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1V6K
Asym. Unit
Info
Asym.Unit (159 KB)
Biol.Unit 1 (152 KB)
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(1)
Title
:
PEANUT LECTIN-LACTOSE COMPLEX IN THE PRESENCE OF PEPTIDE(IWSSAGNVA)
Authors
:
S. Kundhavai Natchiar, A. Arockia Jeyaprakash, T. N. C. Ramya, C. J. Thomas, K. Suguna, A. Surolia, M. Vijayan
Date
:
01 Dec 03 (Deposition) - 10 Feb 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Lectin, Open Quaternary Association, Orthorhombic, Carbohydrate Specificity, Protein Crystallography, Agglutinin, Peptide, Sugar Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Kundhavai Natchiar, A. Arockia Jeyaprakash, T. N. Ramya, C. J. Thomas, K. Suguna, A. Surolia, M. Vijayan
Structural Plasticity Of Peanut Lectin: An X-Ray Analysis Involving Variation In Ph, Ligand Binding And Crystal Structure.
Acta Crystallogr. , Sect. D V. 60 211 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 16)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: BETA-D-GALACTOSE (GALa)
2b: BETA-D-GALACTOSE (GALb)
2c: BETA-D-GALACTOSE (GALc)
2d: BETA-D-GALACTOSE (GALd)
3a: ALPHA-D-GLUCOSE (GLCa)
3b: ALPHA-D-GLUCOSE (GLCb)
3c: ALPHA-D-GLUCOSE (GLCc)
3d: ALPHA-D-GLUCOSE (GLCd)
4a: MANGANESE (II) ION (MNa)
4b: MANGANESE (II) ION (MNb)
4c: MANGANESE (II) ION (MNc)
4d: MANGANESE (II) ION (MNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
GAL
4
Ligand/Ion
BETA-D-GALACTOSE
3
GLC
4
Ligand/Ion
ALPHA-D-GLUCOSE
4
MN
4
Ligand/Ion
MANGANESE (II) ION
[
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]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:80 , ASP A:83 , GLY A:103 , GLY A:104 , TYR A:125 , ASN A:127 , SER A:211 , GLY A:214 , GLC A:236 , HOH A:278 , HOH A:318
BINDING SITE FOR RESIDUE GAL A 235
02
AC2
SOFTWARE
SER A:211 , LEU A:212 , GLY A:213 , GAL A:235
BINDING SITE FOR RESIDUE GLC A 236
03
AC3
SOFTWARE
ASP B:80 , ALA B:82 , ASP B:83 , GLY B:103 , GLY B:104 , TYR B:125 , ASN B:127 , SER B:211 , GLY B:214 , GLC B:236 , HOH B:266 , HOH B:301
BINDING SITE FOR RESIDUE GAL B 235
04
AC4
SOFTWARE
SER B:211 , LEU B:212 , GLY B:213 , GAL B:235
BINDING SITE FOR RESIDUE GLC B 236
05
AC5
SOFTWARE
ASP C:80 , ASP C:83 , GLY C:103 , GLY C:104 , TYR C:125 , ASN C:127 , SER C:211 , GLY C:214 , GLC C:236
BINDING SITE FOR RESIDUE GAL C 235
06
AC6
SOFTWARE
SER C:211 , LEU C:212 , GLY C:213 , GLY C:214 , GAL C:235
BINDING SITE FOR RESIDUE GLC C 236
07
AC7
SOFTWARE
ASP D:80 , ALA D:82 , ASP D:83 , GLY D:103 , GLY D:104 , TYR D:125 , ASN D:127 , SER D:211 , GLY D:214 , GLC D:236 , HOH D:278
BINDING SITE FOR RESIDUE GAL D 235
08
AC8
SOFTWARE
SER D:211 , LEU D:212 , GLY D:213 , GAL D:235
BINDING SITE FOR RESIDUE GLC D 236
09
AC9
SOFTWARE
ASP A:123 , TYR A:125 , ASN A:127 , ASP A:132 , HOH A:237 , HOH A:238
BINDING SITE FOR RESIDUE CA A 233
10
BC1
SOFTWARE
GLU A:121 , ASP A:123 , ASP A:132 , HIS A:137 , HOH A:239 , HOH A:240
BINDING SITE FOR RESIDUE MN A 234
11
BC2
SOFTWARE
ASP B:123 , TYR B:125 , ASN B:127 , ASP B:132 , HOH B:237 , HOH B:238
BINDING SITE FOR RESIDUE CA B 233
12
BC3
SOFTWARE
GLU B:121 , ASP B:123 , ASP B:132 , HIS B:137 , HOH B:239 , HOH B:240
BINDING SITE FOR RESIDUE MN B 234
13
BC4
SOFTWARE
ASP C:123 , TYR C:125 , ASN C:127 , ASP C:132 , HOH C:237 , HOH C:238
BINDING SITE FOR RESIDUE CA C 233
14
BC5
SOFTWARE
GLU C:121 , ASP C:123 , ASP C:132 , HIS C:137 , HOH C:239 , HOH C:240
BINDING SITE FOR RESIDUE MN C 234
15
BC6
SOFTWARE
ASP D:123 , TYR D:125 , ASN D:127 , ASP D:132 , HOH D:237 , HOH D:238
BINDING SITE FOR RESIDUE CA D 233
16
BC7
SOFTWARE
GLU D:121 , ASP D:123 , ASP D:132 , HIS D:137 , HOH D:239 , HOH D:240
BINDING SITE FOR RESIDUE MN D 234
[
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]
SAPs(SNPs)/Variants
(3, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_LECG_ARAHY_001 (E92V, chain A/B/C/D, )
2: VAR_LECG_ARAHY_002 (K149A, chain A/B/C/D, )
3: VAR_LECG_ARAHY_003 (K162I, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_LECG_ARAHY_001
*
E
115
V
LECG_ARAHY
---
---
A/B/C/D
E
92
V
2
UniProt
VAR_LECG_ARAHY_002
*
K
172
A
LECG_ARAHY
---
---
A/B/C/D
K
149
A
3
UniProt
VAR_LECG_ARAHY_003
*
K
185
I
LECG_ARAHY
---
---
A/B/C/D
K
162
I
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: LECTIN_LEGUME_BETA (A:118-124,B:118-124,C:118-124,D:11...)
2: LECTIN_LEGUME_ALPHA (A:198-207,B:198-207,C:198-207,D:19...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LECTIN_LEGUME_BETA
PS00307
Legume lectins beta-chain signature.
LECG_ARAHY
141-147
4
A:118-124
B:118-124
C:118-124
D:118-124
2
LECTIN_LEGUME_ALPHA
PS00308
Legume lectins alpha-chain signature.
LECG_ARAHY
221-230
4
A:198-207
B:198-207
C:198-207
D:198-207
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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.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1v6ka_ (A:)
1b: SCOP_d1v6kb_ (B:)
1c: SCOP_d1v6kc_ (C:)
1d: SCOP_d1v6kd_ (D:)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Concanavalin A-like lectins/glucanases
(797)
Superfamily
:
Concanavalin A-like lectins/glucanases
(797)
Family
:
Legume lectins
(238)
Protein domain
:
Legume lectin
(110)
Peanut (Arachis hypogaea) [TaxId: 3818]
(23)
1a
d1v6ka_
A:
1b
d1v6kb_
B:
1c
d1v6kc_
C:
1d
d1v6kd_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1v6kA00 (A:1-232)
1b: CATH_1v6kB00 (B:1-232)
1c: CATH_1v6kC00 (C:1-232)
1d: CATH_1v6kD00 (D:1-232)
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.200, no name defined]
(421)
Peanut (Arachis hypogaea)
(22)
1a
1v6kA00
A:1-232
1b
1v6kB00
B:1-232
1c
1v6kC00
C:1-232
1d
1v6kD00
D:1-232
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Lectin_legB_1v6kD01 (D:2-226)
1b: PFAM_Lectin_legB_1v6kD02 (D:2-226)
1c: PFAM_Lectin_legB_1v6kD03 (D:2-226)
1d: PFAM_Lectin_legB_1v6kD04 (D:2-226)
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)
Clan
:
Concanavalin
(293)
Family
:
Lectin_legB
(93)
Arachis hypogaea (Peanut)
(11)
1a
Lectin_legB-1v6kD01
D:2-226
1b
Lectin_legB-1v6kD02
D:2-226
1c
Lectin_legB-1v6kD03
D:2-226
1d
Lectin_legB-1v6kD04
D:2-226
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