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...
Getting 'PROSITE' information from database.
4BSW
Biol. Unit 1
Info
Asym.Unit (160 KB)
Biol.Unit 1 (149 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT 2
Authors
:
M. D. L. Suits, T. Spreter, E. E. Cabrera, S. B. Dixit, P. I. Lario, D. K. Y. I. E. P. D'Angelo, M. J. Boulanger
Date
:
11 Jun 13 (Deposition) - 21 Aug 13 (Release) - 23 Sep 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Immune System, Bispecific, Scaffold, Antibody Engineering, Fc Domain, Igg, Igg1, Immunoglobulin G, Zymeworks Inc.
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. S. Von Kreudenstein, E. Escobar-Carbrera, P. I. Lario, I. D'Angelo, K. Brault, J. Kelly, Y. Durocher, J. Baardsnes, R. J. Woods, M. H. Xie, P. Girod, M. D. L. Suits, M. J. Boulanger, D. K. Y. Poon, G. Y. K. Ng, S. B. Dixit
Improving Biophysical Properties Of A Bispecific Antibody Scaffold To Aid Developability: Quality By Molecular Design
Mabs V. 5 646 2013
[
close entry info
]
Hetero Components
(7, 26)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
3a: ALPHA-L-FUCOSE (FUCa)
3b: ALPHA-L-FUCOSE (FUCb)
4a: BETA-D-GALACTOSE (GALa)
4b: BETA-D-GALACTOSE (GALb)
5a: IODIDE ION (IODa)
5b: IODIDE ION (IODb)
5c: IODIDE ION (IODc)
6a: ALPHA-D-MANNOSE (MANa)
6b: ALPHA-D-MANNOSE (MANb)
6c: ALPHA-D-MANNOSE (MANc)
6d: ALPHA-D-MANNOSE (MANd)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
7g: N-ACETYL-D-GLUCOSAMINE (NAGg)
7h: N-ACETYL-D-GLUCOSAMINE (NAGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
3
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
4
GAL
2
Ligand/Ion
BETA-D-GALACTOSE
5
IOD
3
Ligand/Ion
IODIDE ION
6
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
7
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:251 , HOH A:2165 , HOH A:2166
BINDING SITE FOR RESIDUE EDO A1446
02
AC2
SOFTWARE
ARG A:255
BINDING SITE FOR RESIDUE IOD A1447
03
AC3
SOFTWARE
NAG A:505
BINDING SITE FOR RESIDUE EDO A1449
04
AC4
SOFTWARE
SER A:254
BINDING SITE FOR RESIDUE IOD A1451
05
AC5
SOFTWARE
ILE B:377 , ALA B:378 , VAL B:379 , EDO B:1448 , HOH B:2128 , HOH B:2204
BINDING SITE FOR RESIDUE EDO B1446
06
AC6
SOFTWARE
PHE B:241 , LEU B:242 , LYS B:334 , BMA B:503 , NAG B:508
BINDING SITE FOR RESIDUE EDO B1447
07
AC7
SOFTWARE
PRO B:247 , SER B:375 , ASP B:376 , ILE B:377 , PRO B:396 , EDO B:1446 , HOH B:2122 , HOH B:2204
BINDING SITE FOR RESIDUE EDO B1448
08
AC8
SOFTWARE
PHE A:241 , PHE A:243 , PRO A:244 , LYS A:246 , GLU A:258 , THR A:260 , VAL A:264 , ASP A:265 , ASN A:297 , THR A:299 , ARG A:301 , EDO A:1449 , HOH A:2005 , HOH A:2006 , HOH A:2007 , HOH A:2021 , HOH A:2022 , HOH A:2037 , HOH A:2159 , HOH A:2160 , HOH A:2163 , HOH A:2164 , ASN B:384 , VAL B:422 , HOH B:2145 , HOH B:2147
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 500 THROUGH NAG A 508 BOUND TO ASN A 297
09
AC9
SOFTWARE
ASN A:384 , PHE B:243 , PRO B:244 , LYS B:246 , GLU B:258 , THR B:260 , VAL B:262 , VAL B:264 , ASP B:265 , GLU B:272 , GLN B:295 , TYR B:296 , ASN B:297 , ARG B:301 , MAN B:507 , EDO B:1447 , HOH B:2008 , HOH B:2203
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 500 THROUGH GAL B 506 BOUND TO ASN B 297
10
BC1
SOFTWARE
BMA B:503 , EDO B:1447
BINDING SITE FOR POLY-SACCHARIDE RESIDUES MAN B 507 THROUGH NAG B 508
[
close Site info
]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_003887 (D356E, chain A/B, )
2: VAR_003888 (L358M, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_003887
D
239
E
IGHG1_HUMAN
Unclassified
---
A/B
D
356
E
2
UniProt
VAR_003888
L
241
M
IGHG1_HUMAN
Unclassified
---
A/B
L
358
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (A:423-429,B:423-429)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
IGHG1_HUMAN
81-87
306-312
2
-
A:423-429
B:423-429
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d4bswa1 (A:236-341)
1b: SCOP_d4bswa2 (A:342-445)
1c: SCOP_d4bswb1 (B:236-341)
1d: SCOP_d4bswb2 (B:342-445)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Human (Homo sapiens) [TaxId: 9606]
(448)
1a
d4bswa1
A:236-341
1b
d4bswa2
A:342-445
1c
d4bswb1
B:236-341
1d
d4bswb2
B:342-445
[
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 A
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 (160 KB)
Header - Asym.Unit
Biol.Unit 1 (149 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
4BSW
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
