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.
4C16
Biol. Unit 1
Info
Asym.Unit (119 KB)
Biol.Unit 1 (58 KB)
Biol.Unit 2 (57 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
E-SELECTIN LECTIN, EGF-LIKE AND TWO SCR DOMAINS COMPLEXED WITH GLYCOMIMETIC ANTAGONIST
Authors
:
R. C. Preston, R. P. Jakob, F. P. C. Binder, C. P. Sager, B. Ernst, T. Maier
Date
:
09 Aug 13 (Deposition) - 20 Aug 14 (Release) - 27 Jan 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.93
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Cell Adhesion, Cell-Adhesion Molecule, C-Type Lectin, Inflammation, Leukocyte, Glycomimetic, Antagonist, Catch- Bond
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. C. Preston, R. P. Jakob, F. P. Binder, C. P. Sager, B. Ernst, T. Maier
E-Selectin Ligand Complexes Adopt An Extended High-Affinity Conformation.
J. Mol. Cell. Biol. V. 8 62 2016
[
close entry info
]
Hetero Components
(5, 11)
Info
All Hetero Components
1a: (S)-CYCLOHEXYL LACTIC ACID (4WCa)
1b: (S)-CYCLOHEXYL LACTIC ACID (4WCb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: ALPHA-L-FUCOSE (FUCa)
3b: ALPHA-L-FUCOSE (FUCb)
4a: BETA-D-GALACTOSE (GALa)
4b: BETA-D-GALACTOSE (GALb)
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)
5i: N-ACETYL-D-GLUCOSAMINE (NAGi)
5j: N-ACETYL-D-GLUCOSAMINE (NAGj)
5k: N-ACETYL-D-GLUCOSAMINE (NAGk)
5l: N-ACETYL-D-GLUCOSAMINE (NAGl)
5m: N-ACETYL-D-GLUCOSAMINE (NAGm)
5n: N-ACETYL-D-GLUCOSAMINE (NAGn)
6a: (1R,2R,3S)-3-METHYLCYCLOHEXANE-1,2... (Q6Za)
6b: (1R,2R,3S)-3-METHYLCYCLOHEXANE-1,2... (Q6Zb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4WC
1
Ligand/Ion
(S)-CYCLOHEXYL LACTIC ACID
2
CA
-1
Ligand/Ion
CALCIUM ION
3
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
4
GAL
1
Ligand/Ion
BETA-D-GALACTOSE
5
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
Q6Z
1
Ligand/Ion
(1R,2R,3S)-3-METHYLCYCLOHEXANE-1,2-DIOL
[
close Hetero Component info
]
Sites
(13, 13)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC4 (SOFTWARE)
04: AC5 (SOFTWARE)
05: AC6 (SOFTWARE)
06: AC7 (SOFTWARE)
07: AC8 (SOFTWARE)
08: AC9 (SOFTWARE)
09: BC3 (SOFTWARE)
10: BC4 (SOFTWARE)
11: BC5 (SOFTWARE)
12: BC8 (SOFTWARE)
13: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:80 , ASN A:82 , GLU A:88 , ASN A:105 , ASP A:106 , FUC A:305
BINDING SITE FOR RESIDUE CA A 301
02
AC3
SOFTWARE
ASN A:4 , ARG A:22 , GLU A:208 , NAG B:282
BINDING SITE FOR MONO-SACCHARIDE NAG A 285 BOUND TO ASN A 4
03
AC4
SOFTWARE
ASN A:124 , VAL B:59 , TRP B:60 , LEU B:69 , LYS B:74 , TRP B:76 , HOH B:2087 , HOH B:2098
BINDING SITE FOR MONO-SACCHARIDE NAG A 286 BOUND TO ASN A 124
04
AC5
SOFTWARE
ASN A:139 , TYR A:140 , LEU A:151 , HOH A:2125 , HOH A:2127
BINDING SITE FOR MONO-SACCHARIDE NAG A 282 BOUND TO ASN A 139
05
AC6
SOFTWARE
SER A:149 , GLN A:155 , ILE A:156 , ASN A:158 , HOH A:2145 , HOH A:2270 , HOH A:2271 , ASN B:158 , NAG B:283
BINDING SITE FOR MONO-SACCHARIDE NAG A 283 BOUND TO ASN A 158
06
AC7
SOFTWARE
ASN A:178 , VAL A:224 , VAL A:232 , GLU A:233 , CYS A:234 , PHE A:241 , HOH A:2176 , HOH A:2272 , GLU B:233 , NAG B:284
BINDING SITE FOR MONO-SACCHARIDE NAG A 284 BOUND TO ASN A 178
07
AC8
SOFTWARE
ASN A:182 , HOH A:2180 , HOH A:2182 , HOH A:2183 , HOH A:2268
BINDING SITE FOR MONO-SACCHARIDE NAG A 281 BOUND TO ASN A 182
08
AC9
SOFTWARE
TYR A:193 , TRP A:243 , ASN A:244 , HOH A:2194 , GLU B:253
BINDING SITE FOR MONO-SACCHARIDE NAG A 287 BOUND TO ASN A 244
09
BC3
SOFTWARE
NAG A:285 , ASN B:139 , TYR B:140
BINDING SITE FOR MONO-SACCHARIDE NAG B 282 BOUND TO ASN B 139
10
BC4
SOFTWARE
ASN A:158 , NAG A:283 , HOH A:2146 , HOH A:2150 , GLN B:155 , ILE B:156 , ASN B:158 , HOH B:2150 , HOH B:2169 , HOH B:2170 , HOH B:2246 , HOH B:2247
BINDING SITE FOR MONO-SACCHARIDE NAG B 283 BOUND TO ASN B 158
11
BC5
SOFTWARE
NAG A:284 , HOH A:2272 , ASN B:178 , VAL B:224 , THR B:225 , VAL B:232 , GLU B:233 , CYS B:234 , PRO B:238 , GLY B:239 , PHE B:241 , HOH B:2216 , HOH B:2248 , HOH B:2249
BINDING SITE FOR MONO-SACCHARIDE NAG B 284 BOUND TO ASN B 178
12
BC8
SOFTWARE
TYR A:48 , GLU A:80 , ASN A:82 , ARG A:84 , GLN A:85 , GLU A:88 , GLU A:92 , TYR A:94 , ARG A:97 , ASN A:105 , ASP A:106 , GLU A:107 , CA A:301 , HOH A:2053 , HOH A:2273 , HOH A:2274
BINDING SITE FOR POLY-SACCHARIDE RESIDUES 4WC A 302 THROUGH FUC A 305
13
BC9
SOFTWARE
TYR A:48 , GLU A:80 , ASN A:82 , ARG A:84 , GLN A:85 , GLU A:88 , GLU A:92 , TYR A:94 , ARG A:97 , ASN A:105 , ASP A:106 , GLU A:107 , CA A:301 , HOH A:2053 , HOH A:2273 , HOH A:2274 , TYR B:48 , GLU B:80 , ASN B:82 , GLN B:85 , GLU B:88 , GLU B:92 , TYR B:94 , ARG B:97 , ASN B:105 , ASP B:106 , GLU B:107 , GLN B:261 , CA B:301 , HOH B:2060 , HOH B:2253
BINDING SITE FOR POLY-SACCHARIDE RESIDUES 4WC B 302 THROUGH FUC B 305
[
close Site info
]
SAPs(SNPs)/Variants
(5, 5)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_014301 (M10I, chain A, )
2: VAR_011790 (C109W, chain A, )
3: VAR_004191 (S128R, chain A, )
4: VAR_014302 (Q236P, chain A, )
5: VAR_011791 (E274K, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_014301
M
31
I
LYAM2_HUMAN
Polymorphism
3917408
A
M
10
I
2
UniProt
VAR_011790
C
130
W
LYAM2_HUMAN
Polymorphism
5360
A
C
109
W
3
UniProt
VAR_004191
S
149
R
LYAM2_HUMAN
Polymorphism
5361
A
S
128
R
4
UniProt
VAR_014302
Q
257
P
LYAM2_HUMAN
Polymorphism
3917422
A
Q
236
P
5
UniProt
VAR_011791
E
295
K
LYAM2_HUMAN
Polymorphism
5364
A
E
274
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(5, 6)
Info
All PROSITE Patterns/Profiles
1: C_TYPE_LECTIN_1 (A:90-117)
2: EGF_3 (A:118-154)
3: EGF_1 (A:142-153)
4: EGF_2 (A:142-153)
5: SUSHI (A:157-218,A:219-280)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
C_TYPE_LECTIN_1
PS00615
C-type lectin domain signature.
LYAM2_HUMAN
111-138
1
A:90-117
-
2
EGF_3
PS50026
EGF-like domain profile.
LYAM2_HUMAN
139-175
1
A:118-154
-
3
EGF_1
PS00022
EGF-like domain signature 1.
LYAM2_HUMAN
163-174
1
A:142-153
-
4
EGF_2
PS01186
EGF-like domain signature 2.
LYAM2_HUMAN
163-174
1
A:142-153
-
5
SUSHI
PS50923
Sushi/CCP/SCR domain profile.
LYAM2_HUMAN
178-239
240-301
315-364
378-427
441-490
491-549
2
A:157-218
-
A:219-280
-
-
-
-
-
[
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
(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
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 (119 KB)
Header - Asym.Unit
Biol.Unit 1 (58 KB)
Header - Biol.Unit 1
Biol.Unit 2 (57 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
4C16
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help