PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1V6L
Asym. Unit
Info
Asym.Unit (159 KB)
Biol.Unit 1 (152 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PEANUT LECTIN-LACTOSE COMPLEX IN THE PRESENCE OF 9MER PEPTIDE (PVIWSSATG)
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) - 04 Aug 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
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
)
[
close entry info
]
Hetero Components
(5, 16)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
1b: BETA-D-GLUCOSE (BGCb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: BETA-D-GALACTOSE (GALa)
3b: BETA-D-GALACTOSE (GALb)
3c: BETA-D-GALACTOSE (GALc)
3d: BETA-D-GALACTOSE (GALd)
4a: ALPHA-D-GLUCOSE (GLCa)
4b: ALPHA-D-GLUCOSE (GLCb)
5a: MANGANESE (II) ION (MNa)
5b: MANGANESE (II) ION (MNb)
5c: MANGANESE (II) ION (MNc)
5d: MANGANESE (II) ION (MNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
2
Ligand/Ion
BETA-D-GLUCOSE
2
CA
4
Ligand/Ion
CALCIUM ION
3
GAL
4
Ligand/Ion
BETA-D-GALACTOSE
4
GLC
2
Ligand/Ion
ALPHA-D-GLUCOSE
5
MN
4
Ligand/Ion
MANGANESE (II) ION
[
close Hetero Component info
]
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:274 , HOH A:308
BINDING SITE FOR RESIDUE GAL A 235
02
AC2
SOFTWARE
SER A:211 , LEU A:212 , GLY A:213 , GAL A:235 , HOH A:327 , HOH A:329
BINDING SITE FOR RESIDUE GLC A 236
03
AC3
SOFTWARE
ASP A:123 , TYR A:125 , ASN A:127 , ASP A:132 , HOH A:239 , HOH A:240
BINDING SITE FOR RESIDUE CA A 237
04
AC4
SOFTWARE
GLU A:121 , ASP A:123 , ASP A:132 , HIS A:137 , HOH A:241 , HOH A:242
BINDING SITE FOR RESIDUE MN A 238
05
AC5
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 , BGC B:236 , HOH B:270 , HOH B:310 , HOH B:349
BINDING SITE FOR RESIDUE GAL B 235
06
AC6
SOFTWARE
SER B:211 , LEU B:212 , GLY B:213 , GAL B:235
BINDING SITE FOR RESIDUE BGC B 236
07
AC7
SOFTWARE
ASP B:123 , TYR B:125 , ASN B:127 , ASP B:132 , HOH B:239 , HOH B:240
BINDING SITE FOR RESIDUE CA B 237
08
AC8
SOFTWARE
GLU B:121 , ASP B:123 , ASP B:132 , HIS B:137 , HOH B:241 , HOH B:242
BINDING SITE FOR RESIDUE MN B 238
09
AC9
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 , BGC C:236
BINDING SITE FOR RESIDUE GAL C 235
10
BC1
SOFTWARE
SER C:211 , LEU C:212 , GLY C:213 , GLY C:214 , GAL C:235
BINDING SITE FOR RESIDUE BGC C 236
11
BC2
SOFTWARE
ASP C:123 , TYR C:125 , ASN C:127 , ASP C:132 , HOH C:239 , HOH C:240
BINDING SITE FOR RESIDUE CA C 237
12
BC3
SOFTWARE
GLU C:121 , ASP C:123 , ASP C:132 , HIS C:137 , HOH C:241 , HOH C:242
BINDING SITE FOR RESIDUE MN C 238
13
BC4
SOFTWARE
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:255
BINDING SITE FOR RESIDUE GAL D 235
14
BC5
SOFTWARE
SER D:211 , LEU D:212 , GLY D:213 , GAL D:235
BINDING SITE FOR RESIDUE GLC D 236
15
BC6
SOFTWARE
ASP D:123 , TYR D:125 , ASN D:127 , ASP D:132 , HOH D:239 , HOH D:240
BINDING SITE FOR RESIDUE CA D 237
16
BC7
SOFTWARE
GLU D:121 , ASP D:123 , ASP D:132 , HIS D:137 , HOH D:241 , HOH D:242
BINDING SITE FOR RESIDUE MN D 238
[
close Site info
]
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)
[
close SNP/Variant info
]
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
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1v6la_ (A:)
1b: SCOP_d1v6lb_ (B:)
1c: SCOP_d1v6lc_ (C:)
1d: SCOP_d1v6ld_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d1v6la_
A:
1b
d1v6lb_
B:
1c
d1v6lc_
C:
1d
d1v6ld_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1v6lA00 (A:1-232)
1b: CATH_1v6lB00 (B:1-232)
1c: CATH_1v6lC00 (C:1-232)
1d: CATH_1v6lD00 (D:1-232)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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
1v6lA00
A:1-232
1b
1v6lB00
B:1-232
1c
1v6lC00
C:1-232
1d
1v6lD00
D:1-232
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Lectin_legB_1v6lD01 (D:2-226)
1b: PFAM_Lectin_legB_1v6lD02 (D:2-226)
1c: PFAM_Lectin_legB_1v6lD03 (D:2-226)
1d: PFAM_Lectin_legB_1v6lD04 (D:2-226)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Concanavalin
(293)
Family
:
Lectin_legB
(93)
Arachis hypogaea (Peanut)
(11)
1a
Lectin_legB-1v6lD01
D:2-226
1b
Lectin_legB-1v6lD02
D:2-226
1c
Lectin_legB-1v6lD03
D:2-226
1d
Lectin_legB-1v6lD04
D:2-226
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (159 KB)
Header - Asym.Unit
Biol.Unit 1 (152 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1V6L
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help