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.
3VE2
Biol. Unit 5
Info
Asym.Unit (371 KB)
Biol.Unit 1 (718 KB)
Biol.Unit 2 (718 KB)
Biol.Unit 3 (361 KB)
Biol.Unit 4 (183 KB)
Biol.Unit 5 (183 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE 2.1 ANGSTROM CRYSTAL STRUCTURE OF TRANSFERRIN BINDING PROTEIN B (TBPB) FROM SEROGROUP B M982 NEISSERIA MENINGITIDIS
Authors
:
C. Calmettes, T. F. Moraes
Date
:
06 Jan 12 (Deposition) - 22 Feb 12 (Release) - 05 Sep 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.14
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Biol. Unit 2: A,B (2x)
Biol. Unit 3: A,B (1x)
Biol. Unit 4: A (1x)
Biol. Unit 5: B (1x)
Keywords
:
Lipoprotein, Transferrin Receptor, Iron Acquisition, Vaccine Candidate, Host Pathogen Interaction, Beta Barrel, Receptor, Transferrin, Outermembrane, Transferrin-Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Calmettes, J. Alcantara, R. H. Yu, A. B. Schryvers, T. F. Moraes
The Structural Basis Of Transferrin Sequestration By Transferrin-Binding Protein B.
Nat. Struct. Mol. Biol. V. 19 358 2012
[
close entry info
]
Hetero Components
(2, 11)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
3a: SODIUM ION (NAa)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
-1
Ligand/Ion
ACETATE ION
2
GOL
5
Ligand/Ion
GLYCEROL
3
NA
-1
Ligand/Ion
SODIUM ION
4
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(15, 15)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC8 (SOFTWARE)
04: AC9 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC7 (SOFTWARE)
12: BC8 (SOFTWARE)
13: BC9 (SOFTWARE)
14: CC1 (SOFTWARE)
15: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:93 , ASP A:94 , GLY A:95 , SER A:97 , PHE A:150 , SER A:151 , HOH A:801 , HOH A:929 , HOH A:1031 , HOH B:888
BINDING SITE FOR RESIDUE GOL A 701
02
AC2
SOFTWARE
LYS A:194 , ACT A:708 , HOH A:855 , HOH A:923 , PRO B:54
BINDING SITE FOR RESIDUE GOL A 702
03
AC8
SOFTWARE
ARG A:50 , TRP A:52 , GLU A:57 , LYS A:207 , ARG A:211 , GOL A:702 , HOH A:820 , HOH A:855 , PRO B:54
BINDING SITE FOR RESIDUE ACT A 708
04
AC9
SOFTWARE
LYS A:207 , ARG A:211 , HOH A:980 , HOH A:981 , HOH A:1022 , TYR B:53 , LYS B:153 , HOH B:873
BINDING SITE FOR RESIDUE GOL B 701
05
BC1
SOFTWARE
ARG B:46 , HOH B:847 , HOH B:1024 , HOH B:1109
BINDING SITE FOR RESIDUE GOL B 702
06
BC2
SOFTWARE
LYS B:193 , LYS B:337 , HOH B:1078
BINDING SITE FOR RESIDUE GOL B 703
07
BC3
SOFTWARE
ASN B:131 , GLN B:133 , LYS B:345 , ASP B:348 , LYS B:349 , HOH B:1076
BINDING SITE FOR RESIDUE GOL B 704
08
BC4
SOFTWARE
HIS B:129 , LYS B:183 , LYS B:347 , HOH B:883
BINDING SITE FOR RESIDUE GOL B 705
09
BC5
SOFTWARE
HOH A:970 , ARG B:50 , TRP B:52 , GLU B:57 , LYS B:194 , ARG B:211 , HOH B:831 , HOH B:875
BINDING SITE FOR RESIDUE SO4 B 706
10
BC6
SOFTWARE
GLY B:178 , LYS B:179 , LYS B:232 , HIS B:273 , HOH B:834 , HOH B:1031 , HOH B:1032 , HOH B:1045 , HOH B:1046 , HOH B:1047 , HOH B:1068
BINDING SITE FOR RESIDUE SO4 B 707
11
BC7
SOFTWARE
TRP B:68 , GLU B:69 , ALA B:70 , HOH B:887
BINDING SITE FOR RESIDUE SO4 B 708
12
BC8
SOFTWARE
GLU B:58 , SER B:59 , GLU B:60
BINDING SITE FOR RESIDUE SO4 B 709
13
BC9
SOFTWARE
TYR A:53 , THR A:303 , ARG B:211 , HOH B:1075
BINDING SITE FOR RESIDUE SO4 B 710
14
CC1
SOFTWARE
THR B:75 , LYS B:82 , HOH B:856 , HOH B:1002
BINDING SITE FOR RESIDUE SO4 B 711
15
CC2
SOFTWARE
TYR B:41 , GLY B:72 , HOH B:941
BINDING SITE FOR RESIDUE NA B 712
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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 B
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 (371 KB)
Header - Asym.Unit
Biol.Unit 1 (718 KB)
Header - Biol.Unit 1
Biol.Unit 2 (718 KB)
Header - Biol.Unit 2
Biol.Unit 3 (361 KB)
Header - Biol.Unit 3
Biol.Unit 4 (183 KB)
Header - Biol.Unit 4
Biol.Unit 5 (183 KB)
Header - Biol.Unit 5
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
3VE2
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help