 , GLU A:664
BINDING SITE FOR RESIDUE NAG A 4
06
AC6
SOFTWARE
NAG A:4 , BMA A:6 , BMA A:7 , HOH A:3091
BINDING SITE FOR RESIDUE MAN A 5
07
AC7
SOFTWARE
MAN A:5 , BMA A:7
BINDING SITE FOR RESIDUE BMA A 6
08
AC8
SOFTWARE
MAN A:5 , BMA A:6 , HOH A:3105
BINDING SITE FOR RESIDUE BMA A 7
09
AC9
SOFTWARE
NAG A:9 , ASN A:545 , ASP A:546 , TRP A:549 , GLN A:585
BINDING SITE FOR RESIDUE NAG A 8
10
BC1
SOFTWARE
NAG A:8 , MAN A:10 , TRP A:549
BINDING SITE FOR RESIDUE NAG A 9
11
BC2
SOFTWARE
NAG A:9 , BMA A:11 , LYS A:416
BINDING SITE FOR RESIDUE MAN A 10
12
BC3
SOFTWARE
MAN A:10
BINDING SITE FOR RESIDUE BMA A 11
13
BC4
SOFTWARE
ASP A:395 , TYR A:433 , TYR A:526 , HIS A:595 , CO3 A:689
BINDING SITE FOR RESIDUE FE A 688
14
BC5
SOFTWARE
ASP A:395 , TYR A:433 , THR A:459 , ARG A:463 , ALA A:465 , GLY A:466 , TYR A:526 , HIS A:595 , FE A:688
BINDING SITE FOR RESIDUE CO3 A 689
15
BC6
SOFTWARE
GLU A:659
BINDING SITE FOR RESIDUE ZN A 3016
16
BC7
SOFTWARE
HIS A:588 , HOH A:3145
BINDING SITE FOR RESIDUE ZN A 3017
17
BC8
SOFTWARE
LYS A:441 , ARG A:570 , ARG A:578
BINDING SITE FOR RESIDUE SO4 A 3018
[
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
(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_d2dqva_ (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
d2dqva_
A:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2dqvA01 (A:343-414,A:596-657)
1b: CATH_2dqvA02 (A:415-595,A:658-668)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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)
Cattle (Bos taurus)
(37)
1a
2dqvA01
A:343-414,A:596-657
1b
2dqvA02
A:415-595,A:658-668
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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 (67 KB)
Header - Asym.Unit
Biol.Unit 1 (61 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
2DQV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help