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1RZO
Biol. Unit 1
Info
Asym.Unit (186 KB)
Biol.Unit 1 (94 KB)
Biol.Unit 2 (91 KB)
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(1)
Title
:
AGGLUTININ FROM RICINUS COMMUNIS WITH GALACTOAZA
Authors
:
A. G. Gabdoulkhakov, Y. Savochkina, N. Konareva, R. Krauspenhaar, S. S S. V. Nikonov, W. Voelter, C. Betzel, A. M. Mikhailov
Date
:
26 Dec 03 (Deposition) - 28 Dec 04 (Release) - 05 Oct 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.63
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Ribosome-Inactivating Protein, Immunotoxin, Agglutinin Ricin, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. G. Gabdoulkhakov, Y. Savochkina, N. Konareva, R. Krauspenhaar, S. Stoeva, S. V. Nikonov, W. Voelter, C. Betzel, A. M. Mikhailov
Structure-Function Investigation Complex Of Agglutinin From Ricinus Communis With Galactoaza
To Be Published
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: BETA-D-GALACTOSE (GALa)
1b: BETA-D-GALACTOSE (GALb)
1c: BETA-D-GALACTOSE (GALc)
1d: BETA-D-GALACTOSE (GALd)
1e: BETA-D-GALACTOSE (GALe)
1f: BETA-D-GALACTOSE (GALf)
1g: BETA-D-GALACTOSE (GALg)
1h: BETA-D-GALACTOSE (GALh)
1i: BETA-D-GALACTOSE (GALi)
1j: BETA-D-GALACTOSE (GALj)
1k: BETA-D-GALACTOSE (GALk)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GAL
6
Ligand/Ion
BETA-D-GALACTOSE
2
SO4
6
Ligand/Ion
SULFATE ION
[
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Sites
(13, 13)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC7 (SOFTWARE)
12: BC8 (SOFTWARE)
13: BC9 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE A:1008 , ASN A:1010 , HOH A:7101 , HOH A:7117 , HOH A:7222 , HOH A:7268 , HOH A:7392
BINDING SITE FOR RESIDUE GAL A 5001
02
AC2
SOFTWARE
TRP B:2093 , ASN B:2095 , TYR B:2125 , HOH B:7121 , HOH B:7168 , HOH B:7244 , HOH B:7399
BINDING SITE FOR RESIDUE GAL B 5002
03
AC3
SOFTWARE
ASP B:2022 , VAL B:2023 , THR B:2024 , GLY B:2025 , GLU B:2026 , GLN B:2035 , TRP B:2037 , LYS B:2040 , ASN B:2046 , SO4 B:6006
BINDING SITE FOR RESIDUE GAL B 5003
04
AC4
SOFTWARE
ILE B:2010 , LEU B:2048 , ASN B:2135 , HOH B:7055 , HOH B:7186 , HOH B:7209 , HOH B:7240
BINDING SITE FOR RESIDUE GAL B 5004
05
AC5
SOFTWARE
ASN B:2079 , GAL B:5006 , SO4 B:6003
BINDING SITE FOR RESIDUE GAL B 5005
06
AC6
SOFTWARE
GAL B:5005
BINDING SITE FOR RESIDUE GAL B 5006
07
BC3
SOFTWARE
PHE A:1119 , GLY A:1120 , ASN A:1122 , ARG A:1125 , HOH A:7110 , HOH A:7363
BINDING SITE FOR RESIDUE SO4 A 6001
08
BC4
SOFTWARE
ASP B:2234 , ARG B:2236 , ARG B:2237 , HIS B:2248 , HIS B:2251
BINDING SITE FOR RESIDUE SO4 B 6002
09
BC5
SOFTWARE
CYS B:2080 , SER B:2081 , GAL B:5005
BINDING SITE FOR RESIDUE SO4 B 6003
10
BC6
SOFTWARE
ARG A:1212
BINDING SITE FOR RESIDUE SO4 A 6004
11
BC7
SOFTWARE
ARG A:1026 , GLU A:1184 , ASP B:2221 , ILE B:2257
BINDING SITE FOR RESIDUE SO4 A 6005
12
BC8
SOFTWARE
GLU B:2026 , GAL B:5003
BINDING SITE FOR RESIDUE SO4 B 6006
13
BC9
SOFTWARE
LYS B:2198 , ASN C:1194 , ARG C:1196
BINDING SITE FOR RESIDUE SO4 C 6501
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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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 (A:1171-1187)
2: RICIN_B_LECTIN (B:2007-2134)
;
View:
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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_RICCO
195-211
1
A:1171-1187
-
2
RICIN_B_LECTIN
PS50231
Lectin domain of ricin B chain profile.
AGGL_RICCO
309-436
439-563
2
B:2007-2134
-
B:2137-2261
-
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_d1rzob1 (B:2001-2135)
1b: SCOP_d1rzob2 (B:2136-2262)
1c: SCOP_d1rzod1 (D:2001-2135)
1d: SCOP_d1rzod2 (D:2136-2262)
2a: SCOP_d1rzoa_ (A:)
2b: SCOP_d1rzoc_ (C:)
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Protein Domains
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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
:
Plant cytotoxin B-chain (lectin)
(21)
Castor bean (Ricinus communis), Ricin [TaxId: 3988]
(3)
1a
d1rzob1
B:2001-2135
1b
d1rzob2
B:2136-2262
1c
d1rzod1
D:2001-2135
1d
d1rzod2
D:2136-2262
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
:
Ricin A-chain
(36)
Castor bean (Ricinus communis) [TaxId: 3988]
(36)
2a
d1rzoa_
A:
2b
d1rzoc_
C:
[
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CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_1rzoA01 (A:1004-1178)
1b: CATH_1rzoC01 (C:1003-1178)
2a: CATH_1rzoA02 (A:1179-1262)
2b: CATH_1rzoC02 (C:1179-1262)
3a: CATH_1rzoB01 (B:2001-2138)
3b: CATH_1rzoD01 (D:2001-2138)
3c: CATH_1rzoB02 (B:2139-2262)
3d: CATH_1rzoD02 (D:2139-2262)
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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)
Castor bean (Ricinus communis)
(28)
1a
1rzoA01
A:1004-1178
1b
1rzoC01
C:1003-1178
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Ricin (A Subunit), domain 2
(112)
Homologous Superfamily
:
Ricin (A Subunit), domain 2
(112)
Castor bean (Ricinus communis)
(28)
2a
1rzoA02
A:1179-1262
2b
1rzoC02
C:1179-1262
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)
Castor bean (Ricinus communis)
(2)
3a
1rzoB01
B:2001-2138
3b
1rzoD01
D:2001-2138
3c
1rzoB02
B:2139-2262
3d
1rzoD02
D:2139-2262
[
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Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Ricin_B_lectin_1rzoD01 (D:2138-2258)
1b: PFAM_Ricin_B_lectin_1rzoD02 (D:2138-2258)
1c: PFAM_Ricin_B_lectin_1rzoD03 (D:2138-2258)
1d: PFAM_Ricin_B_lectin_1rzoD04 (D:2138-2258)
2a: PFAM_RIP_1rzoC01 (C:1010-1220)
2b: PFAM_RIP_1rzoC02 (C:1010-1220)
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Clan
:
Trefoil
(131)
Family
:
Ricin_B_lectin
(25)
Ricinus communis (Castor bean)
(1)
1a
Ricin_B_lectin-1rzoD01
D:2138-2258
1b
Ricin_B_lectin-1rzoD02
D:2138-2258
1c
Ricin_B_lectin-1rzoD03
D:2138-2258
1d
Ricin_B_lectin-1rzoD04
D:2138-2258
Clan
:
no clan defined [family: RIP]
(62)
Family
:
RIP
(62)
Ricinus communis (Castor bean)
(13)
2a
RIP-1rzoC01
C:1010-1220
2b
RIP-1rzoC02
C:1010-1220
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