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1G1S
Biol. Unit 1
Info
Asym.Unit (77 KB)
Biol.Unit 1 (68 KB)
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(1)
Title
:
P-SELECTIN LECTIN/EGF DOMAINS COMPLEXED WITH PSGL-1 PEPTIDE
Authors
:
W. S. Somers, R. T. Camphausen
Date
:
13 Oct 00 (Deposition) - 13 Oct 01 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Selectin, Lectin, Egf, Sulphated, 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 An Rolling Revealed By Structures Of P- And E-Selectin Bound T Sle(X) And Psgl-1.
Cell(Cambridge, Mass. ) V. 103 467 2000
[
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Hetero Components
(7, 24)
Info
All Hetero Components
1a: ALPHA-L-FUCOSE (FUCa)
1b: ALPHA-L-FUCOSE (FUCb)
2a: BETA-D-GALACTOSE (GALa)
2b: BETA-D-GALACTOSE (GALb)
2c: BETA-D-GALACTOSE (GALc)
2d: BETA-D-GALACTOSE (GALd)
3a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
3b: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDb)
3c: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDc)
3d: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDd)
3e: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDe)
3f: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDf)
3g: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDg)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
6a: N-ACETYL-D-GALACTOSAMINE (NGAa)
6b: N-ACETYL-D-GALACTOSAMINE (NGAb)
7a: O-SIALIC ACID (SIAa)
7b: O-SIALIC ACID (SIAb)
8a: STRONTIUM ION (SRa)
8b: STRONTIUM ION (SRb)
9a: O-SULFO-L-TYROSINE (TYSa)
9b: O-SULFO-L-TYROSINE (TYSb)
9c: O-SULFO-L-TYROSINE (TYSc)
9d: O-SULFO-L-TYROSINE (TYSd)
9e: O-SULFO-L-TYROSINE (TYSe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
2
GAL
4
Ligand/Ion
BETA-D-GALACTOSE
3
MRD
7
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
4
NA
-1
Ligand/Ion
SODIUM ION
5
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
NGA
2
Ligand/Ion
N-ACETYL-D-GALACTOSAMINE
7
SIA
2
Ligand/Ion
O-SIALIC ACID
8
SR
-1
Ligand/Ion
STRONTIUM ION
9
TYS
5
Mod. Amino Acid
O-SULFO-L-TYROSINE
[
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]
Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR B:48 , SER B:99 , HOH C:39 , GAL C:630
BINDING SITE FOR RESIDUE SIA C 629
02
AC2
SOFTWARE
TYR B:48 , GLU B:92 , TYR B:94 , GLU B:107 , HOH C:51 , HOH C:154 , SIA C:629 , NAG C:631 , FUC C:632
BINDING SITE FOR RESIDUE GAL C 630
03
AC3
SOFTWARE
LYS B:84 , ARG B:85 , HOH B:946 , HOH C:68 , HOH C:212 , THR C:616 , GAL C:630 , FUC C:632 , NGA C:633
BINDING SITE FOR RESIDUE NAG C 631
04
AC4
SOFTWARE
GLU B:80 , ASN B:82 , GLU B:88 , ASN B:105 , ASP B:106 , GLU B:107 , SR B:902 , HOH C:68 , GAL C:630 , NAG C:631
BINDING SITE FOR RESIDUE FUC C 632
05
AC5
SOFTWARE
TYS C:610 , THR C:616 , GLU C:617 , NAG C:631 , GAL C:634
BINDING SITE FOR RESIDUE NGA C 633
06
AC6
SOFTWARE
NGA C:633
BINDING SITE FOR RESIDUE GAL C 634
07
AC7
SOFTWARE
TYR A:48 , SER A:99 , HOH A:950 , HOH A:963 , HOH D:117 , HOH D:173 , GAL D:630
BINDING SITE FOR RESIDUE SIA D 629
08
AC8
SOFTWARE
GLU A:92 , TYR A:94 , GLU A:107 , HOH D:49 , HOH D:69 , SIA D:629 , NAG D:631 , FUC D:632
BINDING SITE FOR RESIDUE GAL D 630
09
AC9
SOFTWARE
ARG A:85 , HOH A:927 , HOH D:52 , HOH D:192 , HOH D:210 , THR D:616 , GAL D:630 , FUC D:632 , NGA D:633
BINDING SITE FOR RESIDUE NAG D 631
10
BC1
SOFTWARE
GLU A:80 , ASN A:82 , GLU A:88 , ASN A:105 , ASP A:106 , GLU A:107 , SR A:901 , HOH D:52 , HOH D:183 , GAL D:630 , NAG D:631
BINDING SITE FOR RESIDUE FUC D 632
11
BC2
SOFTWARE
HOH D:218 , TYS D:610 , THR D:616 , GLU D:617 , NAG D:631 , GAL D:634
BINDING SITE FOR RESIDUE NGA D 633
12
BC3
SOFTWARE
NGA D:633
BINDING SITE FOR RESIDUE GAL D 634
13
BC4
SOFTWARE
GLU A:80 , ASN A:82 , GLU A:88 , ASN A:105 , ASP A:106 , FUC D:632
BINDING SITE FOR RESIDUE SR A 901
14
BC5
SOFTWARE
GLU B:80 , ASN B:82 , GLU B:88 , ASN B:105 , ASP B:106 , FUC C:632
BINDING SITE FOR RESIDUE SR B 902
15
BC6
SOFTWARE
HOH B:954 , HOH D:201 , HOH D:202 , HOH D:203 , ASP D:609 , ASP D:611
BINDING SITE FOR RESIDUE NA B 903
16
BC7
SOFTWARE
HOH C:55 , HOH C:185 , HOH C:199 , HOH C:200 , ASP C:609 , ASP C:611
BINDING SITE FOR RESIDUE NA C 904
17
BC8
SOFTWARE
TRP B:1 , ALA B:28 , GLN B:30 , TYR B:118
BINDING SITE FOR RESIDUE MRD B 805
18
BC9
SOFTWARE
TYR B:3 , TYR B:37 , VAL B:41 , TYR B:149 , HOH B:909 , HOH B:962
BINDING SITE FOR RESIDUE MRD B 806
19
CC1
SOFTWARE
ALA A:28 , GLU A:34 , TYR A:118
BINDING SITE FOR RESIDUE MRD A 807
20
CC2
SOFTWARE
TRP B:1 , GLN B:30 , ASN B:31 , ASN B:33 , GLU B:34 , ILE B:137 , HOH B:955
BINDING SITE FOR RESIDUE MRD B 808
21
CC3
SOFTWARE
ASP B:36 , PRO B:101 , GLU B:132 , SER B:143 , CYS B:144
BINDING SITE FOR RESIDUE MRD B 809
22
CC4
SOFTWARE
TYR B:10 , ILE B:14 , LYS B:17 , TYR B:18 , TYS D:610 , GLU D:615
BINDING SITE FOR RESIDUE MRD B 810
23
CC5
SOFTWARE
ASN A:139 , TYR A:140 , PRO A:151 , GLU A:152 , HOH A:960
BINDING SITE FOR RESIDUE MRD A 811
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_019381 (G138R, chain A/B, )
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
G
138
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(5, 10)
Info
All PROSITE Patterns/Profiles
1: C_TYPE_LECTIN_1 (A:90-117,B:90-117)
2: EGF_3 (A:118-154,B:118-154)
3: EGF_1 (A:142-153,B:142-153)
4: EGF_2 (A:142-153,B:142-153)
5: SUSHI (A:157-157,B:157-157|-|-|-|-|-|-|-|...)
;
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
2
A:90-117
B:90-117
2
EGF_3
PS50026
EGF-like domain profile.
LYAM3_HUMAN
159-195
2
A:118-154
B:118-154
3
EGF_1
PS00022
EGF-like domain signature 1.
LYAM3_HUMAN
183-194
2
A:142-153
B:142-153
4
EGF_2
PS01186
EGF-like domain signature 2.
LYAM3_HUMAN
183-194
2
A:142-153
B: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
2
A:157-157
B:157-157
-
-
-
-
-
-
-
-
[
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]
Exons
(0, 0)
Info
All Exons
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1g1sa1 (A:1-118)
1b: SCOP_d1g1sb1 (B:1-118)
2a: SCOP_d1g1sa2 (A:119-158)
2b: SCOP_d1g1sb2 (B:119-157)
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Classes
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Folds
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Superfamilies
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)
(
)
Families
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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
d1g1sa1
A:1-118
1b
d1g1sb1
B: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
d1g1sa2
A:119-158
2b
d1g1sb2
B:119-157
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1g1sA01 (A:1-119)
1b: CATH_1g1sB01 (B:1-119)
2a: CATH_1g1sA02 (A:120-157)
2b: CATH_1g1sB02 (B: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
1g1sA01
A:1-119
1b
1g1sB01
B:1-119
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
Human (Homo sapiens)
(195)
2a
1g1sA02
A:120-157
2b
1g1sB02
B: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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Asymmetric Unit 1
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