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2VMC
Biol. Unit 1
Info
Asym.Unit (57 KB)
Biol.Unit 1 (148 KB)
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(1)
Title
:
STRUCTURE OF THE COMPLEX OF DISCOIDIN II FROM DICTYOSTELIUM DISCOIDEUM WITH N-ACETYL-GALACTOSAMINE
Authors
:
K. Saboia, M. Satre, A. Imberty, A. Varrot
Date
:
25 Jan 08 (Deposition) - 01 Jul 08 (Release) - 08 Jun 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (3x)
Keywords
:
Ddr, Lectin, Aggregation, Cell Adhesion
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. S. Aragao, M. Satre, A. Imberty, A. Varrot
Structure Determination Of Discoidin Ii From Dictyostelium Discoideum And Carbohydrate Binding Properties Of The Lectin Domain.
Proteins V. 73 43 2008
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Hetero Components
(4, 15)
Info
All Hetero Components
1a: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHO... (1PGa)
1b: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHO... (1PGb)
2a: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Ga)
3a: CALCIUM ION (CAa)
4a: CHLORIDE ION (CLa)
4b: CHLORIDE ION (CLb)
5a: 1,2-ETHANEDIOL (EDOa)
6a: N-ACETYL-D-GALACTOSAMINE (NGAa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
1PG
6
Ligand/Ion
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2
A2G
3
Ligand/Ion
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
3
CA
-1
Ligand/Ion
CALCIUM ION
4
CL
-1
Ligand/Ion
CHLORIDE ION
5
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
6
NGA
3
Ligand/Ion
N-ACETYL-D-GALACTOSAMINE
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:212
BINDING SITE FOR RESIDUE CL A 498
2
AC2
SOFTWARE
TRP A:219
BINDING SITE FOR RESIDUE CL A 499
3
AC3
SOFTWARE
ASN A:39 , SER A:40 , ASP A:47 , HOH A:2078 , HOH A:2082 , HOH A:2098 , HOH A:2099
BINDING SITE FOR RESIDUE CA A 500
4
AC4
SOFTWARE
ASP A:209 , GLN A:216 , ARG A:218 , TRP A:238 , TYR A:244 , NGA A:505 , HOH A:2336 , HOH A:2352 , HOH A:2353 , HOH A:2354 , HOH A:2355 , HOH A:2356
BINDING SITE FOR RESIDUE A2G A 501
5
AC5
SOFTWARE
ASP A:209 , GLN A:216 , ARG A:218 , TRP A:238 , TYR A:244 , A2G A:501 , HOH A:2336 , HOH A:2352 , HOH A:2354 , HOH A:2355 , HOH A:2356
BINDING SITE FOR RESIDUE NGA A 505
6
AC6
SOFTWARE
SER A:9 , ALA A:12 , ARG A:94 , TRP A:102 , ALA A:135 , HIS A:137 , HOH A:2162
BINDING SITE FOR RESIDUE 1PG A 502
7
AC7
SOFTWARE
TYR A:24 , HIS A:28 , SER A:53 , ARG A:81 , HIS A:84 , GLN A:86 , HOH A:2057 , HOH A:2358
BINDING SITE FOR RESIDUE 1PG A 503
8
AC8
SOFTWARE
SER A:7
BINDING SITE FOR RESIDUE EDO A 504
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: FA58C_3 (A:10-154)
2: FA58C_1 (A:51-80)
;
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.
DIS2_DICDI
10-154
3
A:10-154
2
FA58C_1
PS01285
Coagulation factors 5/8 type C domain (FA58C) signature 1.
DIS2_DICDI
51-80
3
A:51-80
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Exons
(0, 0)
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All Exons
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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
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CATH Domains
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all CATH domains
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_F5_F8_type_C_2vmcA01 (A:17-151)
2a: PFAM_H_lectin_2vmcA02 (A:183-255)
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Clans
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Families
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)
(
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Organisms
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)
(
)
Clan
:
GBD
(153)
Family
:
F5_F8_type_C
(45)
Dictyostelium discoideum (Slime mold)
(8)
1a
F5_F8_type_C-2vmcA01
A:17-151
Clan
:
no clan defined [family: H_lectin]
(8)
Family
:
H_lectin
(8)
Dictyostelium discoideum (Slime mold)
(8)
2a
H_lectin-2vmcA02
A:183-255
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Chain A
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Asym.Unit (57 KB)
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Header - Biol.Unit 1
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