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2ZR1
Biol. Unit 3
Info
Asym.Unit (173 KB)
Biol.Unit 1 (168 KB)
Biol.Unit 2 (87 KB)
Biol.Unit 3 (87 KB)
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(1)
Title
:
AGGLUTININ FROM ABRUS PRECATORIUS
Authors
:
J. Cheng, T. H. Lu, C. L. Liu, J. Y. Lin
Date
:
22 Aug 08 (Deposition) - 25 Aug 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B (1x)
Biol. Unit 3: C,D (1x)
Keywords
:
Ribosome-Inactivating Protein, Immunotoxin, Agglutinin Abrin, Glycoprotein, Hydrolase, Lectin, Plant Defense, Protein Synthesis Inhibitor, Pyrrolidone Carboxylic Acid, Toxin, Plant Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
J. Cheng, T. H. Lu, C. L. Liu, J. Y. Lin
A Biophysical Elucidation For Less Toxicity Of Agglutinin Than Abrin-A From The Seeds Of Abrus Precatorius In Consequence Of Crystal Structure
J. Biomed. Sci. V. 17 34 2010
(for further references see the
PDB file header
)
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
NDG
-1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
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Sites
(1, 1)
Info
All Sites
1: AC3 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
ASN C:215 , THR D:15 , VAL D:16 , LEU D:48 , ASN D:140 , HOH D:289
BINDING SITE FOR RESIDUE NAG D 268
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 3)
Info
All PROSITE Patterns/Profiles
1: SHIGA_RICIN (C:158-174)
2: RICIN_B_LECTIN (D:142-266)
;
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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.
AGGL_ABRPR
178-194
1
-
C:158-174
2
RICIN_B_LECTIN
PS50231
Lectin domain of ricin B chain profile.
AGGL_ABRPR
292-419
422-546
2
-
D:12-139
-
D:142-266
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Exons
(0, 0)
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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
(2, 6)
Info
All SCOP Domains
1a: SCOP_d2zr1b1 (B:5-140)
1b: SCOP_d2zr1b2 (B:141-267)
1c: SCOP_d2zr1d1 (D:5-140)
1d: SCOP_d2zr1d2 (D:141-267)
2a: SCOP_d2zr1a_ (A:)
2b: SCOP_d2zr1c_ (C:)
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Organisms
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Class
:
All beta proteins
(24004)
Fold
:
beta-Trefoil
(385)
Superfamily
:
Ricin B-like lectins
(91)
Family
:
Ricin B-like
(65)
Protein domain
:
Agglutinin-1 chain B
(2)
Abrus precatorius [TaxId: 3816]
(2)
1a
d2zr1b1
B:5-140
1b
d2zr1b2
B:141-267
1c
d2zr1d1
D:5-140
1d
d2zr1d2
D:141-267
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ribosome inactivating proteins (RIP)
(180)
Superfamily
:
Ribosome inactivating proteins (RIP)
(180)
Family
:
Plant cytotoxins
(166)
Protein domain
:
automated matches
(73)
Abrus precatorius [TaxId: 3816]
(1)
2a
d2zr1a_
A:
2b
d2zr1c_
C:
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CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_2zr1A01 (A:1-167)
1b: CATH_2zr1C01 (C:1-167)
2a: CATH_2zr1A02 (A:168-250)
2b: CATH_2zr1C02 (C:168-250)
3a: CATH_2zr1B01 (B:5-143)
3b: CATH_2zr1D01 (D:5-143)
3c: CATH_2zr1B02 (B:144-267)
3d: CATH_2zr1D02 (D:144-267)
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)
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)
Indian licorice (Abrus precatorius)
(3)
1a
2zr1A01
A:1-167
1b
2zr1C01
C:1-167
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Ricin (A Subunit), domain 2
(112)
Homologous Superfamily
:
Ricin (A Subunit), domain 2
(112)
Indian licorice (Abrus precatorius)
(3)
2a
2zr1A02
A:168-250
2b
2zr1C02
C:168-250
Class
:
Mainly Beta
(13760)
Architecture
:
Trefoil
(289)
Topology
:
Trefoil (Acidic Fibroblast Growth Factor, subunit A)
(289)
Homologous Superfamily
:
[code=2.80.10.50, no name defined]
(289)
Indian licorice (Abrus precatorius)
(3)
3a
2zr1B01
B:5-143
3b
2zr1D01
D:5-143
3c
2zr1B02
B:144-267
3d
2zr1D02
D:144-267
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Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Ricin_B_lectin_2zr1D01 (D:142-263)
1b: PFAM_Ricin_B_lectin_2zr1D02 (D:142-263)
1c: PFAM_Ricin_B_lectin_2zr1D03 (D:142-263)
1d: PFAM_Ricin_B_lectin_2zr1D04 (D:142-263)
2a: PFAM_RIP_2zr1C01 (C:5-207)
2b: PFAM_RIP_2zr1C02 (C:5-207)
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Clan
:
Trefoil
(131)
Family
:
Ricin_B_lectin
(25)
Abrus precatorius (Indian licorice) (Glycine abrus)
(2)
1a
Ricin_B_lectin-2zr1D01
D:142-263
1b
Ricin_B_lectin-2zr1D02
D:142-263
1c
Ricin_B_lectin-2zr1D03
D:142-263
1d
Ricin_B_lectin-2zr1D04
D:142-263
Clan
:
no clan defined [family: RIP]
(62)
Family
:
RIP
(62)
Abrus precatorius (Indian licorice) (Glycine abrus)
(2)
2a
RIP-2zr1C01
C:5-207
2b
RIP-2zr1C02
C:5-207
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Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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Show PDB file:
Asym.Unit (173 KB)
Header - Asym.Unit
Biol.Unit 1 (168 KB)
Header - Biol.Unit 1
Biol.Unit 2 (87 KB)
Header - Biol.Unit 2
Biol.Unit 3 (87 KB)
Header - Biol.Unit 3
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