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1G1R
Asym. Unit
Info
Asym.Unit (120 KB)
Biol.Unit 1 (112 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF P-SELECTIN LECTIN/EGF DOMAINS COMPLEXED WITH SLEX
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
:
3.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Lectin, Egf, Adhesion Molecule, Slex, 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
)
[
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Hetero Components
(6, 18)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: ALPHA-L-FUCOSE (FUCa)
2b: ALPHA-L-FUCOSE (FUCb)
2c: ALPHA-L-FUCOSE (FUCc)
3a: BETA-D-GALACTOSE (GALa)
3b: BETA-D-GALACTOSE (GALb)
3c: BETA-D-GALACTOSE (GALc)
4a: BETA-METHYL-N-ACETYL-D-GLUCOSAMINE (MAGa)
4b: BETA-METHYL-N-ACETYL-D-GLUCOSAMINE (MAGb)
4c: BETA-METHYL-N-ACETYL-D-GLUCOSAMINE (MAGc)
5a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
5b: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDb)
6a: O-SIALIC ACID (SIAa)
6b: O-SIALIC ACID (SIAb)
6c: O-SIALIC ACID (SIAc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
FUC
3
Ligand/Ion
ALPHA-L-FUCOSE
3
GAL
3
Ligand/Ion
BETA-D-GALACTOSE
4
MAG
3
Ligand/Ion
BETA-METHYL-N-ACETYL-D-GLUCOSAMINE
5
MRD
2
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
6
SIA
3
Ligand/Ion
O-SIALIC ACID
[
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Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:48 , SER A:99 , GAL A:902
BINDING SITE FOR RESIDUE SIA A 901
02
AC2
SOFTWARE
GLU A:92 , TYR A:94 , ASN A:105 , GLU A:107 , SIA A:901 , MAG A:903 , FUC A:904
BINDING SITE FOR RESIDUE GAL A 902
03
AC3
SOFTWARE
GAL A:902 , FUC A:904
BINDING SITE FOR RESIDUE MAG A 903
04
AC4
SOFTWARE
GLU A:80 , ASN A:82 , ASN A:105 , ASP A:106 , GLU A:107 , CA A:801 , GAL A:902 , MAG A:903
BINDING SITE FOR RESIDUE FUC A 904
05
AC5
SOFTWARE
TYR B:48 , TYR B:94 , PRO B:98 , SER B:99 , GAL B:902
BINDING SITE FOR RESIDUE SIA B 901
06
AC6
SOFTWARE
GLU B:92 , TYR B:94 , ASN B:105 , SIA B:901 , MAG B:903 , FUC B:904
BINDING SITE FOR RESIDUE GAL B 902
07
AC7
SOFTWARE
GAL B:902 , FUC B:904
BINDING SITE FOR RESIDUE MAG B 903
08
AC8
SOFTWARE
GLU B:80 , ASN B:82 , ASN B:105 , ASP B:106 , GLU B:107 , CA B:802 , GAL B:902 , MAG B:903
BINDING SITE FOR RESIDUE FUC B 904
09
AC9
SOFTWARE
TYR D:48 , TYR D:94 , PRO D:98 , SER D:99 , GAL D:902
BINDING SITE FOR RESIDUE SIA D 901
10
BC1
SOFTWARE
GLU D:92 , TYR D:94 , GLU D:107 , SIA D:901 , MAG D:903 , FUC D:904
BINDING SITE FOR RESIDUE GAL D 902
11
BC2
SOFTWARE
GAL D:902 , FUC D:904
BINDING SITE FOR RESIDUE MAG D 903
12
BC3
SOFTWARE
GLU D:80 , ASN D:82 , ASN D:83 , ASN D:105 , ASP D:106 , GLU D:107 , CA D:804 , GAL D:902 , MAG D:903
BINDING SITE FOR RESIDUE FUC D 904
13
BC4
SOFTWARE
GLU A:80 , ASN A:82 , ASN A:83 , ASN A:105 , ASP A:106 , FUC A:904
BINDING SITE FOR RESIDUE CA A 801
14
BC5
SOFTWARE
GLU B:80 , ASN B:82 , ASN B:83 , ASN B:105 , ASP B:106 , FUC B:904
BINDING SITE FOR RESIDUE CA B 802
15
BC6
SOFTWARE
GLU C:80 , ASN C:82 , ASN C:83 , ASN C:105 , ASP C:106
BINDING SITE FOR RESIDUE CA C 803
16
BC7
SOFTWARE
GLU D:80 , ASN D:82 , ASN D:83 , ASN D:105 , ASP D:106 , FUC D:904
BINDING SITE FOR RESIDUE CA D 804
17
BC8
SOFTWARE
THR C:2 , TYR C:3 , TYR C:37 , GLY C:138
BINDING SITE FOR RESIDUE MRD C 805
18
BC9
SOFTWARE
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 not available)
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, 16)
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
(3, 12)
Info
All Exons
Exon 1.3 (A:1-120 | B:1-120 | C:1-120 | D:1-...)
Exon 1.4 (A:120-156 | B:120-156 | C:120-156 ...)
Exon 1.5 (A:156-160 | B:156-160 | C:156-159 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2b/1.3
2: Boundary 1.3/1.4
3: Boundary 1.4/1.5
4: Boundary 1.5/1.6
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1b
ENST00000263686
1b
ENSE00001384287
chr1:
169599377-169599310
68
LYAM3_HUMAN
1-1
1
0
-
-
1.2b
ENST00000263686
2b
ENSE00001172331
chr1:
169588457-169588367
91
LYAM3_HUMAN
2-32
31
0
-
-
1.3
ENST00000263686
3
ENSE00000814471
chr1:
169586652-169586266
387
LYAM3_HUMAN
32-161
130
4
A:1-120
B:1-120
C:1-120
D:1-120
120
120
120
120
1.4
ENST00000263686
4
ENSE00000814474
chr1:
169582931-169582824
108
LYAM3_HUMAN
161-197
37
4
A:120-156
B:120-156
C:120-156
D:120-156
37
37
37
37
1.5
ENST00000263686
5
ENSE00000789626
chr1:
169582352-169582167
186
LYAM3_HUMAN
197-259
63
4
A:156-160
B:156-160
C:156-159
D:156-160
5
5
4
5
1.6
ENST00000263686
6
ENSE00000789625
chr1:
169581640-169581455
186
LYAM3_HUMAN
259-321
63
0
-
-
1.7
ENST00000263686
7
ENSE00000814478
chr1:
169580915-169580730
186
LYAM3_HUMAN
321-383
63
0
-
-
1.8
ENST00000263686
8
ENSE00000789623
chr1:
169578927-169578742
186
LYAM3_HUMAN
383-445
63
0
-
-
1.9a
ENST00000263686
9a
ENSE00000814480
chr1:
169576372-169576187
186
LYAM3_HUMAN
445-507
63
0
-
-
1.10
ENST00000263686
10
ENSE00000814483
chr1:
169572449-169572264
186
LYAM3_HUMAN
507-569
63
0
-
-
1.11
ENST00000263686
11
ENSE00000814484
chr1:
169566414-169566229
186
LYAM3_HUMAN
569-631
63
0
-
-
1.12
ENST00000263686
12
ENSE00000450611
chr1:
169565372-169565163
210
LYAM3_HUMAN
631-701
71
0
-
-
1.13
ENST00000263686
13
ENSE00000958551
chr1:
169564115-169563930
186
LYAM3_HUMAN
701-763
63
0
-
-
1.14
ENST00000263686
14
ENSE00000450613
chr1:
169562962-169562843
120
LYAM3_HUMAN
763-803
41
0
-
-
1.15b
ENST00000263686
15b
ENSE00001168517
chr1:
169560694-169560664
31
LYAM3_HUMAN
803-813
11
0
-
-
1.16b
ENST00000263686
16b
ENSE00001168504
chr1:
169559440-169559385
56
LYAM3_HUMAN
813-830
18
0
-
-
1.17h
ENST00000263686
17h
ENSE00001359830
chr1:
169558699-169558090
610
LYAM3_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1g1ra1 (A:1-118)
1b: SCOP_d1g1rb1 (B:1-118)
1c: SCOP_d1g1rc1 (C:1-118)
1d: SCOP_d1g1rd1 (D:1-118)
2a: SCOP_d1g1ra2 (A:119-160)
2b: SCOP_d1g1rc2 (C:119-159)
2c: SCOP_d1g1rd2 (D:119-160)
2d: SCOP_d1g1rb2 (B:119-160)
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(
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(
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Folds
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Superfamilies
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(
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)
(
)
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
d1g1ra1
A:1-118
1b
d1g1rb1
B:1-118
1c
d1g1rc1
C:1-118
1d
d1g1rd1
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
d1g1ra2
A:119-160
2b
d1g1rc2
C:119-159
2c
d1g1rd2
D:119-160
2d
d1g1rb2
B:119-160
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1g1rA01 (A:1-119)
1b: CATH_1g1rB01 (B:1-119)
1c: CATH_1g1rC01 (C:1-119)
1d: CATH_1g1rD01 (D:1-119)
2a: CATH_1g1rA02 (A:120-157)
2b: CATH_1g1rB02 (B:120-157)
2c: CATH_1g1rC02 (C:120-157)
2d: CATH_1g1rD02 (D:120-157)
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Architectures
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Topologies
(
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(
)
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
1g1rA01
A:1-119
1b
1g1rB01
B:1-119
1c
1g1rC01
C:1-119
1d
1g1rD01
D:1-119
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
Human (Homo sapiens)
(195)
2a
1g1rA02
A:120-157
2b
1g1rB02
B:120-157
2c
1g1rC02
C:120-157
2d
1g1rD02
D:120-157
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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