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.
4MMZ
Asym. Unit
Info
Asym.Unit (600 KB)
Biol.Unit 1 (586 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
INTEGRIN ALPHAVBETA3 ECTODOMAIN BOUND TO AN ANTAGONISTIC TENTH DOMAIN OF FIBRONECTIN
Authors
:
J. Van Agthoven, J. Xiong, M. A. Arnaout
Date
:
09 Sep 13 (Deposition) - 26 Mar 14 (Release) - 30 Apr 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Integrin, A Domain, Hybrid Domain, Psi, Egf Repeats, Beta Tail, Calf, Thigh, Beta Propeller, Rgd Motif, Fibronectin, Vitronectin, Cell Adhesion
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. F. Van Agthoven, J. P. Xiong, J. L. Alonso, X. Rui, B. D. Adair, S. L. Goodman, M. A. Arnaout
Structural Basis For Pure Antagonism Of Integrin Alpha V Beta 3 By A High-Affinity Form Of Fibronectin.
Nat. Struct. Mol. Biol. V. 21 383 2014
[
close entry info
]
Hetero Components
(7, 38)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
5a: MANGANESE (II) ION (MNa)
5b: MANGANESE (II) ION (MNb)
5c: MANGANESE (II) ION (MNc)
5d: MANGANESE (II) ION (MNd)
5e: MANGANESE (II) ION (MNe)
5f: MANGANESE (II) ION (MNf)
5g: MANGANESE (II) ION (MNg)
5h: MANGANESE (II) ION (MNh)
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)
7i: N-ACETYL-D-GLUCOSAMINE (NAGi)
7j: N-ACETYL-D-GLUCOSAMINE (NAGj)
7k: N-ACETYL-D-GLUCOSAMINE (NAGk)
7l: N-ACETYL-D-GLUCOSAMINE (NAGl)
7m: N-ACETYL-D-GLUCOSAMINE (NAGm)
7n: N-ACETYL-D-GLUCOSAMINE (NAGn)
7o: N-ACETYL-D-GLUCOSAMINE (NAGo)
7p: N-ACETYL-D-GLUCOSAMINE (NAGp)
7q: N-ACETYL-D-GLUCOSAMINE (NAGq)
7r: N-ACETYL-D-GLUCOSAMINE (NAGr)
7s: N-ACETYL-D-GLUCOSAMINE (NAGs)
6a: SODIUM ION (NAa)
6b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
3
Ligand/Ion
BETA-D-MANNOSE
2
CL
2
Ligand/Ion
CHLORIDE ION
3
GOL
2
Ligand/Ion
GLYCEROL
4
MAN
2
Ligand/Ion
ALPHA-D-MANNOSE
5
MN
8
Ligand/Ion
MANGANESE (II) ION
6
NA
2
Ligand/Ion
SODIUM ION
7
NAG
19
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(27, 27)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:230 , ASN A:232 , ASP A:234 , ILE A:236 , ASP A:238
BINDING SITE FOR RESIDUE MN A 1018
02
AC2
SOFTWARE
ASP A:284 , ASN A:286 , ASP A:288 , TYR A:290 , ASP A:292
BINDING SITE FOR RESIDUE MN A 1019
03
AC3
SOFTWARE
ASP A:349 , ASP A:351 , ASP A:353 , PHE A:355 , ASP A:357
BINDING SITE FOR RESIDUE MN A 1020
04
AC4
SOFTWARE
ASP A:413 , ASP A:415 , ASN A:417 , TYR A:419 , ASP A:421
BINDING SITE FOR RESIDUE MN A 1021
05
AC5
SOFTWARE
CYS A:596 , ASP A:599 , VAL A:601 , GLU A:636
BINDING SITE FOR RESIDUE MN A 1022
06
AC6
SOFTWARE
ASP A:544 , GLU A:545 , SER A:546 , GLU A:547
BINDING SITE FOR RESIDUE NA A 1023
07
AC7
SOFTWARE
ASP A:148 , ASP A:150 , GLU A:930
BINDING SITE FOR RESIDUE GOL A 1024
08
AC8
SOFTWARE
SER B:121 , GLU B:220 , HOH B:801 , HOH B:802 , ASP C:1495 , HOH C:1701
BINDING SITE FOR RESIDUE MN B 708
09
AC9
SOFTWARE
SER B:123 , MET B:124 , ASP B:126 , ASP B:127 , MET B:335 , HOH C:1702
BINDING SITE FOR RESIDUE MN B 709
10
BC1
SOFTWARE
ASP B:158 , ASN B:215 , ASP B:217 , PRO B:219 , GLU B:220
BINDING SITE FOR RESIDUE MN B 710
11
BC2
SOFTWARE
ASP B:647 , ASN B:654 , CL B:712 , CL B:713
BINDING SITE FOR RESIDUE NA B 711
12
BC3
SOFTWARE
LEU B:645 , ASP B:647 , NA B:711
BINDING SITE FOR RESIDUE CL B 712
13
BC4
SOFTWARE
ASP B:647 , ASN B:654 , NA B:711
BINDING SITE FOR RESIDUE CL B 713
14
BC5
SOFTWARE
THR C:1491 , ASN C:1497 , GLU C:1498
BINDING SITE FOR RESIDUE GOL C 1601
15
BC6
SOFTWARE
GLU A:15 , LYS A:42 , ASN A:44 , GLU A:52
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 44 RESIDUES 1001 TO 1002
16
BC7
SOFTWARE
ASP A:257 , LYS A:259 , ASN A:260 , SER A:262
BINDING SITE FOR MONO-SACCHARIDE NAG A1003 BOUND TO ASN A 260
17
BC8
SOFTWARE
GLN A:214 , PHE A:217 , TYR A:254 , SER A:263 , LEU A:264 , ASN A:266
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 266 RESIDUES 1004 TO 1009
18
BC9
SOFTWARE
TYR A:450 , PRO A:451 , ASN A:458 , THR A:460 , CYS A:472 , ASN A:474
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 458 RESIDUES 1010 TO 1011
19
CC1
SOFTWARE
LYS A:501 , ASN A:585 , ASP B:512
BINDING SITE FOR MONO-SACCHARIDE NAG A1012 BOUND TO ASN A 585
20
CC2
SOFTWARE
ASN A:805
BINDING SITE FOR MONO-SACCHARIDE NAG A1013 BOUND TO ASN A 805
21
CC3
SOFTWARE
ASN A:821 , GLY A:887
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 821 RESIDUES 1014 TO 1015
22
CC4
SOFTWARE
THR A:942 , ASN A:943
BINDING SITE FOR MONO-SACCHARIDE NAG A1016 BOUND TO ASN A 943
23
CC5
SOFTWARE
ASP A:751 , HIS A:752 , ASN A:950
BINDING SITE FOR MONO-SACCHARIDE NAG A1017 BOUND TO ASN A 950
24
CC6
SOFTWARE
ASN B:99 , NAG B:703
BINDING SITE FOR MONO-SACCHARIDE NAG B 701 BOUND TO ASN B 99
25
CC7
SOFTWARE
ARG A:248 , MET A:272 , ASN B:316 , LEU B:317 , ASN B:320
BINDING SITE FOR MONO-SACCHARIDE NAG B 702 BOUND TO ASN B 320
26
CC8
SOFTWARE
ASN B:371 , SER B:398 , GLU B:400 , NAG B:701
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 371 RESIDUES 703 TO 704
27
CC9
SOFTWARE
ASP A:621 , TYR B:531 , TYR B:557 , ASN B:559
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 559 RESIDUES 705 TO 707
[
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 C
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 (600 KB)
Header - Asym.Unit
Biol.Unit 1 (586 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
4MMZ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
