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2DTY
Asym. Unit
Info
Asym.Unit (173 KB)
Biol.Unit 1 (85 KB)
Biol.Unit 2 (84 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BASIC WINGED BEAN LECTIN COMPLEXED WITH N-ACETYL-D-GALACTOSAMINE
Authors
:
K. A. Kulkarni, S. Katiyar, A. Surolia, M. Vijayan, K. Suguna
Date
:
19 Jul 06 (Deposition) - 07 Nov 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.65
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, Sugar Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. A. Kulkarni, S. Katiyar, A. Surolia, M. Vijayan, K. Suguna
Structural Basis For The Carbohydrate-Specificity Of Basic Winged-Bean Lectin And Its Differential Affinity For Gal An Galnac
Acta Crystallogr. , Sect. D V. 62 1319 2006
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(7, 37)
Info
All Hetero Components
1a: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Ga)
1b: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Gb)
1c: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Gc)
1d: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Gd)
2a: BETA-D-MANNOSE (BMAa)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
3d: CALCIUM ION (CAd)
4a: ALPHA-L-FUCOSE (FUCa)
4b: ALPHA-L-FUCOSE (FUCb)
4c: ALPHA-L-FUCOSE (FUCc)
4d: ALPHA-L-FUCOSE (FUCd)
4e: ALPHA-L-FUCOSE (FUCe)
4f: ALPHA-L-FUCOSE (FUCf)
4g: ALPHA-L-FUCOSE (FUCg)
5a: BETA-L-FUCOSE (FULa)
6a: MANGANESE (II) ION (MNa)
6b: MANGANESE (II) ION (MNb)
6c: MANGANESE (II) ION (MNc)
6d: MANGANESE (II) ION (MNd)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
7g: N-ACETYL-D-GLUCOSAMINE (NAGg)
7h: N-ACETYL-D-GLUCOSAMINE (NAGh)
7i: N-ACETYL-D-GLUCOSAMINE (NAGi)
7j: N-ACETYL-D-GLUCOSAMINE (NAGj)
7k: N-ACETYL-D-GLUCOSAMINE (NAGk)
7l: N-ACETYL-D-GLUCOSAMINE (NAGl)
7m: N-ACETYL-D-GLUCOSAMINE (NAGm)
7n: N-ACETYL-D-GLUCOSAMINE (NAGn)
7o: N-ACETYL-D-GLUCOSAMINE (NAGo)
7p: N-ACETYL-D-GLUCOSAMINE (NAGp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
A2G
4
Ligand/Ion
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2
BMA
1
Ligand/Ion
BETA-D-MANNOSE
3
CA
4
Ligand/Ion
CALCIUM ION
4
FUC
7
Ligand/Ion
ALPHA-L-FUCOSE
5
FUL
1
Ligand/Ion
BETA-L-FUCOSE
6
MN
4
Ligand/Ion
MANGANESE (II) ION
7
NAG
16
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(37, 37)
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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:84 , ASP A:87 , GLY A:104 , GLY A:105 , PHE A:126 , ASN A:128 , GLY A:211 , ASP A:212 , GLY A:215 , ALA A:220
BINDING SITE FOR RESIDUE A2G A 1401
02
AC2
SOFTWARE
ARG A:82 , PRO A:83 , GLN A:217 , ASN A:219 , FUC A:502 , NAG A:503
BINDING SITE FOR RESIDUE NAG A 501
03
AC3
SOFTWARE
NAG A:501 , NAG A:503 , ASN D:8 , GLN D:9
BINDING SITE FOR RESIDUE FUC A 502
04
AC4
SOFTWARE
NAG A:501 , FUC A:502 , GLN D:9 , LYS D:53
BINDING SITE FOR RESIDUE NAG A 503
05
AC5
SOFTWARE
ASN A:44 , PRO A:213 , FUC A:602 , NAG A:603
BINDING SITE FOR RESIDUE NAG A 601
06
AC6
SOFTWARE
NAG A:601 , NAG A:603 , SER D:60
BINDING SITE FOR RESIDUE FUC A 602
07
AC7
SOFTWARE
NAG A:601 , FUC A:602
BINDING SITE FOR RESIDUE NAG A 603
08
AC8
SOFTWARE
HIS B:84 , ASP B:87 , GLY B:104 , GLY B:105 , PHE B:126 , ASN B:128 , GLY B:211 , ASP B:212 , GLY B:215 , ALA B:220 , HOH B:2443 , HOH B:2447
BINDING SITE FOR RESIDUE A2G B 2401
09
AC9
SOFTWARE
LEU A:113 , PHE B:80 , PRO B:83 , ASN B:219 , FUC B:502 , NAG B:503
BINDING SITE FOR RESIDUE NAG B 501
10
BC1
SOFTWARE
ARG B:82 , NAG B:501 , NAG B:503
BINDING SITE FOR RESIDUE FUC B 502
11
BC2
SOFTWARE
ARG B:82 , NAG B:501 , FUC B:502
BINDING SITE FOR RESIDUE NAG B 503
12
BC3
SOFTWARE
ASN B:44 , FUC B:602 , NAG B:603 , HOH B:2423
BINDING SITE FOR RESIDUE NAG B 601
13
BC4
SOFTWARE
NAG B:601 , NAG B:603 , LEU D:113 , SER D:114 , PRO D:115
BINDING SITE FOR RESIDUE FUC B 602
14
BC5
SOFTWARE
NAG B:601 , FUC B:602
BINDING SITE FOR RESIDUE NAG B 603
15
BC6
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
BINDING SITE FOR RESIDUE A2G C 3401
16
BC7
SOFTWARE
PHE C:80 , GLN C:217 , ASN C:219 , FUC C:502 , NAG C:503 , HOH C:3465
BINDING SITE FOR RESIDUE NAG C 501
17
BC8
SOFTWARE
NAG C:501 , NAG C:503
BINDING SITE FOR RESIDUE FUC C 502
18
BC9
SOFTWARE
SER B:181 , NAG C:501 , FUC C:502 , BMA C:504
BINDING SITE FOR RESIDUE NAG C 503
19
CC1
SOFTWARE
GLN B:56 , ASP B:59 , THR B:61 , GLU B:200 , NAG C:503
BINDING SITE FOR RESIDUE BMA C 504
20
CC2
SOFTWARE
ASN C:44 , FUL C:602 , NAG C:603
BINDING SITE FOR RESIDUE NAG C 601
21
CC3
SOFTWARE
NAG C:601 , NAG C:603
BINDING SITE FOR RESIDUE FUL C 602
22
CC4
SOFTWARE
NAG C:601 , FUL C:602 , SER D:27
BINDING SITE FOR RESIDUE NAG C 603
23
CC5
SOFTWARE
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 , HOH D:4437
BINDING SITE FOR RESIDUE A2G D 4401
24
CC6
SOFTWARE
PHE D:80 , GLN D:217 , ASN D:219 , FUC D:502 , NAG D:503
BINDING SITE FOR RESIDUE NAG D 501
25
CC7
SOFTWARE
SER D:214 , NAG D:501 , NAG D:503
BINDING SITE FOR RESIDUE FUC D 502
26
CC8
SOFTWARE
NAG D:501 , FUC D:502
BINDING SITE FOR RESIDUE NAG D 503
27
CC9
SOFTWARE
ASN D:44 , FUC D:602 , NAG D:603
BINDING SITE FOR RESIDUE NAG D 601
28
DC1
SOFTWARE
NAG D:601 , NAG D:603
BINDING SITE FOR RESIDUE FUC D 602
29
DC2
SOFTWARE
NAG D:601 , FUC D:602
BINDING SITE FOR RESIDUE NAG D 603
30
DC3
SOFTWARE
GLU A:122 , ASP A:124 , ASP A:131 , HIS A:136 , HOH A:1402 , HOH A:1403
BINDING SITE FOR RESIDUE MN A 1300
31
DC4
SOFTWARE
ASP A:124 , PHE A:126 , ASN A:128 , ASP A:131 , HOH A:1404 , HOH A:1405
BINDING SITE FOR RESIDUE CA A 1303
32
DC5
SOFTWARE
GLU B:122 , ASP B:124 , ASP B:131 , HIS B:136 , HOH B:2402 , HOH B:2403
BINDING SITE FOR RESIDUE MN B 2300
33
DC6
SOFTWARE
ASP B:124 , PHE B:126 , ASN B:128 , ASP B:131 , HOH B:2404 , HOH B:2405
BINDING SITE FOR RESIDUE CA B 2303
34
DC7
SOFTWARE
GLU C:122 , ASP C:124 , ASP C:131 , HIS C:136 , HOH C:3402
BINDING SITE FOR RESIDUE MN C 3300
35
DC8
SOFTWARE
ASP C:124 , PHE C:126 , ASN C:128 , ASP C:131 , HOH C:3403 , HOH C:3404
BINDING SITE FOR RESIDUE CA C 3303
36
DC9
SOFTWARE
GLU D:122 , ASP D:124 , ASP D:131 , HIS D:136 , HOH D:4402 , HOH D:4403
BINDING SITE FOR RESIDUE MN D 4300
37
EC1
SOFTWARE
ASP D:124 , PHE D:126 , ASN D:128 , ASP D:131 , HOH D:4404
BINDING SITE FOR RESIDUE CA D 4303
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: LECTIN_LEGUME_BETA (A:119-125,B:119-125,C:119-125,D:11...)
;
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
4
A:119-125
B:119-125
C:119-125
D:119-125
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2dtya_ (A:)
1b: SCOP_d2dtyb_ (B:)
1c: SCOP_d2dtyc_ (C:)
1d: SCOP_d2dtyd_ (D:)
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)
(
)
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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)
Winged bean (Psophocarpus tetragonolobus), basic agglutinin [TaxId: 3891]
(13)
1a
d2dtya_
A:
1b
d2dtyb_
B:
1c
d2dtyc_
C:
1d
d2dtyd_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2dtyA00 (A:1-237)
1b: CATH_2dtyB00 (B:1-237)
1c: CATH_2dtyC00 (C:1-237)
1d: CATH_2dtyD00 (D:1-237)
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(
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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)
Winged bean (Psophocarpus tetragonolobus)
(13)
1a
2dtyA00
A:1-237
1b
2dtyB00
B:1-237
1c
2dtyC00
C:1-237
1d
2dtyD00
D:1-237
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
[
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