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2VME
Biol. Unit 2
Info
Asym.Unit (264 KB)
Biol.Unit 1 (132 KB)
Biol.Unit 2 (128 KB)
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(1)
Title
:
STRUCTURE OF THE WILD-TYPE DISCOIDIN II FROM DICTYOSTELIUM DISCOIDEUM
Authors
:
K. S. Aragao, M. Satre, A. Imberty, A. Varrot
Date
:
25 Jan 08 (Deposition) - 01 Jul 08 (Release) - 08 Jun 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.45
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Lectin, Aggregation, Ddr, 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
(2, 11)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
3o: GLYCEROL (GOLo)
4a: ND1-PHOSPHONOHISTIDINE (HIPa)
4b: ND1-PHOSPHONOHISTIDINE (HIPb)
4c: ND1-PHOSPHONOHISTIDINE (HIPc)
4d: ND1-PHOSPHONOHISTIDINE (HIPd)
4e: ND1-PHOSPHONOHISTIDINE (HIPe)
4f: ND1-PHOSPHONOHISTIDINE (HIPf)
5a: TETRAETHYLENE GLYCOL (PG4a)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
GOL
8
Ligand/Ion
GLYCEROL
4
HIP
3
Mod. Amino Acid
ND1-PHOSPHONOHISTIDINE
5
PG4
-1
Ligand/Ion
TETRAETHYLENE GLYCOL
6
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(12, 12)
Info
All Sites
01: BC5 (SOFTWARE)
02: BC6 (SOFTWARE)
03: BC7 (SOFTWARE)
04: BC8 (SOFTWARE)
05: BC9 (SOFTWARE)
06: CC1 (SOFTWARE)
07: CC2 (SOFTWARE)
08: CC3 (SOFTWARE)
09: CC4 (SOFTWARE)
10: CC5 (SOFTWARE)
11: CC6 (SOFTWARE)
12: CC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
BC5
SOFTWARE
ASN D:39 , SER D:40 , ASP D:47 , HOH D:2016 , HOH D:2017
BINDING SITE FOR RESIDUE CA D 500
02
BC6
SOFTWARE
ASP D:68 , ASP E:68 , ASP F:68
BINDING SITE FOR RESIDUE ZN D 501
03
BC7
SOFTWARE
ASP D:209 , TYR D:244 , GLN E:216 , ARG E:218 , TRP E:238
BINDING SITE FOR RESIDUE GOL D 504
04
BC8
SOFTWARE
TYR D:24 , HIS D:28 , ARG D:81 , GLN D:86
BINDING SITE FOR RESIDUE GOL D 506
05
BC9
SOFTWARE
ASN E:39 , SER E:40 , ASP E:47 , HOH E:2017
BINDING SITE FOR RESIDUE CA E 500
06
CC1
SOFTWARE
PHE E:62 , ARG E:94 , TRP E:102 , HIS E:137
BINDING SITE FOR RESIDUE GOL E 504
07
CC2
SOFTWARE
TYR E:24 , HIS E:28 , ARG E:81 , GLN E:86 , HIS E:144
BINDING SITE FOR RESIDUE GOL E 506
08
CC3
SOFTWARE
SER E:182 , GLU E:220
BINDING SITE FOR RESIDUE GOL E 507
09
CC4
SOFTWARE
ASN F:39 , SER F:40 , ASP F:47 , HOH F:2013
BINDING SITE FOR RESIDUE CA F 500
10
CC5
SOFTWARE
PHE F:62 , ARG F:94 , TRP F:102 , HIS F:137
BINDING SITE FOR RESIDUE GOL F 503
11
CC6
SOFTWARE
GLN D:216 , ARG D:218 , TRP D:238 , ASP F:209 , TYR F:244
BINDING SITE FOR RESIDUE GOL F 504
12
CC7
SOFTWARE
HIS F:28 , ARG F:81 , GLN F:86
BINDING SITE FOR RESIDUE GOL F 506
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: FA58C_3 (D:10-154,E:10-154,F:10-154)
2: FA58C_1 (D:51-80,E:51-80,F: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
-
-
-
D:10-154
E:10-154
F:10-154
2
FA58C_1
PS01285
Coagulation factors 5/8 type C domain (FA58C) signature 1.
DIS2_DICDI
51-80
3
-
-
-
D:51-80
E:51-80
F:51-80
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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
(0, 0)
Info
All SCOP Domains
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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
(2, 12)
Info
all PFAM domains
1a: PFAM_F5_F8_type_C_2vmeF01 (F:17-151)
1b: PFAM_F5_F8_type_C_2vmeF02 (F:17-151)
1c: PFAM_F5_F8_type_C_2vmeF03 (F:17-151)
1d: PFAM_F5_F8_type_C_2vmeF04 (F:17-151)
1e: PFAM_F5_F8_type_C_2vmeF05 (F:17-151)
1f: PFAM_F5_F8_type_C_2vmeF06 (F:17-151)
2a: PFAM_H_lectin_2vmeF07 (F:183-255)
2b: PFAM_H_lectin_2vmeF08 (F:183-255)
2c: PFAM_H_lectin_2vmeF09 (F:183-255)
2d: PFAM_H_lectin_2vmeF10 (F:183-255)
2e: PFAM_H_lectin_2vmeF11 (F:183-255)
2f: PFAM_H_lectin_2vmeF12 (F:183-255)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GBD
(153)
Family
:
F5_F8_type_C
(45)
Dictyostelium discoideum (Slime mold)
(8)
1a
F5_F8_type_C-2vmeF01
F:17-151
1b
F5_F8_type_C-2vmeF02
F:17-151
1c
F5_F8_type_C-2vmeF03
F:17-151
1d
F5_F8_type_C-2vmeF04
F:17-151
1e
F5_F8_type_C-2vmeF05
F:17-151
1f
F5_F8_type_C-2vmeF06
F:17-151
Clan
:
no clan defined [family: H_lectin]
(8)
Family
:
H_lectin
(8)
Dictyostelium discoideum (Slime mold)
(8)
2a
H_lectin-2vmeF07
F:183-255
2b
H_lectin-2vmeF08
F:183-255
2c
H_lectin-2vmeF09
F:183-255
2d
H_lectin-2vmeF10
F:183-255
2e
H_lectin-2vmeF11
F:183-255
2f
H_lectin-2vmeF12
F:183-255
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Asym.Unit (264 KB)
Header - Asym.Unit
Biol.Unit 1 (132 KB)
Header - Biol.Unit 1
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Header - Biol.Unit 2
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