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1PUM
Asym. Unit
Info
Asym.Unit (100 KB)
Biol.Unit 1 (93 KB)
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(1)
Title
:
MISTLETOE LECTIN I IN COMPLEX WITH GALACTOSE
Authors
:
R. Krauspenhaar, W. Voelter, S. Stoeva, A. Mikhailov, N. Konareva, C. B
Date
:
25 Jun 03 (Deposition) - 25 Jun 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Protein-Sugar Complex, Sugar Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Mikeska, R. Wacker, R. Arni, T. P. Singh, A. Mikhailov, A. Gabdoulkhakov, W. Voelter, C. Betzel
Mistletoe Lectin I In Complex With Galactose And Lactose Reveals Distinct Sugar-Binding Properties
Acta Crystallogr. , Sect. F V. 61 17 2005
[
close entry info
]
Hetero Components
(7, 29)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: BETA-L-FUCOSE (FULa)
3a: BETA-D-GALACTOSE (GALa)
3b: BETA-D-GALACTOSE (GALb)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
4g: GLYCEROL (GOLg)
4h: GLYCEROL (GOLh)
4i: GLYCEROL (GOLi)
4j: GLYCEROL (GOLj)
4k: GLYCEROL (GOLk)
4l: GLYCEROL (GOLl)
4m: GLYCEROL (GOLm)
4n: GLYCEROL (GOLn)
4o: GLYCEROL (GOLo)
4p: GLYCEROL (GOLp)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
7a: SULFATE ION (SO4a)
7b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
2
Ligand/Ion
CHLORIDE ION
2
FUL
1
Ligand/Ion
BETA-L-FUCOSE
3
GAL
2
Ligand/Ion
BETA-D-GALACTOSE
4
GOL
16
Ligand/Ion
GLYCEROL
5
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
7
SO4
2
Ligand/Ion
SULFATE 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
ILE B:11 , ASN B:44 , NAG B:265 , GOL B:1016
BINDING SITE FOR RESIDUE NDG B 264
02
AC2
SOFTWARE
PHE A:214 , PRO A:217 , ILE B:11 , ASN B:44 , ASN B:136 , NDG B:264 , HOH B:1077
BINDING SITE FOR RESIDUE NAG B 265
03
AC3
SOFTWARE
TRP B:94 , ASN B:96 , TYR B:126 , LEU B:228 , NAG B:267 , GOL B:1019 , HOH B:1100
BINDING SITE FOR RESIDUE NAG B 266
04
AC4
SOFTWARE
TRP B:94 , NAG B:266 , GOL B:1021
BINDING SITE FOR RESIDUE NAG B 267
05
AC5
SOFTWARE
LYS A:90 , ASP A:91 , ASN A:112
BINDING SITE FOR RESIDUE NAG A 1004
06
AC6
SOFTWARE
ASP B:27 , PHE B:29 , ASN B:61 , FUL B:269 , HOH B:1082 , HOH B:1194
BINDING SITE FOR RESIDUE NAG B 268
07
AC7
SOFTWARE
NAG B:268
BINDING SITE FOR RESIDUE FUL B 269
08
AC8
SOFTWARE
ASP B:23 , VAL B:24 , ARG B:25 , ASP B:26 , ASP B:27 , GLN B:36 , TRP B:38 , LYS B:41 , ASN B:47 , HOH B:1150 , HOH B:1192
BINDING SITE FOR RESIDUE GAL B 1008
09
AC9
SOFTWARE
ASP B:235 , GLN B:238 , ILE B:247 , TYR B:249 , ASN B:256 , HOH B:1239
BINDING SITE FOR RESIDUE GAL B 1009
10
BC1
SOFTWARE
LEU A:4 , SER A:5
BINDING SITE FOR RESIDUE CL A 1026
11
BC2
SOFTWARE
HIS A:208 , ASN A:216
BINDING SITE FOR RESIDUE CL A 1027
12
BC3
SOFTWARE
GLY A:95 , ALA A:96 , GLU A:97 , THR A:98
BINDING SITE FOR RESIDUE SO4 A 1028
13
BC4
SOFTWARE
TYR A:76 , TYR A:115 , ILE A:160 , GLU A:165 , ARG A:168
BINDING SITE FOR RESIDUE SO4 A 1029
14
BC5
SOFTWARE
ARG A:41 , GLN A:42 , THR A:44 , ILE A:45
BINDING SITE FOR RESIDUE GOL A 1010
15
BC6
SOFTWARE
PRO A:171 , ARG A:175 , GLN A:178 , ASP B:150
BINDING SITE FOR RESIDUE GOL A 1011
16
BC7
SOFTWARE
SER A:148 , THR A:149 , ARG A:150 , ASN B:105
BINDING SITE FOR RESIDUE GOL A 1012
17
BC8
SOFTWARE
ARG A:234 , ASP A:235 , GOL A:1024 , LEU B:133 , LEU B:176 , TYR B:177 , GLY B:178
BINDING SITE FOR RESIDUE GOL B 1013
18
BC9
SOFTWARE
GLY A:63 , ASP A:64 , SER A:65 , ARG A:143
BINDING SITE FOR RESIDUE GOL A 1014
19
CC1
SOFTWARE
GLU B:142 , GLU B:170 , ARG B:173 , LYS B:185
BINDING SITE FOR RESIDUE GOL B 1015
20
CC2
SOFTWARE
PRO B:46 , LEU B:49 , THR B:51 , ARG B:59 , SER B:60 , ASN B:61 , NDG B:264 , HOH B:1030
BINDING SITE FOR RESIDUE GOL B 1016
21
CC3
SOFTWARE
ASP A:84 , ARG A:143
BINDING SITE FOR RESIDUE GOL A 1017
22
CC4
SOFTWARE
THR A:59 , ARG B:196 , SER B:198
BINDING SITE FOR RESIDUE GOL B 1018
23
CC5
SOFTWARE
ASN B:96 , ASN B:227 , LEU B:228 , GLY B:231 , NAG B:266 , HOH B:1221
BINDING SITE FOR RESIDUE GOL B 1019
24
CC6
SOFTWARE
ARG A:177 , GLY B:147 , PHE B:148 , ARG B:149 , ASP B:150 , PRO B:255 , MET B:258
BINDING SITE FOR RESIDUE GOL B 1020
25
CC7
SOFTWARE
GLN B:92 , TRP B:94 , PRO B:102 , ASN B:105 , NAG B:267
BINDING SITE FOR RESIDUE GOL B 1021
26
CC8
SOFTWARE
ARG B:59 , ASN B:82 , ARG B:86 , HOH B:1090
BINDING SITE FOR RESIDUE GOL B 1022
27
CC9
SOFTWARE
PRO A:129 , GLN A:134 , HOH A:7792 , HOH A:7835 , PHE B:79 , ALA B:84 , VAL B:85 , HOH B:1049
BINDING SITE FOR RESIDUE GOL B 1023
28
DC1
SOFTWARE
VAL A:228 , ARG A:234 , ASP A:235 , ARG B:141 , PRO B:261 , GOL B:1013 , HOH B:1105
BINDING SITE FOR RESIDUE GOL A 1024
29
DC2
SOFTWARE
GLU A:119 , HIS A:124 , ARG A:125 , ASP A:126
BINDING SITE FOR RESIDUE GOL A 1025
[
close Site info
]
SAPs(SNPs)/Variants
(19, 19)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_ML1_VISAL_001 (A15D, chain A, )
02: VAR_ML1_VISAL_013 (N18S, chain B, )
03: VAR_ML1_VISAL_014 (G56N, chain B, )
04: VAR_ML1_VISAL_002 (N112T, chain A, )
05: VAR_ML1_VISAL_003 (P116T, chain A, )
06: VAR_ML1_VISAL_004 (T140S, chain A, )
07: VAR_ML1_VISAL_005 (F144Y, chain A, )
08: VAR_ML1_VISAL_006 (T151A, chain A, )
09: VAR_ML1_VISAL_015 (G157Q, chain B, )
10: VAR_ML1_VISAL_007 (Y179D, chain A, )
11: VAR_ML1_VISAL_008 (A184E, chain A, )
12: VAR_ML1_VISAL_009 (V190M, chain A, )
13: VAR_ML1_VISAL_016 (N194V, chain B, )
14: VAR_ML1_VISAL_010 (I218F, chain A, )
15: VAR_ML1_VISAL_017 (G223Y, chain B, )
16: VAR_ML1_VISAL_018 (N230S, chain B, )
17: VAR_ML1_VISAL_019 (N230T, chain B, )
18: VAR_ML1_VISAL_011 (T231S, chain A, )
19: VAR_ML1_VISAL_012 (D235S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_ML1_VISAL_001
*
E
48
D
ML1_VISAL
---
---
A
A
15
D
02
UniProt
VAR_ML1_VISAL_013
*
N
319
S
ML1_VISAL
---
---
B
N
18
S
03
UniProt
VAR_ML1_VISAL_014
*
G
357
N
ML1_VISAL
---
---
B
G
56
N
04
UniProt
VAR_ML1_VISAL_002
*
N
145
T
ML1_VISAL
---
---
A
N
112
T
05
UniProt
VAR_ML1_VISAL_003
*
P
149
T
ML1_VISAL
---
---
A
P
116
T
06
UniProt
VAR_ML1_VISAL_004
*
T
173
S
ML1_VISAL
---
---
A
T
140
S
07
UniProt
VAR_ML1_VISAL_005
*
F
177
Y
ML1_VISAL
---
---
A
F
144
Y
08
UniProt
VAR_ML1_VISAL_006
*
T
184
A
ML1_VISAL
---
---
A
T
151
A
09
UniProt
VAR_ML1_VISAL_015
*
G
458
Q
ML1_VISAL
---
---
B
G
157
Q
10
UniProt
VAR_ML1_VISAL_007
*
Y
212
D
ML1_VISAL
---
---
A
Y
179
D
11
UniProt
VAR_ML1_VISAL_008
*
A
217
E
ML1_VISAL
---
---
A
A
184
E
12
UniProt
VAR_ML1_VISAL_009
*
V
223
M
ML1_VISAL
---
---
A
V
190
M
13
UniProt
VAR_ML1_VISAL_016
*
C
495
V
ML1_VISAL
---
---
B
N
194
V
14
UniProt
VAR_ML1_VISAL_010
*
I
251
F
ML1_VISAL
---
---
A
I
218
F
15
UniProt
VAR_ML1_VISAL_017
*
G
524
Y
ML1_VISAL
---
---
B
G
223
Y
16
UniProt
VAR_ML1_VISAL_018
*
N
531
S
ML1_VISAL
---
---
B
N
230
S
17
UniProt
VAR_ML1_VISAL_019
*
N
531
T
ML1_VISAL
---
---
B
N
230
T
18
UniProt
VAR_ML1_VISAL_011
*
T
264
S
ML1_VISAL
---
---
A
T
231
S
19
UniProt
VAR_ML1_VISAL_012
*
D
268
S
ML1_VISAL
---
---
A
D
235
S
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: RICIN_B_LECTIN (B:8-135|B:139-262)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RICIN_B_LECTIN
PS50231
Lectin domain of ricin B chain profile.
ML1_VISAL
309-436
440-563
2
B:8-135
B:139-262
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 3)
Info
All SCOP Domains
1a: SCOP_d1pumb1 (B:1-137)
1b: SCOP_d1pumb2 (B:138-263)
2a: SCOP_d1puma_ (A:)
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Classes
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)
(
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Folds
(
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(
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Superfamilies
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)
(
)
Families
(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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)
European mistletoe (Viscum album) [TaxId: 3972]
(12)
1a
d1pumb1
B:1-137
1b
d1pumb2
B:138-263
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
:
Mistletoe lectin I A-chain
(11)
European mistletoe (Viscum album) [TaxId: 3972]
(11)
2a
d1puma_
A:
[
close SCOP info
]
CATH Domains
(3, 4)
Info
all CATH domains
1a: CATH_1pumA01 (A:1-167)
2a: CATH_1pumA02 (A:168-247)
3a: CATH_1pumB01 (B:2-139)
3b: CATH_1pumB02 (B:140-263)
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Architectures
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Topologies
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(
)
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)
European mistletoe (Viscum album)
(14)
1a
1pumA01
A: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)
European mistletoe (Viscum album)
(14)
2a
1pumA02
A:168-247
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)
European mistletoe (Viscum album)
(14)
3a
1pumB01
B:2-139
3b
1pumB02
B:140-263
[
close CATH info
]
Pfam Domains
(2, 3)
Info
all PFAM domains
1a: PFAM_Ricin_B_lectin_1pumB01 (B:139-259)
1b: PFAM_Ricin_B_lectin_1pumB02 (B:139-259)
2a: PFAM_RIP_1pumA01 (A:6-209)
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Clans
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Families
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Organisms
(
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(
)
Clan
:
Trefoil
(131)
Family
:
Ricin_B_lectin
(25)
Viscum album (European mistletoe)
(9)
1a
Ricin_B_lectin-1pumB01
B:139-259
1b
Ricin_B_lectin-1pumB02
B:139-259
Clan
:
no clan defined [family: RIP]
(62)
Family
:
RIP
(62)
Viscum album (European mistletoe)
(9)
2a
RIP-1pumA01
A:6-209
[
close Pfam info
]
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