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.
1G1Q
Biol. Unit 1
Info
Asym.Unit (116 KB)
Biol.Unit 1 (111 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF P-SELECTIN LECTIN/EGF DOMAINS
Authors
:
W. S. Somers, R. T. Camphausen
Date
:
13 Oct 00 (Deposition) - 13 Oct 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Lectin, Egf, Adhesion Molecule, Immune System, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. S. Somers, J. Tang, G. D. Shaw, R. T. Camphausen
Insights Into The Molecular Basis Of Leukocyte Tethering And Rolling Revealed By Structures Of P- And E-Selectin Bound To Sle(X) And Psgl-1.
Cell(Cambridge, Mass. ) V. 103 467 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
2b: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
MRD
2
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:80 , ASN A:82 , ASN A:105 , ASP A:106 , HOH A:810 , HOH A:857
BINDING SITE FOR RESIDUE CA A 801
2
AC2
SOFTWARE
GLU B:80 , ASN B:82 , ASN B:105 , ASP B:106 , HOH B:826 , HOH B:833
BINDING SITE FOR RESIDUE CA B 802
3
AC3
SOFTWARE
GLU C:80 , ASN C:82 , ASN C:105 , ASP C:106
BINDING SITE FOR RESIDUE CA C 803
4
AC4
SOFTWARE
GLU D:80 , ASN D:82 , ASN D:105 , ASP D:106
BINDING SITE FOR RESIDUE CA D 804
5
AC5
SOFTWARE
THR C:2 , TYR C:3 , TYR C:37 , GLY C:138 , HOH C:814
BINDING SITE FOR RESIDUE MRD C 805
6
AC6
SOFTWARE
THR A:2 , TYR A:3 , TYR A:37 , ILE A:137 , GLY A:138
BINDING SITE FOR RESIDUE MRD A 806
[
close Site info
]
SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_019381 (G138R, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_019381
G
179
R
LYAM3_HUMAN
Polymorphism
3917718
A/B/C/D
G
138
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(5, 20)
Info
All PROSITE Patterns/Profiles
1: C_TYPE_LECTIN_1 (A:90-117,B:90-117,C:90-117,D:90-11...)
2: EGF_3 (A:118-154,B:118-154,C:118-154,D:11...)
3: EGF_1 (A:142-153,B:142-153,C:142-153,D:14...)
4: EGF_2 (A:142-153,B:142-153,C:142-153,D:14...)
5: SUSHI (A:157-157,B:157-157,C:157-157,D:15...)
;
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.
LYAM3_HUMAN
131-158
4
A:90-117
B:90-117
C:90-117
D:90-117
2
EGF_3
PS50026
EGF-like domain profile.
LYAM3_HUMAN
159-195
4
A:118-154
B:118-154
C:118-154
D:118-154
3
EGF_1
PS00022
EGF-like domain signature 1.
LYAM3_HUMAN
183-194
4
A:142-153
B:142-153
C:142-153
D:142-153
4
EGF_2
PS01186
EGF-like domain signature 2.
LYAM3_HUMAN
183-194
4
A:142-153
B:142-153
C:142-153
D:142-153
5
SUSHI
PS50923
Sushi/CCP/SCR domain profile.
LYAM3_HUMAN
198-259
260-321
322-383
384-445
446-507
508-569
570-631
640-701
702-763
4
A:157-157
B:157-157
C:157-157
D:157-157
-
-
-
-
-
-
-
-
[
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, 8)
Info
All SCOP Domains
1a: SCOP_d1g1qa1 (A:1-118)
1b: SCOP_d1g1qb1 (B:1-118)
1c: SCOP_d1g1qc1 (C:1-118)
1d: SCOP_d1g1qd1 (D:1-118)
2a: SCOP_d1g1qa2 (A:119-160)
2b: SCOP_d1g1qb2 (B:119-160)
2c: SCOP_d1g1qc2 (C:119-159)
2d: SCOP_d1g1qd2 (D:119-160)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
C-type lectin-like
(322)
Superfamily
:
C-type lectin-like
(322)
Family
:
C-type lectin domain
(182)
Protein domain
:
P-selectin, C-lectin domain
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d1g1qa1
A:1-118
1b
d1g1qb1
B:1-118
1c
d1g1qc1
C:1-118
1d
d1g1qd1
D:1-118
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
EGF/Laminin
(347)
Family
:
EGF-type module
(304)
Protein domain
:
E-selectin, EGF-domain
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
2a
d1g1qa2
A:119-160
2b
d1g1qb2
B:119-160
2c
d1g1qc2
C:119-159
2d
d1g1qd2
D:119-160
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1g1qA01 (A:1-119)
1b: CATH_1g1qB01 (B:1-119)
1c: CATH_1g1qC01 (C:1-119)
1d: CATH_1g1qD01 (D:1-119)
2a: CATH_1g1qA02 (A:120-157)
2b: CATH_1g1qB02 (B:120-157)
2c: CATH_1g1qC02 (C:120-157)
2d: CATH_1g1qD02 (D:120-157)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Mannose-Binding Protein A; Chain A
(180)
Homologous Superfamily
:
Mannose-Binding Protein A, subunit A
(180)
Human (Homo sapiens)
(80)
1a
1g1qA01
A:1-119
1b
1g1qB01
B:1-119
1c
1g1qC01
C:1-119
1d
1g1qD01
D:1-119
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
Human (Homo sapiens)
(195)
2a
1g1qA02
A:120-157
2b
1g1qB02
B:120-157
2c
1g1qC02
C:120-157
2d
1g1qD02
D:120-157
[
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
Chain D
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 (116 KB)
Header - Asym.Unit
Biol.Unit 1 (111 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
1G1Q
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
