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.
4TPR
Asym. Unit
Info
Asym.Unit (171 KB)
Biol.Unit 1 (166 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 TAU5 ANTIBODY FAB FRAGMENT
Authors
:
O. Cehlar, R. Skrabana, M. Novak
Date
:
09 Jun 14 (Deposition) - 29 Jul 15 (Release) - 29 Jul 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : H,L
Biol. Unit 1: H,L (1x)
Keywords
:
Immune System, Monoclonal Antibody
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
O. Cehlar, R. Skrabana, M. Novak
Structure Of Tau5 Antibody Fab Fragment
To Be Published
[
close entry info
]
Hetero Components
(7, 16)
Info
All Hetero Components
1a: 3,6,9,12,15,18,21,24,27,30,33,36-D... (33Oa)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
3a: SODIUM ION (NAa)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
4c: DI(HYDROXYETHYL)ETHER (PEGc)
4d: DI(HYDROXYETHYL)ETHER (PEGd)
4e: DI(HYDROXYETHYL)ETHER (PEGe)
5a: TETRAETHYLENE GLYCOL (PG4a)
5b: TETRAETHYLENE GLYCOL (PG4b)
6a: TRIETHYLENE GLYCOL (PGEa)
7a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
33O
1
Ligand/Ion
3,6,9,12,15,18,21,24,27,30,33,36-DODECAOXAOCTATRIACONTANE-1,38-DIOL
2
CL
5
Ligand/Ion
CHLORIDE ION
3
NA
1
Ligand/Ion
SODIUM ION
4
PEG
5
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
PG4
2
Ligand/Ion
TETRAETHYLENE GLYCOL
6
PGE
1
Ligand/Ion
TRIETHYLENE GLYCOL
7
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(16, 16)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN H:43 , LEU L:9 , TYR L:92 , GLY L:105 , LYS L:147 , PG4 L:302 , HOH L:545 , HOH L:561
binding site for residue PG4 L 301
02
AC2
SOFTWARE
GLU H:42 , LYS L:147 , ILE L:149 , TRP L:168 , PG4 L:301 , HOH L:498
binding site for residue PG4 L 302
03
AC3
SOFTWARE
LEU L:15 , ARG L:82
binding site for residue CL L 303
04
AC4
SOFTWARE
33O H:304 , ARG L:113
binding site for residue CL L 304
05
AC5
SOFTWARE
SER L:70 , LYS L:79
binding site for residue PGE L 305
06
AC6
SOFTWARE
HOH H:436 , ALA L:117 , PRO L:118 , THR L:119 , ASN L:142 , ASN L:143
binding site for residue NA L 306
07
AC7
SOFTWARE
GLY L:71 , SER L:72 , ASP L:156 , ARG L:193 , ASN L:195 , HOH L:401
binding site for residue PEG L 307
08
AC8
SOFTWARE
LYS L:50 , GLY L:62 , GLU L:86
binding site for residue PEG L 308
09
AC9
SOFTWARE
GLU H:42 , ASN L:166 , SER L:167 , TRP L:168 , HOH L:557
binding site for residue PEG L 309
10
AD1
SOFTWARE
HIS L:31 , SER L:32 , SER L:97 , HIS L:98 , VAL L:99 , ARG L:160 , GLN L:161 , ASN L:162 , TRS L:311 , HOH L:402 , HOH L:467
binding site for residue PEG L 310
11
AD2
SOFTWARE
ASN L:33 , GLY L:96 , PEG L:310 , HOH L:402
binding site for residue TRS L 311
12
AD3
SOFTWARE
TRP H:47 , PHE L:103
binding site for residue CL H 301
13
AD4
SOFTWARE
SER H:164 , ASN H:204 , LYS H:213 , HOH H:429
binding site for residue CL H 302
14
AD5
SOFTWARE
LYS H:151 , GLY H:152 , GLN H:179 , TYR H:183 , THR H:184 , HOH H:542
binding site for residue CL H 303
15
AD6
SOFTWARE
MET H:143 , ASN H:163 , SER H:164 , SER H:166 , LEU H:167 , GLY H:170 , THR H:190 , VAL H:191 , THR H:195 , THR H:200 , THR H:202 , LYS H:213 , ASP H:215 , HOH H:416 , HOH H:419 , HOH H:422 , HOH H:436 , HOH H:470 , HOH H:528 , HOH H:530 , ASP L:115 , ALA L:116 , ALA L:117 , ASN L:143 , THR L:205 , SER L:206 , CL L:304 , HOH L:405
binding site for residue 33O H 304
16
AD7
SOFTWARE
PRO H:41 , THR H:116 , HOH H:556
binding site for residue PEG H 305
[
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
(0, 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.
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 H
Chain L
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 (171 KB)
Header - Asym.Unit
Biol.Unit 1 (166 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
4TPR
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help