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4CSY
Biol. Unit 2
Info
Asym.Unit (213 KB)
Biol.Unit 1 (104 KB)
Biol.Unit 2 (104 KB)
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(1)
Title
:
E-SELECTIN LECTIN, EGF-LIKE AND TWO SCR DOMAINS COMPLEXED WITH SIALYL LEWIS X
Authors
:
R. C. Preston, R. P. Jakob, F. P. C. Binder, C. P. Sager, B. Ernst, T. Maier
Date
:
11 Mar 14 (Deposition) - 24 Sep 14 (Release) - 27 Jan 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.41
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Cell-Adhesion, Human Lectin, C-Type Lectin, Inflammation, Leukocyte, Sialyl Lewis X, Slex, Protein Conformation, Ligand-Induced Conformational Change, 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: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: ALPHA-L-FUCOSE (FUCa)
2b: ALPHA-L-FUCOSE (FUCb)
3a: BETA-D-GALACTOSE (GALa)
3b: BETA-D-GALACTOSE (GALb)
4a: BETA-METHYL-N-ACETYL-D-GLUCOSAMINE (MAGa)
4b: BETA-METHYL-N-ACETYL-D-GLUCOSAMINE (MAGb)
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: O-SIALIC ACID (SIAa)
6b: O-SIALIC ACID (SIAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
3
GAL
1
Ligand/Ion
BETA-D-GALACTOSE
4
MAG
1
Ligand/Ion
BETA-METHYL-N-ACETYL-D-GLUCOSAMINE
5
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
SIA
1
Ligand/Ion
O-SIALIC ACID
[
close Hetero Component info
]
Sites
(14, 14)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC4 (SOFTWARE)
04: AC5 (SOFTWARE)
05: AC6 (SOFTWARE)
06: AC7 (SOFTWARE)
07: BC1 (SOFTWARE)
08: BC2 (SOFTWARE)
09: BC3 (SOFTWARE)
10: BC4 (SOFTWARE)
11: BC5 (SOFTWARE)
12: BC6 (SOFTWARE)
13: BC7 (SOFTWARE)
14: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
GLU B:80 , ASN B:82 , GLU B:88 , ASN B:105 , ASP B:106 , FUC B:304
BINDING SITE FOR RESIDUE CA B 306
02
AC3
SOFTWARE
ASN A:4 , ARG A:22 , GLU A:208 , LEU B:151 , NAG B:282
BINDING SITE FOR MONO-SACCHARIDE NAG A 285 BOUND TO ASN A 4
03
AC4
SOFTWARE
ASN A:124 , GLU B:71 , LYS B:74
BINDING SITE FOR MONO-SACCHARIDE NAG A 286 BOUND TO ASN A 124
04
AC5
SOFTWARE
ASN A:139 , TYR A:140 , NAG B:285
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 , PRO A:238 , NAG A:284 , HOH A:2037 , HOH A:2056 , 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 , THR A:225 , VAL A:232 , CYS A:234 , PHE A:241 , NAG A:283 , HOH A:2048 , GLU B:233 , NAG B:284
BINDING SITE FOR MONO-SACCHARIDE NAG A 284 BOUND TO ASN A 178
07
BC1
SOFTWARE
LEU A:151 , NAG A:282 , ASN B:4 , ARG B:22 , HOH B:2001
BINDING SITE FOR MONO-SACCHARIDE NAG B 285 BOUND TO ASN B 4
08
BC2
SOFTWARE
GLU A:71 , LYS A:74 , ASN B:124 , HOH B:2021
BINDING SITE FOR MONO-SACCHARIDE NAG B 286 BOUND TO ASN B 124
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:2028 , SER B:149 , GLN B:155 , ILE B:156 , ASN B:158 , PRO B:238 , HOH B:2040 , HOH B:2041
BINDING SITE FOR MONO-SACCHARIDE NAG B 283 BOUND TO ASN B 158
11
BC5
SOFTWARE
NAG A:284 , HOH A:2049 , ASN B:178 , ALA B:223 , VAL B:224 , VAL B:232 , GLU B:233 , CYS B:234 , GLY B:239 , PHE B:241 , HOH B:2040 , HOH B:2060
BINDING SITE FOR MONO-SACCHARIDE NAG B 284 BOUND TO ASN B 178
12
BC6
SOFTWARE
ASN B:182
BINDING SITE FOR MONO-SACCHARIDE NAG B 281 BOUND TO ASN B 182
13
BC7
SOFTWARE
TYR B:193 , TRP B:243 , ASN B:244
BINDING SITE FOR MONO-SACCHARIDE NAG B 287 BOUND TO ASN B 244
14
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:306 , TYR B:48 , GLU B:80 , ASN B:82 , ARG B:84 , GLN B:85 , GLU B:88 , GLU B:92 , TYR B:94 , ARG B:97 , GLU B:98 , ASN B:105 , ASP B:106 , GLU B:107 , CA B:306
BINDING SITE FOR POLY-SACCHARIDE RESIDUES SIA B 301 THROUGH FUC B 304
[
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 B, )
2: VAR_011790 (C109W, chain B, )
3: VAR_004191 (S128R, chain B, )
4: VAR_014302 (Q236P, chain B, )
5: VAR_011791 (E274K, chain B, )
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
B
M
10
I
2
UniProt
VAR_011790
C
130
W
LYAM2_HUMAN
Polymorphism
5360
B
C
109
W
3
UniProt
VAR_004191
S
149
R
LYAM2_HUMAN
Polymorphism
5361
B
S
128
R
4
UniProt
VAR_014302
Q
257
P
LYAM2_HUMAN
Polymorphism
3917422
B
Q
236
P
5
UniProt
VAR_011791
E
295
K
LYAM2_HUMAN
Polymorphism
5364
B
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 (B:90-117)
2: EGF_3 (B:118-154)
3: EGF_1 (B:142-153)
4: EGF_2 (B:142-153)
5: SUSHI (B: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
-
B:90-117
2
EGF_3
PS50026
EGF-like domain profile.
LYAM2_HUMAN
139-175
1
-
B:118-154
3
EGF_1
PS00022
EGF-like domain signature 1.
LYAM2_HUMAN
163-174
1
-
B:142-153
4
EGF_2
PS01186
EGF-like domain signature 2.
LYAM2_HUMAN
163-174
1
-
B: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
-
B:157-218
-
B:219-280
-
-
-
-
[
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]
Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain B
Asymmetric Unit 1
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