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2C5C
Biol. Unit 1
Info
Asym.Unit (141 KB)
Biol.Unit 1 (69 KB)
Biol.Unit 2 (66 KB)
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(1)
Title
:
SHIGA-LIKE TOXIN 1 B SUBUNIT COMPLEXED WITH A BIVALENT INHIBITOR
Authors
:
R. B. Dodd, R. J. Read
Date
:
26 Oct 05 (Deposition) - 27 Nov 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.94
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E (1x)
Biol. Unit 2: F,G,H,I,J (1x)
Keywords
:
Bacterial Exotoxin, Gb3 Binding Activity, Bivalent Ligand, Protein-Carbohydrate Recognition, Ob Fold, Toxin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. B. Dodd, R. J. Read
Extensive Cross-Linking Of The Shiga-Like Toxin 1 B Subunit By A Bivalent Ligand
To Be Published
[
close entry info
]
Hetero Components
(5, 38)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
1b: BETA-D-GLUCOSE (BGCb)
1c: BETA-D-GLUCOSE (BGCc)
1d: BETA-D-GLUCOSE (BGCd)
2a: BETA-D-GALACTOSE (GALa)
2b: BETA-D-GALACTOSE (GALb)
2c: BETA-D-GALACTOSE (GALc)
2d: BETA-D-GALACTOSE (GALd)
2e: BETA-D-GALACTOSE (GALe)
2f: BETA-D-GALACTOSE (GALf)
2g: BETA-D-GALACTOSE (GALg)
2h: BETA-D-GALACTOSE (GALh)
2i: BETA-D-GALACTOSE (GALi)
2j: BETA-D-GALACTOSE (GALj)
2k: BETA-D-GALACTOSE (GALk)
2l: BETA-D-GALACTOSE (GALl)
3a: ALPHA D-GALACTOSE (GLAa)
3aa: ALPHA D-GALACTOSE (GLAaa)
3ab: ALPHA D-GALACTOSE (GLAab)
3ac: ALPHA D-GALACTOSE (GLAac)
3b: ALPHA D-GALACTOSE (GLAb)
3c: ALPHA D-GALACTOSE (GLAc)
3d: ALPHA D-GALACTOSE (GLAd)
3e: ALPHA D-GALACTOSE (GLAe)
3f: ALPHA D-GALACTOSE (GLAf)
3g: ALPHA D-GALACTOSE (GLAg)
3h: ALPHA D-GALACTOSE (GLAh)
3i: ALPHA D-GALACTOSE (GLAi)
3j: ALPHA D-GALACTOSE (GLAj)
3k: ALPHA D-GALACTOSE (GLAk)
3l: ALPHA D-GALACTOSE (GLAl)
3m: ALPHA D-GALACTOSE (GLAm)
3n: ALPHA D-GALACTOSE (GLAn)
3o: ALPHA D-GALACTOSE (GLAo)
3p: ALPHA D-GALACTOSE (GLAp)
3q: ALPHA D-GALACTOSE (GLAq)
3r: ALPHA D-GALACTOSE (GLAr)
3s: ALPHA D-GALACTOSE (GLAs)
3t: ALPHA D-GALACTOSE (GLAt)
3u: ALPHA D-GALACTOSE (GLAu)
3v: ALPHA D-GALACTOSE (GLAv)
3w: ALPHA D-GALACTOSE (GLAw)
3x: ALPHA D-GALACTOSE (GLAx)
3y: ALPHA D-GALACTOSE (GLAy)
3z: ALPHA D-GALACTOSE (GLAz)
4a: ALPHA-D-GLUCOSE (GLCa)
4b: ALPHA-D-GLUCOSE (GLCb)
4c: ALPHA-D-GLUCOSE (GLCc)
4d: ALPHA-D-GLUCOSE (GLCd)
4e: ALPHA-D-GLUCOSE (GLCe)
4f: ALPHA-D-GLUCOSE (GLCf)
4g: ALPHA-D-GLUCOSE (GLCg)
4h: ALPHA-D-GLUCOSE (GLCh)
4i: ALPHA-D-GLUCOSE (GLCi)
4j: ALPHA-D-GLUCOSE (GLCj)
5a: DIETHYL PROPANE-1,3-DIYLBISCARBAMA... (S10a)
5b: DIETHYL PROPANE-1,3-DIYLBISCARBAMA... (S10b)
5c: DIETHYL PROPANE-1,3-DIYLBISCARBAMA... (S10c)
5d: DIETHYL PROPANE-1,3-DIYLBISCARBAMA... (S10d)
5e: DIETHYL PROPANE-1,3-DIYLBISCARBAMA... (S10e)
5f: DIETHYL PROPANE-1,3-DIYLBISCARBAMA... (S10f)
5g: DIETHYL PROPANE-1,3-DIYLBISCARBAMA... (S10g)
5h: DIETHYL PROPANE-1,3-DIYLBISCARBAMA... (S10h)
6a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
2
Ligand/Ion
BETA-D-GLUCOSE
2
GAL
9
Ligand/Ion
BETA-D-GALACTOSE
3
GLA
16
Ligand/Ion
ALPHA D-GALACTOSE
4
GLC
7
Ligand/Ion
ALPHA-D-GLUCOSE
5
S10
4
Ligand/Ion
DIETHYL PROPANE-1,3-DIYLBISCARBAMATE
6
SO4
-1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(47, 47)
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)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: EC6 (SOFTWARE)
36: FC5 (SOFTWARE)
37: FC6 (SOFTWARE)
38: FC7 (SOFTWARE)
39: FC8 (SOFTWARE)
40: FC9 (SOFTWARE)
41: GC1 (SOFTWARE)
42: GC3 (SOFTWARE)
43: GC4 (SOFTWARE)
44: GC5 (SOFTWARE)
45: GC6 (SOFTWARE)
46: GC7 (SOFTWARE)
47: GC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:32 , ARG A:33 , TRP A:34 , ASN A:35 , GAL A:1071 , ASP B:18 , ASP F:16 , ARG J:33 , GLA J:1073
BINDING SITE FOR RESIDUE GLA A1070
02
AC2
SOFTWARE
TRP A:34 , GLA A:1070 , GLC A:1072 , S10 A:1076 , ASP F:16 , GAL J:1074 , GLC J:1075
BINDING SITE FOR RESIDUE GAL A1071
03
AC3
SOFTWARE
GAL A:1071 , S10 A:1076 , ASP F:16 , THR J:1 , GLU J:65
BINDING SITE FOR RESIDUE GLC A1072
04
AC4
SOFTWARE
PHE A:30 , THR A:31 , ASN A:32 , ARG A:33 , GLY A:62 , PHE A:63 , GAL A:1074 , ASP B:16 , ASN J:32 , GLA J:1070 , GAL J:1071
BINDING SITE FOR RESIDUE GLA A1073
05
AC5
SOFTWARE
THR A:1 , THR A:54 , ASN A:55 , GLY A:62 , GLA A:1073 , GLC A:1075 , GAL J:1071 , S10 J:1076
BINDING SITE FOR RESIDUE GAL A1074
06
AC6
SOFTWARE
ASN A:55 , GAL A:1074 , GLA I:1070 , ASP J:18 , TRP J:34 , GAL J:1071 , S10 J:1076
BINDING SITE FOR RESIDUE GLC A1075
07
AC7
SOFTWARE
ASN B:32 , ARG B:33 , TRP B:34 , ASN B:35 , GAL B:71 , TYR C:14 , ASP C:18 , TRP C:34
BINDING SITE FOR RESIDUE GLA B 70
08
AC8
SOFTWARE
S10 A:1076 , TRP B:34 , GLA B:70 , GLC B:72 , ASP F:17
BINDING SITE FOR RESIDUE GAL B 71
09
AC9
SOFTWARE
S10 A:1076 , GAL B:71 , ASN F:15 , ASP F:17 , THR F:19 , PHE F:30
BINDING SITE FOR RESIDUE GLC B 72
10
BC1
SOFTWARE
THR B:31 , ASN B:32 , ARG B:33 , GLY B:62 , PHE B:63 , GAL B:1073 , ASP C:16
BINDING SITE FOR RESIDUE GLA B1072
11
BC2
SOFTWARE
THR B:54 , ASN B:55 , GLY B:62 , GLA B:1072 , GLC B:1074
BINDING SITE FOR RESIDUE GAL B1073
12
BC3
SOFTWARE
ASN B:55 , GAL B:1073
BINDING SITE FOR RESIDUE GLC B1074
13
BC4
SOFTWARE
ASN B:15 , ASP B:17 , THR B:19 , PHE B:30 , GAL B:1077 , S10 F:1073
BINDING SITE FOR RESIDUE GLC B1075
14
BC5
SOFTWARE
GAL B:1077 , ARG F:33 , TRP F:34 , ASN F:35 , TYR G:14 , ASP G:18
BINDING SITE FOR RESIDUE GLA B1076
15
BC6
SOFTWARE
ASP B:17 , GLC B:1075 , GLA B:1076 , TRP F:34 , S10 F:1073
BINDING SITE FOR RESIDUE GAL B1077
16
BC7
SOFTWARE
ASN C:32 , ARG C:33 , TRP C:34 , ASN C:35
BINDING SITE FOR RESIDUE GLA C1070
17
BC8
SOFTWARE
THR C:31 , ASN C:32 , ARG C:33 , PHE C:63 , SER C:64 , GLA C:1072 , ASP D:16
BINDING SITE FOR RESIDUE GLA C1071
18
BC9
SOFTWARE
THR C:54 , ASN C:55 , GLY C:62 , GLA C:1071 , S10 C:1073
BINDING SITE FOR RESIDUE GLA C1072
19
CC1
SOFTWARE
GAL C:1075 , PHE F:30 , THR F:31 , ASN F:32 , ARG F:33 , GLY F:62 , PHE F:63 , SER F:64 , ASP G:16
BINDING SITE FOR RESIDUE GLA C1074
20
CC2
SOFTWARE
S10 C:1073 , GLA C:1074 , GLC C:1076 , THR F:1 , THR F:54 , ASN F:55
BINDING SITE FOR RESIDUE GAL C1075
21
CC3
SOFTWARE
S10 C:1073 , GAL C:1075 , ASN F:55
BINDING SITE FOR RESIDUE GLC C1076
22
CC4
SOFTWARE
ASN D:32 , ARG D:33 , TRP D:34 , ASN D:35 , GLA D:1071 , ASP E:18
BINDING SITE FOR RESIDUE GLA D1070
23
CC5
SOFTWARE
TRP D:34 , GLA D:1070
BINDING SITE FOR RESIDUE GLA D1071
24
CC6
SOFTWARE
THR D:31 , ASN D:32 , ARG D:33 , GLY D:62 , PHE D:63 , SER D:64 , GAL D:1073 , GLA D:1076 , GAL D:1077 , ASP E:16
BINDING SITE FOR RESIDUE GLA D1072
25
CC7
SOFTWARE
THR D:54 , ASN D:55 , GLY D:62 , GLA D:1072 , BGC D:1074 , S10 D:1075 , GLA D:1076 , GAL D:1077 , BGC D:1078
BINDING SITE FOR RESIDUE GAL D1073
26
CC8
SOFTWARE
GAL D:1073 , S10 D:1075 , GAL D:1077 , BGC D:1078
BINDING SITE FOR RESIDUE BGC D1074
27
CC9
SOFTWARE
THR D:31 , ASN D:32 , ARG D:33 , GLY D:62 , PHE D:63 , SER D:64 , GLA D:1072 , GAL D:1073 , GAL D:1077 , ASP E:16
BINDING SITE FOR RESIDUE GLA D1076
28
DC1
SOFTWARE
THR D:54 , ASN D:55 , GLY D:62 , GLA D:1072 , GAL D:1073 , BGC D:1074 , S10 D:1075 , GLA D:1076 , BGC D:1078
BINDING SITE FOR RESIDUE GAL D1077
29
DC2
SOFTWARE
GAL D:1073 , BGC D:1074 , S10 D:1075 , GAL D:1077
BINDING SITE FOR RESIDUE BGC D1078
30
DC3
SOFTWARE
ASP A:18 , ASN E:32 , ARG E:33 , TRP E:34 , ASN E:35 , GLA E:1071 , GLC J:1075
BINDING SITE FOR RESIDUE GLA E1070
31
DC4
SOFTWARE
S10 A:1076 , TRP E:34 , GLA E:1070
BINDING SITE FOR RESIDUE GLA E1071
32
DC5
SOFTWARE
ASP A:16 , THR E:31 , ASN E:32 , ARG E:33 , GLY E:62 , PHE E:63 , GAL E:1073
BINDING SITE FOR RESIDUE GLA E1072
33
DC6
SOFTWARE
THR E:54 , ASN E:55 , GLY E:62 , GLA E:1072 , GLC E:1074 , S10 E:1075
BINDING SITE FOR RESIDUE GAL E1073
34
DC7
SOFTWARE
ASN E:55 , GAL E:1073 , THR I:46 , HOH I:2001 , ILE J:45
BINDING SITE FOR RESIDUE GLC E1074
35
EC6
SOFTWARE
GLC A:1075 , ASN I:32 , ARG I:33 , TRP I:34 , ASN I:35 , GLA I:1071 , ASP J:18 , TRP J:34
BINDING SITE FOR RESIDUE GLA I1070
36
FC5
SOFTWARE
ARG A:33 , GLA A:1073 , ASP B:16 , ASP F:18 , TRP F:34 , ARG J:33 , TRP J:34 , ASN J:35 , GAL J:1071
BINDING SITE FOR RESIDUE GLA J1070
37
FC6
SOFTWARE
GLA A:1073 , GAL A:1074 , GLC A:1075 , ASP B:16 , TRP J:34 , GLA J:1070 , GLC J:1072 , S10 J:1077
BINDING SITE FOR RESIDUE GAL J1071
38
FC7
SOFTWARE
THR A:1 , GLU A:65 , ASP B:16 , HOH B:2001 , GAL J:1071 , S10 J:1077
BINDING SITE FOR RESIDUE GLC J1072
39
FC8
SOFTWARE
ASN A:32 , GLA A:1070 , ASP F:16 , THR J:31 , ASN J:32 , ARG J:33 , GLY J:62 , PHE J:63 , SER J:64 , GAL J:1074 , S10 J:1076 , HOH J:2003
BINDING SITE FOR RESIDUE GLA J1073
40
FC9
SOFTWARE
GAL A:1071 , THR J:54 , ASN J:55 , GLY J:62 , GLA J:1073 , GLC J:1075 , S10 J:1076
BINDING SITE FOR RESIDUE GAL J1074
41
GC1
SOFTWARE
ASP A:18 , GAL A:1071 , GLA E:1070 , ASN J:55 , GAL J:1074 , S10 J:1076
BINDING SITE FOR RESIDUE GLC J1075
42
GC3
SOFTWARE
GAL A:1071 , GLC A:1072 , GAL B:71 , GLC B:72 , GLA E:1071
BINDING SITE FOR RESIDUE S10 A1076
43
GC4
SOFTWARE
ASN C:32 , GLA C:1072 , GAL C:1075 , GLC C:1076
BINDING SITE FOR RESIDUE S10 C1073
44
GC5
SOFTWARE
GLY D:60 , GAL D:1073 , BGC D:1074 , GAL D:1077 , BGC D:1078
BINDING SITE FOR RESIDUE S10 D1075
45
GC6
SOFTWARE
GAL E:1073 , ILE F:45
BINDING SITE FOR RESIDUE S10 E1075
46
GC7
SOFTWARE
GLC B:1075 , GAL B:1077
BINDING SITE FOR RESIDUE S10 F1073
47
GC9
SOFTWARE
ASN A:32 , GAL A:1074 , GLC A:1075 , ASP J:17 , THR J:19 , ASN J:32 , GLA J:1073 , GAL J:1074 , GLC J:1075
BINDING SITE FOR RESIDUE S10 J1076
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
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
(1, 10)
Info
All SCOP Domains
1a: SCOP_d2c5ca_ (A:)
1b: SCOP_d2c5cb_ (B:)
1c: SCOP_d2c5cc_ (C:)
1d: SCOP_d2c5cd_ (D:)
1e: SCOP_d2c5ce_ (E:)
1f: SCOP_d2c5cf_ (F:)
1g: SCOP_d2c5cg_ (G:)
1h: SCOP_d2c5ch_ (H:)
1i: SCOP_d2c5ci_ (I:)
1j: SCOP_d2c5cj_ (J:)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
OB-fold
(1179)
Superfamily
:
Bacterial enterotoxins
(188)
Family
:
Bacterial AB5 toxins, B-subunits
(85)
Protein domain
:
Verotoxin-1/shiga-toxin, B-pentamer
(19)
Escherichia coli [TaxId: 562]
(14)
1a
d2c5ca_
A:
1b
d2c5cb_
B:
1c
d2c5cc_
C:
1d
d2c5cd_
D:
1e
d2c5ce_
E:
1f
d2c5cf_
F:
1g
d2c5cg_
G:
1h
d2c5ch_
H:
1i
d2c5ci_
I:
1j
d2c5cj_
J:
[
close SCOP info
]
CATH Domains
(1, 10)
Info
all CATH domains
1a: CATH_2c5cA00 (A:1-69)
1b: CATH_2c5cB00 (B:1-69)
1c: CATH_2c5cC00 (C:1-69)
1d: CATH_2c5cD00 (D:1-69)
1e: CATH_2c5cE00 (E:1-69)
1f: CATH_2c5cF00 (F:1-69)
1g: CATH_2c5cG00 (G:1-69)
1h: CATH_2c5cH00 (H:1-69)
1i: CATH_2c5cI00 (I:1-69)
1j: CATH_2c5cJ00 (J:1-69)
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Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
[code=2.40.50.70, no name defined]
(18)
Bacteriophage h30. Organism_taxid: 12371.
(1)
1a
2c5cA00
A:1-69
1b
2c5cB00
B:1-69
1c
2c5cC00
C:1-69
1d
2c5cD00
D:1-69
1e
2c5cE00
E:1-69
1f
2c5cF00
F:1-69
1g
2c5cG00
G:1-69
1h
2c5cH00
H:1-69
1i
2c5cI00
I:1-69
1j
2c5cJ00
J:1-69
[
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Pfam Domains
(0, 0)
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all PFAM domains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (141 KB)
Header - Asym.Unit
Biol.Unit 1 (69 KB)
Header - Biol.Unit 1
Biol.Unit 2 (66 KB)
Header - Biol.Unit 2
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