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Asym. Unit
Info
Asym.Unit (99 KB)
Biol.Unit 1 (91 KB)
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(1)
Title
:
MISTLETOE LECTIN I IN COMPLEX WITH ZEATIN
Authors
:
A. Meyer, W. Rypniewski, M. Szymanski, W. Voelter, J. Barciszewski, C.
Date
:
22 May 08 (Deposition) - 17 Jun 08 (Release) - 05 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.49
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Mistletoe Lectin I, Cytokinin, Zeatin, Plant Hormones, Microgravity, Glycoprotein, Hydrolase, Lectin, Plant Defense, Protein Synthesis Inhibitor, Toxin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Meyer, W. Rypniewski, M. Szymanski, W. Voelter, J. Barciszewski, C. Betzel
Structure Of Mistletoe Lectin I From Viscum Album In Comple With The Phytohormone Zeatin
Biochim. Biophys. Acta V. 1784 1590 2008
[
close entry info
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Hetero Components
(5, 14)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
4a: (2E)-2-METHYL-4-(9H-PURIN-6-YLAMIN... (ZEAa)
5a: (2Z)-2-METHYL-4-(9H-PURIN-6-YLAMIN... (ZEZa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
4
Ligand/Ion
GLYCEROL
2
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
SO4
2
Ligand/Ion
SULFATE ION
4
ZEA
1
Ligand/Ion
(2E)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL
5
ZEZ
1
Ligand/Ion
(2Z)-2-METHYL-4-(9H-PURIN-6-YLAMINO)BUT-2-EN-1-OL
[
close Hetero Component info
]
Sites
(14, 14)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:91 , ASN A:112 , ASP A:117
BINDING SITE FOR RESIDUE NAG A 500
02
AC2
SOFTWARE
PHE B:276 , ASN B:308 , HOH B:855
BINDING SITE FOR RESIDUE NAG B 600
03
AC3
SOFTWARE
TRP B:341 , ASN B:343 , TYR B:373 , LEU B:475 , HOH B:731 , HOH B:802
BINDING SITE FOR RESIDUE NAG B 602
04
AC4
SOFTWARE
PHE A:214 , ASN A:215 , PRO A:217 , ILE B:258 , ASN B:291 , LEU B:296 , ASN B:383 , HOH B:744
BINDING SITE FOR RESIDUE NAG B 603
05
AC5
SOFTWARE
ILE B:258 , ASN B:291 , LEU B:296 , HOH B:746
BINDING SITE FOR RESIDUE NAG B 604
06
AC6
SOFTWARE
TRP B:341
BINDING SITE FOR RESIDUE NAG B 605
07
AC7
SOFTWARE
GLU A:119 , HIS A:124 , ARG A:125 , ASP A:126
BINDING SITE FOR RESIDUE SO4 A 660
08
AC8
SOFTWARE
GLY A:31 , SER A:32 , PHE A:33 , ASP B:249
BINDING SITE FOR RESIDUE SO4 A 661
09
AC9
SOFTWARE
ARG A:234 , ASP A:235 , HOH A:665 , LEU B:380 , ARG B:388 , LEU B:423 , TYR B:424 , GLY B:425 , PRO B:508 , PRO B:510 , HOH B:872 , HOH B:875
BINDING SITE FOR RESIDUE ZEA B 701
10
BC1
SOFTWARE
ARG A:234 , ASP A:235 , HOH A:665 , ARG B:388 , LEU B:423 , TYR B:424 , GLY B:425 , PRO B:508 , PRO B:510 , HOH B:872 , HOH B:875
BINDING SITE FOR RESIDUE ZEZ B 702
11
BC2
SOFTWARE
PRO A:171 , TRP A:174 , ARG A:175 , GLN A:178 , HOH A:740 , TYR B:393 , ASP B:397
BINDING SITE FOR RESIDUE GOL A 648
12
BC3
SOFTWARE
LEU A:75 , TYR A:76 , GLY A:113 , ILE A:160 , SER A:164 , ARG A:168
BINDING SITE FOR RESIDUE GOL A 652
13
BC4
SOFTWARE
ASP A:133 , SER A:185 , PHE B:326 , THR B:330 , ALA B:331 , HOH B:710 , HOH B:853
BINDING SITE FOR RESIDUE GOL B 650
14
BC5
SOFTWARE
ASP B:270 , ASP B:273 , GLN B:283 , LYS B:288 , ASN B:294 , HOH B:796
BINDING SITE FOR RESIDUE GOL B 651
[
close Site info
]
SAPs(SNPs)/Variants
(19, 19)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_ML1_VISAL_001 (E15D, chain A, )
02: VAR_ML1_VISAL_002 (N112T, chain A, )
03: VAR_ML1_VISAL_003 (P116T, chain A, )
04: VAR_ML1_VISAL_004 (T140S, chain A, )
05: VAR_ML1_VISAL_005 (F144Y, chain A, )
06: VAR_ML1_VISAL_006 (T151A, chain A, )
07: VAR_ML1_VISAL_007 (Y179D, chain A, )
08: VAR_ML1_VISAL_008 (A184E, chain A, )
09: VAR_ML1_VISAL_009 (V190M, chain A, )
10: VAR_ML1_VISAL_010 (I218F, chain A, )
11: VAR_ML1_VISAL_011 (T231S, chain A, )
12: VAR_ML1_VISAL_012 (D235S, chain A, )
13: VAR_ML1_VISAL_013 (N265S, chain B, )
14: VAR_ML1_VISAL_014 (G303N, chain B, )
15: VAR_ML1_VISAL_015 (G404Q, chain B, )
16: VAR_ML1_VISAL_016 (N441V, chain B, )
17: VAR_ML1_VISAL_017 (G470Y, chain B, )
18: VAR_ML1_VISAL_018 (N477S, chain B, )
19: VAR_ML1_VISAL_019 (N477T, chain B, )
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
E
15
D
02
UniProt
VAR_ML1_VISAL_002
*
N
145
T
ML1_VISAL
---
---
A
N
112
T
03
UniProt
VAR_ML1_VISAL_003
*
P
149
T
ML1_VISAL
---
---
A
P
116
T
04
UniProt
VAR_ML1_VISAL_004
*
T
173
S
ML1_VISAL
---
---
A
T
140
S
05
UniProt
VAR_ML1_VISAL_005
*
F
177
Y
ML1_VISAL
---
---
A
F
144
Y
06
UniProt
VAR_ML1_VISAL_006
*
T
184
A
ML1_VISAL
---
---
A
T
151
A
07
UniProt
VAR_ML1_VISAL_007
*
Y
212
D
ML1_VISAL
---
---
A
Y
179
D
08
UniProt
VAR_ML1_VISAL_008
*
A
217
E
ML1_VISAL
---
---
A
A
184
E
09
UniProt
VAR_ML1_VISAL_009
*
V
223
M
ML1_VISAL
---
---
A
V
190
M
10
UniProt
VAR_ML1_VISAL_010
*
I
251
F
ML1_VISAL
---
---
A
I
218
F
11
UniProt
VAR_ML1_VISAL_011
*
T
264
S
ML1_VISAL
---
---
A
T
231
S
12
UniProt
VAR_ML1_VISAL_012
*
D
268
S
ML1_VISAL
---
---
A
D
235
S
13
UniProt
VAR_ML1_VISAL_013
*
N
319
S
ML1_VISAL
---
---
B
N
265
S
14
UniProt
VAR_ML1_VISAL_014
*
G
357
N
ML1_VISAL
---
---
B
G
303
N
15
UniProt
VAR_ML1_VISAL_015
*
G
458
Q
ML1_VISAL
---
---
B
G
404
Q
16
UniProt
VAR_ML1_VISAL_016
*
C
495
V
ML1_VISAL
---
---
B
N
441
V
17
UniProt
VAR_ML1_VISAL_017
*
G
524
Y
ML1_VISAL
---
---
B
G
470
Y
18
UniProt
VAR_ML1_VISAL_018
*
N
531
S
ML1_VISAL
---
---
B
N
477
S
19
UniProt
VAR_ML1_VISAL_019
*
N
531
T
ML1_VISAL
---
---
B
N
477
T
* 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:255-382|B:386-509)
;
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:255-382
B:386-509
[
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.
SCOP Domains
(2, 3)
Info
All SCOP Domains
1a: SCOP_d3d7wb1 (B:249-384)
1b: SCOP_d3d7wb2 (B:385-510)
2a: SCOP_d3d7wa_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
:
automated matches
(10)
European mistletoe (Viscum album) [TaxId: 3972]
(4)
1a
d3d7wb1
B:249-384
1b
d3d7wb2
B:385-510
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)
European mistletoe (Viscum album) [TaxId: 3972]
(5)
2a
d3d7wa_
A:
[
close SCOP info
]
CATH Domains
(3, 4)
Info
all CATH domains
1a: CATH_3d7wA01 (A:1-167)
2a: CATH_3d7wA02 (A:168-249)
3a: CATH_3d7wB01 (B:249-386)
3b: CATH_3d7wB02 (B:387-510)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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
3d7wA01
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
3d7wA02
A:168-249
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
3d7wB01
B:249-386
3b
3d7wB02
B:387-510
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
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Hetero
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
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Asymmetric Unit 1
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