PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
1PTO
Biol. Unit 2
Info
Asym.Unit (303 KB)
Biol.Unit 1 (150 KB)
Biol.Unit 2 (151 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE STRUCTURE OF A PERTUSSIS TOXIN-SUGAR COMPLEX AS A MODEL FOR RECEPTOR BINDING
Authors
:
P. E. Stein, R. J. Read
Date
:
22 Mar 94 (Deposition) - 15 Sep 95 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Keywords
:
Toxin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. E. Stein, A. Boodhoo, G. D. Armstrong, L. D. Heerze, S. A. Cockle, M. H. Klein, R. J. Read
Structure Of A Pertussis Toxin-Sugar Complex As A Model For Receptor Binding.
Nat. Struct. Biol. V. 1 591 1994
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: BETA-D-GALACTOSE (GALa)
1b: BETA-D-GALACTOSE (GALb)
1c: BETA-D-GALACTOSE (GALc)
2a: O-SIALIC ACID (SIAa)
2b: O-SIALIC ACID (SIAb)
2c: O-SIALIC ACID (SIAc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GAL
1
Ligand/Ion
BETA-D-GALACTOSE
2
SIA
1
Ligand/Ion
O-SIALIC ACID
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
HIS I:101 , TYR I:102 , TYR I:103 , SER I:104 , ARG I:125 , GAL I:201
BINDING SITE FOR RESIDUE SIA I 200
2
AC6
SOFTWARE
SER I:104 , ARG I:125 , SIA I:200
BINDING SITE FOR RESIDUE GAL I 201
[
close Site info
]
SAPs(SNPs)/Variants
(6, 6)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_TOX1_BORPE_001 (E34E, chain G, )
2: VAR_TOX1_BORPE_002 (N95S, chain G, )
3: VAR_TOX1_BORPE_003 (S162P, chain G, )
4: VAR_TOX1_BORPE_004 (M194I, chain G, )
5: VAR_TOX1_BORPE_005 (V198M, chain G, )
6: VAR_TOX1_BORPE_006 (V198V, chain G, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_TOX1_BORPE_001
*
D
68
E
TOX1_BORPE
---
---
G
E
34
E
2
UniProt
VAR_TOX1_BORPE_002
*
N
129
S
TOX1_BORPE
---
---
G
N
95
S
3
UniProt
VAR_TOX1_BORPE_003
*
S
196
P
TOX1_BORPE
---
---
G
S
162
P
4
UniProt
VAR_TOX1_BORPE_004
*
M
228
I
TOX1_BORPE
---
---
G
M
194
I
5
UniProt
VAR_TOX1_BORPE_005
*
I
232
M
TOX1_BORPE
---
---
G
V
198
M
6
UniProt
VAR_TOX1_BORPE_006
*
I
232
V
TOX1_BORPE
---
---
G
V
198
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(5, 16)
Info
All SCOP Domains
1a: SCOP_d1ptob1 (B:90-199)
1b: SCOP_d1ptoh1 (H:90-199)
1c: SCOP_d1ptoi1 (I:90-199)
1d: SCOP_d1ptoc1 (C:90-199)
2a: SCOP_d1ptod_ (D:)
2b: SCOP_d1ptoj_ (J:)
2c: SCOP_d1ptok_ (K:)
2d: SCOP_d1ptoe_ (E:)
3a: SCOP_d1ptof_ (F:)
3b: SCOP_d1ptol_ (L:)
4a: SCOP_d1ptoa_ (A:)
4b: SCOP_d1ptog_ (G:)
5a: SCOP_d1ptob2 (B:4-89)
5b: SCOP_d1ptoh2 (H:2-89)
5c: SCOP_d1ptoi2 (I:4-89)
5d: SCOP_d1ptoc2 (C:4-89)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
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
:
Pertussis toxin S2/S3 subunits, C-terminal domain
(3)
Bordetella pertussis [TaxId: 520]
(3)
1a
d1ptob1
B:90-199
1b
d1ptoh1
H:90-199
1c
d1ptoi1
I:90-199
1d
d1ptoc1
C:90-199
Protein domain
:
Pertussis toxin S4 subunit
(3)
Bordetella pertussis [TaxId: 520]
(3)
2a
d1ptod_
D:
2b
d1ptoj_
J:
2c
d1ptok_
K:
2d
d1ptoe_
E:
Protein domain
:
Pertussis toxin S5 subunit
(3)
Bordetella pertussis [TaxId: 520]
(3)
3a
d1ptof_
F:
3b
d1ptol_
L:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ADP-ribosylation
(157)
Superfamily
:
ADP-ribosylation
(157)
Family
:
ADP-ribosylating toxins
(85)
Protein domain
:
Pertussis toxin, S1 subunit
(3)
Bordetella pertussis [TaxId: 520]
(3)
4a
d1ptoa_
A:
4b
d1ptog_
G:
Fold
:
C-type lectin-like
(322)
Superfamily
:
C-type lectin-like
(322)
Family
:
Aerolysin/Pertussis toxin (APT) domain
(9)
Protein domain
:
Pertussis toxin, S2/S3 subunits, N-terminal domain
(3)
Bordetella pertussis [TaxId: 520]
(3)
5a
d1ptob2
B:4-89
5b
d1ptoh2
H:2-89
5c
d1ptoi2
I:4-89
5d
d1ptoc2
C:4-89
[
close SCOP info
]
CATH Domains
(3, 16)
Info
all CATH domains
1a: CATH_1ptoA00 (A:2-235)
1b: CATH_1ptoG00 (G:2-235)
2a: CATH_1ptoB01 (B:4-89)
2b: CATH_1ptoH01 (H:4-89)
2c: CATH_1ptoC01 (C:4-89)
2d: CATH_1ptoI01 (I:4-89)
3a: CATH_1ptoF00 (F:2-99)
3b: CATH_1ptoL00 (L:2-99)
3c: CATH_1ptoB02 (B:90-199)
3d: CATH_1ptoH02 (H:90-199)
3e: CATH_1ptoC02 (C:90-199)
3f: CATH_1ptoI02 (I:90-199)
3g: CATH_1ptoD00 (D:1-110)
3h: CATH_1ptoE00 (E:1-110)
3i: CATH_1ptoJ00 (J:1-110)
3j: CATH_1ptoK00 (K:1-110)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Heat-Labile Enterotoxin; Chain A
(22)
Homologous Superfamily
:
Heat-Labile Enterotoxin, subunit A
(22)
Bordetella pertussis. Organism_taxid: 520. Cell_line: s2. Bordetella pertussis. Organism_taxid: 520. Cell_line: s2. Bordetella pertussis. Organism_taxid: 520. Cell_line: s2. Bordetella pertussis. Organism_taxid: 520. Cell_line: s2. Bordetella pertussis. Organism_taxid: 520. Cell_line: s2.
(1)
1a
1ptoA00
A:2-235
1b
1ptoG00
G:2-235
Architecture
:
Roll
(3276)
Topology
:
Pertussis Toxin; Chain B, domain 1
(10)
Homologous Superfamily
:
Pertussis Toxin, subunit B, domain 1
(10)
Bordetella pertussis. Organism_taxid: 520. Cell_line: s2. Bordetella pertussis. Organism_taxid: 520. Cell_line: s2. Bordetella pertussis. Organism_taxid: 520. Cell_line: s2. Bordetella pertussis. Organism_taxid: 520. Cell_line: s2. Bordetella pertussis. Organism_taxid: 520. Cell_line: s2.
(1)
2a
1ptoB01
B:4-89
2b
1ptoH01
H:4-89
2c
1ptoC01
C:4-89
2d
1ptoI01
I:4-89
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
[code=2.40.50.110, no name defined]
(136)
Bordetella pertussis. Organism_taxid: 520. Cell_line: s2. Bordetella pertussis. Organism_taxid: 520. Cell_line: s2. Bordetella pertussis. Organism_taxid: 520. Cell_line: s2. Bordetella pertussis. Organism_taxid: 520. Cell_line: s2. Bordetella pertussis. Organism_taxid: 520. Cell_line: s2.
(1)
3a
1ptoF00
F:2-99
3b
1ptoL00
L:2-99
3c
1ptoB02
B:90-199
3d
1ptoH02
H:90-199
3e
1ptoC02
C:90-199
3f
1ptoI02
I:90-199
3g
1ptoD00
D:1-110
3h
1ptoE00
E:1-110
3i
1ptoJ00
J:1-110
3j
1ptoK00
K:1-110
[
close CATH info
]
Pfam Domains
(5, 16)
Info
all PFAM domains
1a: PFAM_Pertussis_S1_1ptoG01 (G:2-234)
1b: PFAM_Pertussis_S1_1ptoG02 (G:2-234)
2a: PFAM_APT_1ptoH01 (H:3-89)
2b: PFAM_APT_1ptoH02 (H:3-89)
2c: PFAM_APT_1ptoI01 (I:4-89)
2d: PFAM_APT_1ptoI02 (I:4-89)
3a: PFAM_Pertus_S4_tox_1ptoK01 (K:1-110)
3b: PFAM_Pertus_S4_tox_1ptoK02 (K:1-110)
3c: PFAM_Pertus_S4_tox_1ptoK03 (K:1-110)
3d: PFAM_Pertus_S4_tox_1ptoK04 (K:1-110)
4a: PFAM_Pertus_S5_tox_1ptoL01 (L:3-99)
4b: PFAM_Pertus_S5_tox_1ptoL02 (L:3-99)
5a: PFAM_Pertussis_S2S3_1ptoH03 (H:90-198)
5b: PFAM_Pertussis_S2S3_1ptoH04 (H:90-198)
5c: PFAM_Pertussis_S2S3_1ptoI03 (I:90-198)
5d: PFAM_Pertussis_S2S3_1ptoI04 (I:90-198)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
ADP-ribosyl
(56)
Family
:
Pertussis_S1
(2)
Bordetella pertussis
(2)
1a
Pertussis_S1-1ptoG01
G:2-234
1b
Pertussis_S1-1ptoG02
G:2-234
Clan
:
C_Lectin
(98)
Family
:
APT
(4)
Bordetella pertussis
(2)
2a
APT-1ptoH01
H:3-89
2b
APT-1ptoH02
H:3-89
2c
APT-1ptoI01
I:4-89
2d
APT-1ptoI02
I:4-89
Clan
:
no clan defined [family: Pertus-S4-tox]
(2)
Family
:
Pertus-S4-tox
(2)
Bordetella pertussis
(2)
3a
Pertus-S4-tox-1ptoK01
K:1-110
3b
Pertus-S4-tox-1ptoK02
K:1-110
3c
Pertus-S4-tox-1ptoK03
K:1-110
3d
Pertus-S4-tox-1ptoK04
K:1-110
Clan
:
no clan defined [family: Pertus-S5-tox]
(2)
Family
:
Pertus-S5-tox
(2)
Bordetella pertussis
(2)
4a
Pertus-S5-tox-1ptoL01
L:3-99
4b
Pertus-S5-tox-1ptoL02
L:3-99
Clan
:
no clan defined [family: Pertussis_S2S3]
(2)
Family
:
Pertussis_S2S3
(2)
Bordetella pertussis
(2)
5a
Pertussis_S2S3-1ptoH03
H:90-198
5b
Pertussis_S2S3-1ptoH04
H:90-198
5c
Pertussis_S2S3-1ptoI03
I:90-198
5d
Pertussis_S2S3-1ptoI04
I:90-198
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (303 KB)
Header - Asym.Unit
Biol.Unit 1 (150 KB)
Header - Biol.Unit 1
Biol.Unit 2 (151 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1PTO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help