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.
4XL1
Asym. Unit
Info
Asym.Unit (250 KB)
Biol.Unit 1 (120 KB)
Biol.Unit 2 (121 KB)
Biol.Unit 3 (236 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
COMPLEX OF NOTCH1 (EGF11-13) BOUND TO DELTA-LIKE 4 (N-EGF1)
Authors
:
V. C. Luca, K. M. Jude, K. C. Garcia
Date
:
13 Jan 15 (Deposition) - 04 Mar 15 (Release) - 11 Mar 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,D,E
Biol. Unit 1: A,B (1x)
Biol. Unit 2: D,E (1x)
Biol. Unit 3: A,B,D,E (1x)
Keywords
:
Glycosylation, Egf Domains, Receptor-Ligand Complex, Protein Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. C. Luca, K. M. Jude, N. W. Pierce, M. V. Nachury, S. Fischer, K. C. Garcia
Structural Biology. Structural Basis For Notch1 Engagement Of Delta-Like 4.
Science V. 347 847 2015
[
close entry info
]
Hetero Components
(5, 34)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
1b: BETA-D-GLUCOSE (BGCb)
1c: BETA-D-GLUCOSE (BGCc)
1d: BETA-D-GLUCOSE (BGCd)
1e: BETA-D-GLUCOSE (BGCe)
1f: BETA-D-GLUCOSE (BGCf)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
3a: ALPHA-L-FUCOSE (FUCa)
3b: ALPHA-L-FUCOSE (FUCb)
4a: N-DIMETHYL-LYSINE (MLYa)
4b: N-DIMETHYL-LYSINE (MLYb)
4c: N-DIMETHYL-LYSINE (MLYc)
4d: N-DIMETHYL-LYSINE (MLYd)
4e: N-DIMETHYL-LYSINE (MLYe)
4f: N-DIMETHYL-LYSINE (MLYf)
4g: N-DIMETHYL-LYSINE (MLYg)
4h: N-DIMETHYL-LYSINE (MLYh)
4i: N-DIMETHYL-LYSINE (MLYi)
4j: N-DIMETHYL-LYSINE (MLYj)
4k: N-DIMETHYL-LYSINE (MLYk)
4l: N-DIMETHYL-LYSINE (MLYl)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
6
Ligand/Ion
BETA-D-GLUCOSE
2
CA
6
Ligand/Ion
CALCIUM ION
3
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
4
MLY
12
Mod. Amino Acid
N-DIMETHYL-LYSINE
5
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(20, 20)
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)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:415 , SER A:435 , PHE A:436 , HOH A:714 , HOH A:734 , ASP B:218 , GLU E:51
binding site for residue BGC A 601
02
AC2
SOFTWARE
ASP A:452 , VAL A:453 , GLU A:455 , ASP A:469 , GLN A:470 , HOH A:729 , HOH A:740
binding site for residue CA A 605
03
AC3
SOFTWARE
ASN A:490 , THR A:491 , GLU A:493 , ASP A:507 , LYS A:508 , HOH A:702 , HOH A:727
binding site for residue CA A 606
04
AC4
SOFTWARE
GLU A:415 , ASN A:431 , THR A:432 , LEU A:433 , GLY A:434 , SER A:435 , HOH A:773
binding site for residue CA A 607
05
AC5
SOFTWARE
ASN D:490 , THR D:491 , GLU D:493 , ASP D:507 , LYS D:508 , HOH D:717
binding site for residue CA D 605
06
AC6
SOFTWARE
ASP D:452 , VAL D:453 , GLU D:455 , ASP D:469 , GLN D:470 , HOH D:715 , HOH D:718
binding site for residue CA D 606
07
AC7
SOFTWARE
ASP D:412 , VAL D:413 , GLU D:415 , ASN D:431 , THR D:432 , LEU D:433 , GLY D:434 , SER D:435
binding site for residue CA D 607
08
AC8
SOFTWARE
GLU A:455 , SER A:458 , PHE A:474 , HOH A:741
binding site for Mono-Saccharide BGC A 602 bound to SER A 458
09
AC9
SOFTWARE
ASP A:464 , THR A:466 , ILE A:477 , HOH A:717 , HOH A:718 , HOH A:726 , HOH A:755 , HIS B:64 , TYR B:65 , THR B:114
binding site for Mono-Saccharide FUC A 603 bound to THR A 466
10
AD1
SOFTWARE
GLU A:493 , SER A:496
binding site for Mono-Saccharide BGC A 604 bound to SER A 496
11
AD2
SOFTWARE
PRO B:73 , CYS B:74 , ASN B:78 , HOH B:439 , GLU D:511
binding site for Mono-Saccharide NAG B 301 bound to ASN B 78
12
AD3
SOFTWARE
ILE A:471 , ASN B:108 , SER D:527
binding site for Mono-Saccharide NAG B 302 bound to ASN B 108
13
AD4
SOFTWARE
GLU B:159 , ASN B:161 , HOH B:456 , ASN E:161 , ASN E:162
binding site for Poly-Saccharide residues NAG B 303 through NAG B 304 bound to ASN B 161
14
AD5
SOFTWARE
SER D:435 , PHE D:436 , HOH D:729 , ASP E:218 , GLN E:219
binding site for Mono-Saccharide BGC D 601 bound to SER D 435
15
AD6
SOFTWARE
GLU D:455 , SER D:458 , PHE D:474 , PRO E:135
binding site for Mono-Saccharide BGC D 602 bound to SER D 458
16
AD7
SOFTWARE
ASP D:464 , THR D:466 , ILE D:477 , HIS E:64 , TYR E:65
binding site for Mono-Saccharide FUC D 603 bound to THR D 466
17
AD8
SOFTWARE
GLU D:493 , SER D:496
binding site for Mono-Saccharide BGC D 604 bound to SER D 496
18
AD9
SOFTWARE
GLU A:511 , CYS E:74 , ASN E:78 , HOH E:446
binding site for Mono-Saccharide NAG E 301 bound to ASN E 78
19
AE1
SOFTWARE
GLY E:25 , ASN E:108
binding site for Mono-Saccharide NAG E 302 bound to ASN E 108
20
AE2
SOFTWARE
ASN B:161 , ASN B:162 , ALA D:417 , GLY D:419 , GLU E:159 , ASN E:161 , ARG E:166 , HOH E:463
binding site for Poly-Saccharide residues NAG E 303 through NAG E 304 bound to ASN E 161
[
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 A
Chain B
Chain D
Chain E
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 (250 KB)
Header - Asym.Unit
Biol.Unit 1 (120 KB)
Header - Biol.Unit 1
Biol.Unit 2 (121 KB)
Header - Biol.Unit 2
Biol.Unit 3 (236 KB)
Header - Biol.Unit 3
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
4XL1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
