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1RF2
Asym. Unit
Info
Asym.Unit (195 KB)
Biol.Unit 1 (190 KB)
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(1)
Title
:
CHOLERA TOXIN B-PENTAMER COMPLEXED WITH BIVALENT NITROPHENOL-GALACTOSIDE LIGAND BV4
Authors
:
J. C. Pickens, D. D. Mitchell, J. Liu, X. Tan, Z. Zhang, C. L. Verlinde, W. G. Hol, E. Fan
Date
:
07 Nov 03 (Deposition) - 26 Oct 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.35
Chains
:
Asym. Unit : D,E,F,G,H
Biol. Unit 1: D,E,F,G,H (1x)
Keywords
:
Bivalent, Cholera, Toxin, Pentamer, Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. C. Pickens, D. D. Mitchell, J. Liu, X. Tan, Z. Zhang, C. L. Verlinde, W. G. Hol, E. Fan
Nonspanning Bivalent Ligands As Improved Surface Receptor Binding Inhibitors Of The Cholera Toxin B Pentamer.
Chem. Biol. V. 11 1205 2004
(for further references see the
PDB file header
)
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Hetero Components
(3, 7)
Info
All Hetero Components
1a: 1,3-BIS-([3-[3-[3-(4-{3-[3-NITRO-5... (BV4a)
1b: 1,3-BIS-([3-[3-[3-(4-{3-[3-NITRO-5... (BV4b)
1c: 1,3-BIS-([3-[3-[3-(4-{3-[3-NITRO-5... (BV4c)
1d: 1,3-BIS-([3-[3-[3-(4-{3-[3-NITRO-5... (BV4d)
1e: 1,3-BIS-([3-[3-[3-(4-{3-[3-NITRO-5... (BV4e)
2a: TRIETHYLENE GLYCOL (PGEa)
3a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
BV4
5
Ligand/Ion
1,3-BIS-([3-[3-[3-(4-{3-[3-NITRO-5-(GALACTOPYRANOSYLOXY)-BENZOYLAMINO]-PROPYL}-PIPERAZIN-1-YL)-PROPYLAMINO-3,4-DIOXO-CYCLOBUTENYL]-AMINO-PROPOXY-ETHOXY-ETHOXY]-PROPYL-]AMINO-CARBONYLOXY)-2-AMINO-PROPANE
2
PGE
1
Ligand/Ion
TRIETHYLENE GLYCOL
3
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR D:12 , GLU D:51 , GLN D:56 , HIS D:57 , GLN D:61 , TRP D:88 , ASN D:90 , LYS D:91 , HOH D:1133 , HOH D:1352 , HOH D:1481 , GLY E:33
BINDING SITE FOR RESIDUE BV4 D 104
2
AC2
SOFTWARE
TYR E:12 , GLU E:51 , GLN E:56 , GLN E:61 , TRP E:88 , ASN E:90 , LYS E:91 , HOH E:1262 , HOH E:1480 , GLY F:33
BINDING SITE FOR RESIDUE BV4 E 105
3
AC3
SOFTWARE
TYR F:12 , GLU F:51 , GLN F:56 , HIS F:57 , GLN F:61 , TRP F:88 , ASN F:90 , LYS F:91 , HOH F:1049 , HOH F:1152 , GLY G:33
BINDING SITE FOR RESIDUE BV4 F 106
4
AC4
SOFTWARE
TYR G:12 , GLU G:51 , GLN G:56 , HIS G:57 , GLN G:61 , TRP G:88 , ASN G:90 , LYS G:91 , HOH G:1018 , HOH G:1137 , HOH G:1261 , GLY H:33
BINDING SITE FOR RESIDUE BV4 G 107
5
AC5
SOFTWARE
GLY D:33 , TYR H:12 , GLU H:51 , GLN H:56 , HIS H:57 , GLN H:61 , TRP H:88 , ASN H:90 , LYS H:91 , HOH H:1048 , HOH H:1150 , HOH H:1346 , HOH H:1479
BINDING SITE FOR RESIDUE BV4 H 108
6
AC6
SOFTWARE
ARG D:35 , ASN F:14 , ASN F:89 , ASN F:90 , THR H:1 , PRO H:2 , ASP H:7 , GLU H:11 , HOH H:1075 , HOH H:1496
BINDING SITE FOR RESIDUE TRS H 109
7
AC7
SOFTWARE
LYS D:91 , THR D:92 , ASN F:89 , ASN F:90 , LYS F:91 , THR F:92 , THR H:1 , HOH H:1472
BINDING SITE FOR RESIDUE PGE H 110
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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Exons
(0, 0)
Info
All Exons
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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
(1, 5)
Info
All SCOP Domains
1a: SCOP_d1rf2d_ (D:)
1b: SCOP_d1rf2e_ (E:)
1c: SCOP_d1rf2f_ (F:)
1d: SCOP_d1rf2g_ (G:)
1e: SCOP_d1rf2h_ (H:)
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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
:
Cholera toxin
(24)
Vibrio cholerae [TaxId: 666]
(24)
1a
d1rf2d_
D:
1b
d1rf2e_
E:
1c
d1rf2f_
F:
1d
d1rf2g_
G:
1e
d1rf2h_
H:
[
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CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_1rf2D00 (D:1-103)
1b: CATH_1rf2E00 (E:1-103)
1c: CATH_1rf2F00 (F:1-103)
1d: CATH_1rf2G00 (G:1-103)
1e: CATH_1rf2H00 (H:1-103)
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)
Organisms
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)
(
)
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)
Vibrio cholerae. Organism_taxid: 666.
(15)
1a
1rf2D00
D:1-103
1b
1rf2E00
E:1-103
1c
1rf2F00
F:1-103
1d
1rf2G00
G:1-103
1e
1rf2H00
H:1-103
[
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Pfam Domains
(1, 5)
Info
all PFAM domains
1a: PFAM_Enterotoxin_b_1rf2H01 (H:1-102)
1b: PFAM_Enterotoxin_b_1rf2H02 (H:1-102)
1c: PFAM_Enterotoxin_b_1rf2H03 (H:1-102)
1d: PFAM_Enterotoxin_b_1rf2H04 (H:1-102)
1e: PFAM_Enterotoxin_b_1rf2H05 (H:1-102)
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Clan
:
no clan defined [family: Enterotoxin_b]
(23)
Family
:
Enterotoxin_b
(23)
Vibrio cholerae
(11)
1a
Enterotoxin_b-1rf2H01
H:1-102
1b
Enterotoxin_b-1rf2H02
H:1-102
1c
Enterotoxin_b-1rf2H03
H:1-102
1d
Enterotoxin_b-1rf2H04
H:1-102
1e
Enterotoxin_b-1rf2H05
H:1-102
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Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (195 KB)
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