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1G1R
Biol. Unit 1
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
(5, 14)
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
-1
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
[
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]
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:
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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
-
-
-
-
-
-
-
-
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_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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)
(
)
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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
[
close SCOP info
]
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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Classes
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Architectures
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)
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
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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