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2D3S
Biol. Unit 2
Info
Asym.Unit (171 KB)
Biol.Unit 1 (86 KB)
Biol.Unit 2 (83 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BASIC WINGED BEAN LECTIN WITH TN-ANTIGEN
Authors
:
K. A. Kulkarni, S. Sinha, S. Katiyar, A. Surolia, M. Vijayan, K. Suguna
Date
:
01 Oct 05 (Deposition) - 17 Jan 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Legume Lectin, Glycosylated Protein, Agglutinin, Tn-Antigen, Sugar Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. A. Kulkarni, S. Sinha, S. Katiyar, A. Surolia, M. Vijayan, K. Suguna
Structural Basis For The Specificity Of Basic Winged Bean Lectin For The Tn-Antigen: A Crystallographic, Thermodynami And Modelling Study
Febs Lett. V. 579 6775 2005
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 10)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: ALPHA-L-FUCOSE (FUCa)
3b: ALPHA-L-FUCOSE (FUCb)
3c: ALPHA-L-FUCOSE (FUCc)
3d: ALPHA-L-FUCOSE (FUCd)
3e: ALPHA-L-FUCOSE (FUCe)
3f: ALPHA-L-FUCOSE (FUCf)
4a: MANGANESE (II) ION (MNa)
4b: MANGANESE (II) ION (MNb)
4c: MANGANESE (II) ION (MNc)
4d: MANGANESE (II) ION (MNd)
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)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
5i: N-ACETYL-D-GLUCOSAMINE (NAGi)
5j: N-ACETYL-D-GLUCOSAMINE (NAGj)
5k: N-ACETYL-D-GLUCOSAMINE (NAGk)
5l: N-ACETYL-D-GLUCOSAMINE (NAGl)
6a: O-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GAL... (TNRa)
6b: O-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GAL... (TNRb)
6c: O-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GAL... (TNRc)
6d: O-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GAL... (TNRd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
4
MN
-1
Ligand/Ion
MANGANESE (II) ION
5
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
TNR
2
Ligand/Ion
O-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSYL)-L-SERINE
[
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]
Sites
(17, 17)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC9 (SOFTWARE)
03: BC1 (SOFTWARE)
04: BC3 (SOFTWARE)
05: BC4 (SOFTWARE)
06: BC5 (SOFTWARE)
07: BC6 (SOFTWARE)
08: BC7 (SOFTWARE)
09: BC8 (SOFTWARE)
10: BC9 (SOFTWARE)
11: CC1 (SOFTWARE)
12: CC6 (SOFTWARE)
13: CC7 (SOFTWARE)
14: CC8 (SOFTWARE)
15: CC9 (SOFTWARE)
16: DC3 (SOFTWARE)
17: DC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
TRP A:43 , ASN A:44 , PRO A:213 , FUC A:602 , SER D:60
BINDING SITE FOR RESIDUE NAG A 601
02
AC9
SOFTWARE
ASN B:44 , FUC B:602 , NAG B:603 , LEU D:113
BINDING SITE FOR RESIDUE NAG B 601
03
BC1
SOFTWARE
NAG B:601 , NAG B:603 , LEU D:113 , SER D:114
BINDING SITE FOR RESIDUE FUC B 602
04
BC3
SOFTWARE
PHE C:80 , PRO C:83 , GLN C:217 , ASN C:219 , FUC C:502 , NAG C:503
BINDING SITE FOR RESIDUE NAG C 501
05
BC4
SOFTWARE
NAG C:501 , NAG C:503
BINDING SITE FOR RESIDUE FUC C 502
06
BC5
SOFTWARE
SER B:181 , NAG C:501 , FUC C:502 , BMA C:504 , HOH C:2435
BINDING SITE FOR RESIDUE NAG C 503
07
BC6
SOFTWARE
GLN B:56 , ASP B:59 , SER B:60 , GLU B:200 , NAG C:503
BINDING SITE FOR RESIDUE BMA C 504
08
BC7
SOFTWARE
ARG C:21 , ASN C:44
BINDING SITE FOR RESIDUE NAG C 601
09
BC8
SOFTWARE
ARG D:21 , TRP D:43 , ASN D:44 , PRO D:213 , FUC D:602 , NAG D:603
BINDING SITE FOR RESIDUE NAG D 601
10
BC9
SOFTWARE
NAG D:601 , NAG D:603 , HOH D:3424
BINDING SITE FOR RESIDUE FUC D 602
11
CC1
SOFTWARE
NAG D:601 , FUC D:602
BINDING SITE FOR RESIDUE NAG D 603
12
CC6
SOFTWARE
ASP C:124 , PHE C:126 , ASN C:128 , ASP C:131 , HOH C:2437 , HOH C:2438
BINDING SITE FOR RESIDUE CA C 2303
13
CC7
SOFTWARE
GLU C:122 , ASP C:124 , ASP C:131 , HIS C:136 , HOH C:2436
BINDING SITE FOR RESIDUE MN C 2300
14
CC8
SOFTWARE
ASP D:124 , PHE D:126 , ASN D:128 , ASP D:131 , HOH D:3425 , HOH D:3429
BINDING SITE FOR RESIDUE CA D 3303
15
CC9
SOFTWARE
GLU D:122 , ASP D:124 , ASP D:131 , HIS D:136 , HOH D:3427 , HOH D:3428
BINDING SITE FOR RESIDUE MN D 3300
16
DC3
SOFTWARE
HIS C:84 , ASP C:87 , GLY C:104 , GLY C:105 , PHE C:126 , ASN C:128 , GLY C:211 , ASP C:212 , GLY C:215 , ALA C:220 , HOH C:2432 , HOH C:2455
BINDING SITE FOR RESIDUE TNR C 2401
17
DC4
SOFTWARE
ARG D:82 , HIS D:84 , ASP D:87 , GLY D:104 , GLY D:105 , PHE D:126 , ASN D:128 , GLY D:211 , ASP D:212 , GLY D:215 , ALA D:220 , HOH D:3416 , HOH D:3443
BINDING SITE FOR RESIDUE TNR D 3401
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: LECTIN_LEGUME_BETA (C:119-125,D:119-125)
;
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.
LEC1_PSOTE
120-126
2
-
-
C:119-125
D:119-125
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2d3sa_ (A:)
1b: SCOP_d2d3sb_ (B:)
1c: SCOP_d2d3sc_ (C:)
1d: SCOP_d2d3sd_ (D:)
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(
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(
)
Families
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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
:
automated matches
(63)
Winged bean (Psophocarpus tetragonolobus) [TaxId: 3891]
(1)
1a
d2d3sa_
A:
1b
d2d3sb_
B:
1c
d2d3sc_
C:
1d
d2d3sd_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2d3sA00 (A:1-237)
1b: CATH_2d3sB00 (B:1-237)
1c: CATH_2d3sC00 (C:1-237)
1d: CATH_2d3sD00 (D:1-237)
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(
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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)
Winged bean (Psophocarpus tetragonolobus)
(13)
1a
2d3sA00
A:1-237
1b
2d3sB00
B:1-237
1c
2d3sC00
C:1-237
1d
2d3sD00
D:1-237
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain C
Chain D
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (171 KB)
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