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.
2QQL
Biol. Unit 1
Info
Asym.Unit (165 KB)
Biol.Unit 1 (310 KB)
Biol.Unit 2 (158 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
NEUROPILIN-2 A1A2B1B2 DOMAINS IN COMPLEX WITH A SEMAPHORIN-BLOCKING FAB
Authors
:
B. A. Appleton, C. Wiesmann
Date
:
26 Jul 07 (Deposition) - 20 Nov 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,H,L
Biol. Unit 1: A,H,L (2x)
Biol. Unit 2: A,H,L (1x)
Keywords
:
Vegf Receptor, Semaphorin Receptor, Phage-Derived Antibody, Developmental Protein, Differentiation, Glycoprotein, Membrane, Neurogenesis, Transmembrane, Hormone, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. A. Appleton, P. Wu, J. Maloney, J. Yin, W. C. Liang, S. Stawicki, K. Mortara, K. K. Bowman, J. M. Elliott, W. Desmarais, J. F. Bazan, A. Bagri, M. Tessier-Lavigne, A. W. Koch, Y. Wu, R. J. Watts, C. Wiesman
Structural Studies Of Neuropilin/Antibody Complexes Provide Insights Into Semaphorin And Vegf Binding
Embo J. V. 26 4902 2007
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(5, 10)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_047754 (K123K, chain A, )
2: VAR_066403 (W148R, chain L, )
3: VAR_003897 (V191L, chain L, )
4: VAR_067537 (R334C, chain A, )
5: VAR_067538 (R428W, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_047754
R
123
K
NRP2_HUMAN
Polymorphism
849541
A
K
123
K
2
UniProt
VAR_066403
W
40
R
IGKC_HUMAN
Disease (IGKCD)
---
L
W
148
R
3
UniProt
VAR_003897
V
83
L
IGKC_HUMAN
Unclassified
---
L
V
191
L
4
UniProt
VAR_067537
R
334
C
NRP2_HUMAN
Polymorphism
114144673
A
R
334
C
5
UniProt
VAR_067538
R
428
W
NRP2_HUMAN
Polymorphism
139711818
A
R
428
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(6, 20)
Info
All PROSITE Patterns/Profiles
1: CUB (A:149-267)
2: IG_MHC (L:192-198)
3: FA58C_3 (A:434-592)
4: FA58C_1 (A:473-505)
5: FA58C_2 (A:575-592)
6: MAM_2 (A:601-601)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CUB
PS01180
CUB domain profile.
NRP2_HUMAN
28-142
149-267
4
A:28-142
A:149-267
2
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
IGKC_HUMAN
85-91
2
L:192-198
3
FA58C_3
PS50022
Coagulation factors 5/8 type C domain (FA58C) profile.
NRP2_HUMAN
277-427
434-592
4
A:277-427
A:434-592
4
FA58C_1
PS01285
Coagulation factors 5/8 type C domain (FA58C) signature 1.
NRP2_HUMAN
317-346
473-505
4
A:317-346
A:473-505
5
FA58C_2
PS01286
Coagulation factors 5/8 type C domain (FA58C) signature 2.
NRP2_HUMAN
411-427
575-592
4
A:411-427
A:575-592
6
MAM_2
PS50060
MAM domain profile.
NRP2_HUMAN
644-802
2
A:601-601
[
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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2qqll1 (L:1-106)
2a: SCOP_d2qqll2 (L:107-214)
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
d2qqll1
L:1-106
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Human (Homo sapiens) [TaxId: 9606]
(334)
2a
d2qqll2
L:107-214
[
close SCOP info
]
CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_2qqlL02 (L:109-214)
1b: CATH_2qqlH02 (H:114-216)
1c: CATH_2qqlH01 (H:1-113)
1d: CATH_2qqlL01 (L:1-108)
2a: CATH_2qqlA02 (A:147-274)
2b: CATH_2qqlA01 (A:26-146)
3a: CATH_2qqlA04 (A:432-601)
3b: CATH_2qqlA03 (A:275-431)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
2qqlL02
L:109-214
1b
2qqlH02
H:114-216
1c
2qqlH01
H:1-113
1d
2qqlL01
L:1-108
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.290, no name defined]
(10)
Human (Homo sapiens)
(7)
2a
2qqlA02
A:147-274
2b
2qqlA01
A:26-146
Homologous Superfamily
:
Galactose-binding domain-like
(195)
Human (Homo sapiens)
(39)
3a
2qqlA04
A:432-601
3b
2qqlA03
A:275-431
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_CUB_2qqlA01 (A:149-264)
1b: PFAM_CUB_2qqlA02 (A:149-264)
2a: PFAM_F5_F8_type_C_2qqlA03 (A:449-589)
2b: PFAM_F5_F8_type_C_2qqlA04 (A:449-589)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CUB
(11)
Family
:
CUB
(11)
Homo sapiens (Human)
(8)
1a
CUB-2qqlA01
A:149-264
1b
CUB-2qqlA02
A:149-264
Clan
:
GBD
(153)
Family
:
F5_F8_type_C
(45)
Homo sapiens (Human)
(10)
2a
F5_F8_type_C-2qqlA03
A:449-589
2b
F5_F8_type_C-2qqlA04
A:449-589
[
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 H
Chain L
Asymmetric Unit 1
Asymmetric Unit 2
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 (165 KB)
Header - Asym.Unit
Biol.Unit 1 (310 KB)
Header - Biol.Unit 1
Biol.Unit 2 (158 KB)
Header - Biol.Unit 2
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
2QQL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
