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2WN3
Asym. Unit
Info
Asym.Unit (153 KB)
Biol.Unit 1 (147 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM IN COMPLEX WITH THE DISACCHARIDE GALNAC BETA 1-3 GALACTOSE, AT 1.6 A RESOLUTION.
Authors
:
S. Mathieu, A. Imberty, A. Varrot
Date
:
07 Jul 09 (Deposition) - 26 May 10 (Release) - 21 Jul 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.59
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Type-H Lectin, Cell Adhesion, Discoidin Domain, Lectin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
S. Mathieu, K. Saboia Aragao, A. Imberty, A. Varrot
Discoidin I From Dictyostelium Discoideum And Interactions With Oligosaccharides: Specificity, Affinity, Crystal Structures And Comparison With Discoidin Ii.
J. Mol. Biol. V. 400 540 2010
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Hetero Components
(6, 16)
Info
All Hetero Components
1a: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHO... (1PGa)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
3a: BETA-D-GALACTOSE (GALa)
3b: BETA-D-GALACTOSE (GALb)
3c: BETA-D-GALACTOSE (GALc)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
5a: N-ACETYL-D-GALACTOSAMINE (NGAa)
5b: N-ACETYL-D-GALACTOSAMINE (NGAb)
5c: N-ACETYL-D-GALACTOSAMINE (NGAc)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PG
1
Ligand/Ion
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2
CA
3
Ligand/Ion
CALCIUM ION
3
GAL
3
Ligand/Ion
BETA-D-GALACTOSE
4
GOL
3
Ligand/Ion
GLYCEROL
5
NGA
3
Ligand/Ion
N-ACETYL-D-GALACTOSAMINE
6
SO4
3
Ligand/Ion
SULFATE ION
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Sites
(16, 16)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:206 , TYR A:241 , GAL A:301 , HOH A:2405 , HOH A:2406 , HOH A:2407 , HOH A:2408 , GLN B:213 , ARG B:215 , TRP B:235 , ASN B:236
BINDING SITE FOR RESIDUE NGA A 300
02
AC2
SOFTWARE
NGA A:300 , ASN B:236
BINDING SITE FOR RESIDUE GAL A 301
03
AC3
SOFTWARE
ASP A:164 , ASP A:203 , ASP A:246 , GLN B:219 , HOH B:2309 , HOH B:2310
BINDING SITE FOR RESIDUE CA A 400
04
AC4
SOFTWARE
SER A:157 , VAL A:158 , THR A:159 , SER B:157 , VAL B:158 , THR B:159 , SER C:157 , VAL C:158 , THR C:159
BINDING SITE FOR RESIDUE SO4 A 401
05
AC5
SOFTWARE
ARG B:104 , VAL B:109 , THR B:110 , HIS B:121 , HOH B:2189
BINDING SITE FOR RESIDUE SO4 A 403
06
AC6
SOFTWARE
ARG A:18 , THR A:57 , TYR A:60 , LYS A:90 , ARG A:92 , TRP A:100 , GLU A:102 , HIS A:135 , HOH A:2223 , HOH A:2409 , ALA C:11
BINDING SITE FOR RESIDUE 1PG A 500
07
AC7
SOFTWARE
ASP B:206 , TYR B:241 , GAL B:301 , HOH B:2363 , HOH B:2364 , HOH B:2365 , HOH B:2367 , GLN C:213 , ARG C:215 , TRP C:235 , ASN C:236
BINDING SITE FOR RESIDUE NGA B 300
08
AC8
SOFTWARE
NGA B:300 , ASN C:236
BINDING SITE FOR RESIDUE GAL B 301
09
AC9
SOFTWARE
ASP B:164 , ASP B:203 , ASP B:246 , GLN C:219 , HOH C:2285 , HOH C:2287
BINDING SITE FOR RESIDUE CA B 400
10
BC1
SOFTWARE
ALA A:0 , MET A:1 , ARG B:92 , HOH B:2368 , HOH B:2369
BINDING SITE FOR RESIDUE SO4 B 402
11
BC2
SOFTWARE
ALA A:11 , ARG B:18 , VAL B:62 , ALA B:133 , HIS B:135
BINDING SITE FOR RESIDUE GOL B 500
12
BC3
SOFTWARE
GLN A:213 , ARG A:215 , TRP A:235 , ASN A:236 , ASP C:206 , GAL C:301 , HOH C:2340 , HOH C:2341 , HOH C:2342
BINDING SITE FOR RESIDUE NGA C 300
13
BC4
SOFTWARE
ASN A:236 , NGA C:300
BINDING SITE FOR RESIDUE GAL C 301
14
BC5
SOFTWARE
GLN A:219 , HOH A:2351 , HOH A:2352 , ASP C:164 , ASP C:203 , ASP C:246
BINDING SITE FOR RESIDUE CA C 400
15
BC6
SOFTWARE
ALA B:11 , ARG C:18 , ARG C:92 , TRP C:100 , HIS C:135
BINDING SITE FOR RESIDUE GOL C 500
16
BC7
SOFTWARE
TYR C:23 , HIS C:27 , THR C:41 , ARG C:79 , GLN C:84 , HIS C:142
BINDING SITE FOR RESIDUE GOL C 501
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(2, 5)
Info
All PROSITE Patterns/Profiles
1: FA58C_3 (A:1-152,B:1-152)
2: FA58C_1 (A:49-78,B:49-78,C:49-78)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FA58C_3
PS50022
Coagulation factors 5/8 type C domain (FA58C) profile.
DIS1A_DICDI
1-152
2
A:1-152
B:1-152
2
FA58C_1
PS01285
Coagulation factors 5/8 type C domain (FA58C) signature 1.
DIS1A_DICDI
49-78
3
A:49-78
B:49-78
C:49-78
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
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CATH Domains
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all CATH domains
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Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_F5_F8_type_C_2wn3C01 (C:16-149)
1b: PFAM_F5_F8_type_C_2wn3C02 (C:16-149)
1c: PFAM_F5_F8_type_C_2wn3C03 (C:16-149)
2a: PFAM_H_lectin_2wn3C04 (C:180-252)
2b: PFAM_H_lectin_2wn3C05 (C:180-252)
2c: PFAM_H_lectin_2wn3C06 (C:180-252)
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Clans
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(
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Families
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(
)
Organisms
(
)
(
)
Clan
:
GBD
(153)
Family
:
F5_F8_type_C
(45)
Dictyostelium discoideum (Slime mold)
(8)
1a
F5_F8_type_C-2wn3C01
C:16-149
1b
F5_F8_type_C-2wn3C02
C:16-149
1c
F5_F8_type_C-2wn3C03
C:16-149
Clan
:
no clan defined [family: H_lectin]
(8)
Family
:
H_lectin
(8)
Dictyostelium discoideum (Slime mold)
(8)
2a
H_lectin-2wn3C04
C:180-252
2b
H_lectin-2wn3C05
C:180-252
2c
H_lectin-2wn3C06
C:180-252
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Asym.Unit (153 KB)
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