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1SZ6
Asym. Unit
Info
Asym.Unit (98 KB)
Biol.Unit 1 (179 KB)
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(1)
Title
:
MISTLETOE LECTIN I FROM VISCUM ALBUM. CRYSTAL STRUCTURE AT 2.05 A RESOLUTION
Authors
:
A. G. Gabdoulkhakov, N. E. Guhlistova, A. V. Lyashenko, R. Krauspenhaa S. Stoeva, W. Voelter, S. V. Nikonov, C. Betzel, A. M. Mikhailov
Date
:
04 Apr 04 (Deposition) - 05 Oct 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Ribosome-Inactivating Protein Type Ii, Hydrolase Inhibitor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. G. Gabdoulkhakov, N. E. Guhlistova, A. V. Lyashenko, R. Krauspenhaar, S. Stoeva, W. Voelter, S. V. Nikonov, C. Betzel, A. M. Mikhailov
Crystal Structure Of Viscum Album Mistletoe Lectin I In Native State At 2. 05 A Resolution, Comparison Of Structure Active Site Conformation In Ricin And In Viscumin
To Be Published
[
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Hetero Components
(5, 25)
Info
All Hetero Components
1a: AZIDE ION (AZIa)
1b: AZIDE ION (AZIb)
1c: AZIDE ION (AZIc)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
3o: GLYCEROL (GOLo)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AZI
3
Ligand/Ion
AZIDE ION
2
CL
2
Ligand/Ion
CHLORIDE ION
3
GOL
15
Ligand/Ion
GLYCEROL
4
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE B:11 , VAL B:12 , ASN B:44 , ASN B:136 , HOH B:3109 , HOH B:3132 , HOH B:3159 , HOH B:3294
BINDING SITE FOR RESIDUE NAG B 5001
02
AC2
SOFTWARE
TRP B:94 , ASN B:96 , TYR B:126 , LEU B:228 , HOH B:3166 , HOH B:3318 , GOL B:4013
BINDING SITE FOR RESIDUE NAG B 5002
03
AC3
SOFTWARE
LYS A:90 , ASP A:91 , ASN A:112 , HOH A:3213 , HOH A:3224 , HOH A:3271
BINDING SITE FOR RESIDUE NAG A 5003
04
AC4
SOFTWARE
ASP B:27 , PHE B:29 , ASN B:61 , HOH B:3134 , HOH B:3136 , HOH B:3296
BINDING SITE FOR RESIDUE NAG B 5004
05
AC5
SOFTWARE
GLU A:119 , HIS A:124 , ARG A:125 , ASP A:126
BINDING SITE FOR RESIDUE SO4 A 4001
06
AC6
SOFTWARE
GLN B:30 , ASP B:31 , HOH B:3135
BINDING SITE FOR RESIDUE AZI B 4003
07
AC7
SOFTWARE
ASP A:211 , ASN A:232 , HOH A:3242 , ILE B:93 , LEU B:133 , ALA B:134
BINDING SITE FOR RESIDUE AZI A 4004
08
AC8
SOFTWARE
VAL B:218 , PHE B:219 , HOH B:3144 , HOH B:3145 , HOH B:3146
BINDING SITE FOR RESIDUE AZI B 4005
09
AC9
SOFTWARE
GLN A:205 , HIS A:208 , ASN A:216
BINDING SITE FOR RESIDUE CL A 4021
10
BC1
SOFTWARE
ASP B:235 , GLN B:238 , TYR B:249 , ASN B:256 , HOH B:3152
BINDING SITE FOR RESIDUE GOL B 4006
11
BC2
SOFTWARE
TYR A:1 , ARG A:3 , LEU A:55 , HOH A:3055
BINDING SITE FOR RESIDUE GOL A 4007
12
BC3
SOFTWARE
SER A:32 , ARG A:41 , GLN A:42
BINDING SITE FOR RESIDUE GOL A 4008
13
BC4
SOFTWARE
GLY A:63 , ASP A:64 , SER A:65 , ARG A:143 , HOH A:3038 , HOH A:3039 , GOL A:4019
BINDING SITE FOR RESIDUE GOL A 4009
14
BC5
SOFTWARE
ALA A:92 , PRO A:93 , GLY A:95 , ALA A:96 , GLU A:97 , THR A:98
BINDING SITE FOR RESIDUE GOL A 4010
15
BC6
SOFTWARE
ARG A:175 , ASP A:189 , LEU A:222 , PRO A:223 , TYR B:146
BINDING SITE FOR RESIDUE GOL A 4011
16
BC7
SOFTWARE
ASP B:23 , VAL B:24 , ARG B:25 , ASP B:26 , GLN B:36 , TRP B:38 , LYS B:41 , ASN B:47 , HOH B:3101 , HOH B:3238
BINDING SITE FOR RESIDUE GOL B 4012
17
BC8
SOFTWARE
LEU B:228 , HOH B:3228 , NAG B:5002
BINDING SITE FOR RESIDUE GOL B 4013
18
BC9
SOFTWARE
ARG A:154 , TYR B:68 , ALA B:72 , GLN B:122 , THR B:123 , HOH B:3097 , HOH B:3173 , HOH B:3178
BINDING SITE FOR RESIDUE GOL B 4014
19
CC1
SOFTWARE
PRO A:129 , GLN A:134 , PHE B:79 , ALA B:84 , VAL B:85 , HOH B:3079 , HOH B:3143 , HOH B:3174
BINDING SITE FOR RESIDUE GOL B 4015
20
CC2
SOFTWARE
PRO A:171 , ARG A:175 , GLN A:178 , HOH A:3009 , TYR B:146 , ASP B:150
BINDING SITE FOR RESIDUE GOL A 4016
21
CC3
SOFTWARE
ARG B:59 , ASN B:82 , HOH B:3316
BINDING SITE FOR RESIDUE GOL B 4017
22
CC4
SOFTWARE
ARG A:234 , ASP A:235 , HOH A:3022 , ARG B:141 , LEU B:176 , HOH B:3021 , HOH B:3052 , HOH B:3085
BINDING SITE FOR RESIDUE GOL B 4018
23
CC5
SOFTWARE
GLN A:84 , ARG A:143 , HOH A:3201 , GOL A:4009
BINDING SITE FOR RESIDUE GOL A 4019
24
CC6
SOFTWARE
SER A:148 , THR A:149 , ARG A:150 , HOH A:3266 , ASN B:105
BINDING SITE FOR RESIDUE GOL A 4020
[
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
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
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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_d1sz6b1 (B:1-137)
1b: SCOP_d1sz6b2 (B:138-263)
2a: SCOP_d1sz6a_ (A:)
View:
Select:
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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
:
Plant cytotoxin B-chain (lectin)
(21)
European mistletoe (Viscum album) [TaxId: 3972]
(12)
1a
d1sz6b1
B:1-137
1b
d1sz6b2
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
d1sz6a_
A:
[
close SCOP info
]
CATH Domains
(3, 4)
Info
all CATH domains
1a: CATH_1sz6A01 (A:1-167)
2a: CATH_1sz6A02 (A:168-248)
3a: CATH_1sz6B01 (B:2-139)
3b: CATH_1sz6B02 (B:140-263)
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Classes
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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
1sz6A01
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
1sz6A02
A:168-248
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
1sz6B01
B:2-139
3b
1sz6B02
B:140-263
[
close CATH info
]
Pfam Domains
(2, 3)
Info
all PFAM domains
1a: PFAM_Ricin_B_lectin_1sz6B01 (B:139-259)
1b: PFAM_Ricin_B_lectin_1sz6B02 (B:139-259)
2a: PFAM_RIP_1sz6A01 (A:6-209)
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Clans
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Families
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Organisms
(
)
(
)
Clan
:
Trefoil
(131)
Family
:
Ricin_B_lectin
(25)
Viscum album (European mistletoe)
(9)
1a
Ricin_B_lectin-1sz6B01
B:139-259
1b
Ricin_B_lectin-1sz6B02
B:139-259
Clan
:
no clan defined [family: RIP]
(62)
Family
:
RIP
(62)
Viscum album (European mistletoe)
(9)
2a
RIP-1sz6A01
A:6-209
[
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]
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