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1R4P
Asym. Unit
Info
Asym.Unit (122 KB)
Biol.Unit 1 (116 KB)
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(1)
Title
:
SHIGA TOXIN TYPE 2
Authors
:
M. E. Fraser, M. Fujinaga, M. M. Cherney, A. R. Melton-Celsa, E. M. Twiddy, A. D. O'Brien, M. N. G. James
Date
:
07 Oct 03 (Deposition) - 11 May 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.77
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Ab5 Toxin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. E. Fraser, M. Fujinaga, M. M. Cherney, A. R. Melton-Celsa, E. M. Twiddy, A. D. O'Brien, M. N. G. James
Structure Of Shiga Toxin Type 2 (Stx2) From Escherichia Coli O157:H7.
J. Biol. Chem. V. 279 27511 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 29)
Info
All Hetero Components
1a: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONA... (1PSa)
1b: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONA... (1PSb)
1c: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONA... (1PSc)
1d: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONA... (1PSd)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
3a: FORMIC ACID (FMTa)
3b: FORMIC ACID (FMTb)
3c: FORMIC ACID (FMTc)
3d: FORMIC ACID (FMTd)
3e: FORMIC ACID (FMTe)
3f: FORMIC ACID (FMTf)
3g: FORMIC ACID (FMTg)
3h: FORMIC ACID (FMTh)
3i: FORMIC ACID (FMTi)
3j: FORMIC ACID (FMTj)
3k: FORMIC ACID (FMTk)
3l: FORMIC ACID (FMTl)
3m: FORMIC ACID (FMTm)
3n: FORMIC ACID (FMTn)
3o: FORMIC ACID (FMTo)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
4e: SODIUM ION (NAe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PS
4
Ligand/Ion
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
2
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
3
FMT
15
Ligand/Ion
FORMIC ACID
4
NA
5
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(29, 29)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:22 , SER A:25 , HOH A:4021 , HOH A:4110 , HOH A:4168 , HOH A:4173
BINDING SITE FOR RESIDUE NA A 4001
02
AC2
SOFTWARE
ARG A:266 , SER A:278 , ASN A:279 , FMT A:3004 , HOH A:4035 , HOH C:3065
BINDING SITE FOR RESIDUE NA A 4002
03
AC3
SOFTWARE
SER A:15 , SER A:19 , HOH A:4078 , HOH A:4153 , HOH A:4217
BINDING SITE FOR RESIDUE NA A 4003
04
AC4
SOFTWARE
SER F:53 , THR F:55 , SER F:60 , GLY F:61
BINDING SITE FOR RESIDUE NA F 4004
05
AC5
SOFTWARE
SER B:53 , THR B:55 , SER B:60 , GLY B:61
BINDING SITE FOR RESIDUE NA B 4005
06
AC6
SOFTWARE
ASN F:14 , ASP F:16 , THR F:18 , TRP F:29 , HOH F:4018
BINDING SITE FOR RESIDUE 1PS F 1001
07
AC7
SOFTWARE
ASN B:14 , ASP B:16 , THR B:18 , TRP B:29 , HOH B:4010 , HOH B:4044 , HOH B:4046
BINDING SITE FOR RESIDUE 1PS B 1002
08
AC8
SOFTWARE
ASN C:14 , GLU C:15 , ASP C:16 , THR C:18 , TRP C:29 , FMT C:3012 , HOH C:3033 , HOH C:3037 , HOH C:3057 , SER D:58
BINDING SITE FOR RESIDUE 1PS C 1003
09
AC9
SOFTWARE
SER C:58 , ASN D:14 , GLU D:15 , ASP D:16 , THR D:18 , TRP D:29 , FMT D:3003 , HOH D:3020 , HOH D:3040 , HOH D:3047
BINDING SITE FOR RESIDUE 1PS D 1004
10
BC1
SOFTWARE
SER A:229 , PHE A:291 , TYR B:13 , SER F:31 , ARG F:32 , TRP F:33 , ASN F:34 , EDO F:2005
BINDING SITE FOR RESIDUE EDO F 2001
11
BC2
SOFTWARE
THR A:35 , LYS A:288 , GLY A:296 , HOH A:4059 , HOH A:4159 , TRP D:33
BINDING SITE FOR RESIDUE EDO D 2002
12
BC3
SOFTWARE
GLN A:33 , GLY A:34 , THR A:35 , THR A:36 , LYS A:288 , LEU A:292 , HOH A:4159 , TRP C:33 , ASN C:34
BINDING SITE FOR RESIDUE EDO A 2003
13
BC4
SOFTWARE
PHE A:3 , THR A:4 , SER A:16 , SER A:19 , ILE A:20
BINDING SITE FOR RESIDUE EDO A 2004
14
BC5
SOFTWARE
ARG A:176 , HOH A:4235 , SER F:31 , TRP F:33 , EDO F:2001 , FMT F:3005
BINDING SITE FOR RESIDUE EDO F 2005
15
BC6
SOFTWARE
GLN A:175 , ARG A:176 , ARG A:179 , HOH A:4042 , TRP F:33
BINDING SITE FOR RESIDUE FMT A 3001
16
BC7
SOFTWARE
ARG A:179 , THR A:294 , HOH A:4105 , ARG E:32 , TRP E:33 , ASN E:34 , HOH E:3033
BINDING SITE FOR RESIDUE FMT E 3002
17
BC8
SOFTWARE
THR D:20 , GLY D:59 , 1PS D:1004 , HOH D:3042 , HOH D:3058
BINDING SITE FOR RESIDUE FMT D 3003
18
BC9
SOFTWARE
ASN A:207 , THR A:263 , ASP A:265 , ARG A:266 , PRO A:267 , NA A:4002 , HOH A:4142 , HOH C:3065
BINDING SITE FOR RESIDUE FMT A 3004
19
CC1
SOFTWARE
ASN A:227 , SER A:229 , ALA A:230 , SER F:31 , ARG F:32 , EDO F:2005
BINDING SITE FOR RESIDUE FMT F 3005
20
CC2
SOFTWARE
ASN B:68 , ASN B:69 , HOH B:4026 , HOH B:4053 , ILE C:8 , GLU C:9 , GLN C:43
BINDING SITE FOR RESIDUE FMT B 3006
21
CC3
SOFTWARE
ARG C:32 , TRP C:33 , HOH C:3016
BINDING SITE FOR RESIDUE FMT C 3007
22
CC4
SOFTWARE
HOH A:4090 , THR E:30 , SER E:31 , ARG E:32 , PHE E:62
BINDING SITE FOR RESIDUE FMT E 3008
23
CC5
SOFTWARE
ARG A:266 , VAL A:268 , HOH A:4106 , HOH A:4161
BINDING SITE FOR RESIDUE FMT A 3009
24
CC6
SOFTWARE
THR A:110 , VAL A:120 , THR A:149 , HOH A:4130
BINDING SITE FOR RESIDUE FMT A 3010
25
CC7
SOFTWARE
ASN E:68 , ASN E:69 , ILE F:8 , GLU F:9 , GLN F:43 , HOH F:4033 , HOH F:4041
BINDING SITE FOR RESIDUE FMT F 3011
26
CC8
SOFTWARE
THR C:20 , GLY C:59 , 1PS C:1003 , HOH C:3034 , HOH C:3060 , HOH C:3063
BINDING SITE FOR RESIDUE FMT C 3012
27
CC9
SOFTWARE
GLN A:129 , ILE A:130 , SER A:131 , SER A:134
BINDING SITE FOR RESIDUE FMT A 3013
28
DC1
SOFTWARE
ARG A:219 , ARG A:222 , THR E:45 , GLY E:46 , MET E:47 , ASN E:69 , ASP E:70
BINDING SITE FOR RESIDUE FMT E 3014
29
DC2
SOFTWARE
TYR A:77 , VAL A:78 , SER A:112 , VAL A:162 , HOH A:4031 , HOH A:4237
BINDING SITE FOR RESIDUE FMT A 3015
[
close Site info
]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_STXA_BP933_002 (T4M, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_STXA_BP933_002
*
T
26
M
STXA_BP933
---
---
A
T
4
M
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: SHIGA_RICIN (A:162-178)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SHIGA_RICIN
PS00275
Shiga/ricin ribosomal inactivating toxins active site signature.
STXA_BP933
184-200
1
A:162-178
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1r4pb_ (B:)
1b: SCOP_d1r4pc_ (C:)
1c: SCOP_d1r4pd_ (D:)
1d: SCOP_d1r4pe_ (E:)
1e: SCOP_d1r4pf_ (F:)
2a: SCOP_d1r4pa_ (A:)
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)
(
)
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)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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)
Shigella dysenteriae, toxin II [TaxId: 622]
(1)
1a
d1r4pb_
B:
1b
d1r4pc_
C:
1c
d1r4pd_
D:
1d
d1r4pe_
E:
1e
d1r4pf_
F:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ribosome inactivating proteins (RIP)
(180)
Superfamily
:
Ribosome inactivating proteins (RIP)
(180)
Family
:
Shiga toxin, A-chain
(5)
Protein domain
:
Shiga toxin, A-chain
(5)
Shigella dysenteriae, toxin II [TaxId: 622]
(1)
2a
d1r4pa_
A:
[
close SCOP info
]
CATH Domains
(3, 7)
Info
all CATH domains
1a: CATH_1r4pA01 (A:1-170)
2a: CATH_1r4pA02 (A:171-297)
3a: CATH_1r4pB00 (B:1-70)
3b: CATH_1r4pC00 (C:1-70)
3c: CATH_1r4pD00 (D:1-70)
3d: CATH_1r4pE00 (E:1-70)
3e: CATH_1r4pF00 (F:1-70)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Ricin (A subunit); domain 1
(112)
Homologous Superfamily
:
Ricin (A subunit), domain 1
(112)
Escherichia coli. Organism_taxid: 562.
(1)
1a
1r4pA01
A:1-170
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Ricin (A Subunit), domain 2
(112)
Homologous Superfamily
:
Ricin (A Subunit), domain 2
(112)
Escherichia coli. Organism_taxid: 562.
(1)
2a
1r4pA02
A:171-297
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)
Escherichia coli. Organism_taxid: 562.
(1)
3a
1r4pB00
B:1-70
3b
1r4pC00
C:1-70
3c
1r4pD00
D:1-70
3d
1r4pE00
E:1-70
3e
1r4pF00
F:1-70
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_RIP_1r4pA01 (A:2-212)
2a: PFAM_SLT_beta_1r4pF01 (F:1-68)
2b: PFAM_SLT_beta_1r4pF02 (F:1-68)
2c: PFAM_SLT_beta_1r4pF03 (F:1-68)
2d: PFAM_SLT_beta_1r4pF04 (F:1-68)
2e: PFAM_SLT_beta_1r4pF05 (F:1-68)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: RIP]
(62)
Family
:
RIP
(62)
Enterobacteria phage 933W (Bacteriophage 933W)
(1)
1a
RIP-1r4pA01
A:2-212
Clan
:
no clan defined [family: SLT_beta]
(6)
Family
:
SLT_beta
(6)
Enterobacteria phage 933W (Bacteriophage 933W)
(1)
2a
SLT_beta-1r4pF01
F:1-68
2b
SLT_beta-1r4pF02
F:1-68
2c
SLT_beta-1r4pF03
F:1-68
2d
SLT_beta-1r4pF04
F:1-68
2e
SLT_beta-1r4pF05
F:1-68
[
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]
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