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2VME
Asym. Unit
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
(6, 32)
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
6
Ligand/Ion
CALCIUM ION
2
CL
2
Ligand/Ion
CHLORIDE ION
3
GOL
15
Ligand/Ion
GLYCEROL
4
HIP
6
Mod. Amino Acid
ND1-PHOSPHONOHISTIDINE
5
PG4
1
Ligand/Ion
TETRAETHYLENE GLYCOL
6
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
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Sites
(25, 25)
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)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:39 , SER A:40 , ASP A:47 , HOH A:2023 , HOH A:2024
BINDING SITE FOR RESIDUE CA A 500
02
AC2
SOFTWARE
ASP A:68 , ASP B:68 , ASP C:68
BINDING SITE FOR RESIDUE ZN A 501
03
AC3
SOFTWARE
TRP B:219
BINDING SITE FOR RESIDUE CL A 502
04
AC4
SOFTWARE
ARG A:19 , VAL A:64 , ARG A:94 , TRP A:102 , ALA A:135 , HIS A:137 , ALA C:12
BINDING SITE FOR RESIDUE GOL A 503
05
AC5
SOFTWARE
ASP A:209 , TYR A:244 , GLN B:216 , ARG B:218 , TRP B:238
BINDING SITE FOR RESIDUE GOL A 504
06
AC6
SOFTWARE
ASN B:39 , SER B:40 , ASP B:47 , HOH B:2021 , HOH B:2022 , HOH B:2025
BINDING SITE FOR RESIDUE CA B 500
07
AC7
SOFTWARE
ARG B:19 , ARG B:94 , ALA B:135 , HIS B:137
BINDING SITE FOR RESIDUE GOL B 503
08
AC8
SOFTWARE
ASP B:209 , GLN C:216 , ARG C:218 , TRP C:238
BINDING SITE FOR RESIDUE GOL B 504
09
AC9
SOFTWARE
TYR B:24 , HIS B:28 , ARG B:81 , GLN B:86 , HIS B:144 , HOH B:2076
BINDING SITE FOR RESIDUE GOL B 506
10
BC1
SOFTWARE
ASN C:39 , SER C:40 , ASP C:47 , HOH C:2020 , HOH C:2022
BINDING SITE FOR RESIDUE CA C 500
11
BC2
SOFTWARE
GLN A:216 , ARG A:218 , TRP A:238 , ASP C:209 , TYR C:244
BINDING SITE FOR RESIDUE GOL C 504
12
BC3
SOFTWARE
SER B:7 , VAL B:8 , SER B:9 , ALA B:12 , ASN B:13 , ARG C:94 , ASN C:99 , VAL C:100 , TRP C:102 , HIS C:137 , HOH C:2110
BINDING SITE FOR RESIDUE PG4 C 505
13
BC4
SOFTWARE
HIS C:28 , ARG C:81 , GLN C:86 , HIS C:144 , HOH C:2064
BINDING SITE FOR RESIDUE GOL C 506
14
BC5
SOFTWARE
ASN D:39 , SER D:40 , ASP D:47 , HOH D:2016 , HOH D:2017
BINDING SITE FOR RESIDUE CA D 500
15
BC6
SOFTWARE
ASP D:68 , ASP E:68 , ASP F:68
BINDING SITE FOR RESIDUE ZN D 501
16
BC7
SOFTWARE
ASP D:209 , TYR D:244 , GLN E:216 , ARG E:218 , TRP E:238
BINDING SITE FOR RESIDUE GOL D 504
17
BC8
SOFTWARE
TYR D:24 , HIS D:28 , ARG D:81 , GLN D:86
BINDING SITE FOR RESIDUE GOL D 506
18
BC9
SOFTWARE
ASN E:39 , SER E:40 , ASP E:47 , HOH E:2017
BINDING SITE FOR RESIDUE CA E 500
19
CC1
SOFTWARE
PHE E:62 , ARG E:94 , TRP E:102 , HIS E:137
BINDING SITE FOR RESIDUE GOL E 504
20
CC2
SOFTWARE
TYR E:24 , HIS E:28 , ARG E:81 , GLN E:86 , HIS E:144
BINDING SITE FOR RESIDUE GOL E 506
21
CC3
SOFTWARE
SER E:182 , GLU E:220
BINDING SITE FOR RESIDUE GOL E 507
22
CC4
SOFTWARE
ASN F:39 , SER F:40 , ASP F:47 , HOH F:2013
BINDING SITE FOR RESIDUE CA F 500
23
CC5
SOFTWARE
PHE F:62 , ARG F:94 , TRP F:102 , HIS F:137
BINDING SITE FOR RESIDUE GOL F 503
24
CC6
SOFTWARE
GLN D:216 , ARG D:218 , TRP D:238 , ASP F:209 , TYR F:244
BINDING SITE FOR RESIDUE GOL F 504
25
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 not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: FA58C_3 (A:10-154,B:10-154,C:10-154,D:10-15...)
2: FA58C_1 (A:51-80,B:51-80,C:51-80,D:51-80,E:...)
;
View:
Select:
Label:
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
6
A:10-154
B:10-154
C:10-154
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
6
A:51-80
B:51-80
C:51-80
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.
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
(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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