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2DU1
Biol. Unit 1
Info
Asym.Unit (170 KB)
Biol.Unit 1 (85 KB)
Biol.Unit 2 (83 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BASIC WINGED BEAN LECTIN IN COMPLEX WITH METHYL-ALPHA-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
:
2.60
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
)
[
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: ALPHA-L-FUCOSE (FUCa)
2b: ALPHA-L-FUCOSE (FUCb)
2c: ALPHA-L-FUCOSE (FUCc)
2d: ALPHA-L-FUCOSE (FUCd)
3a: ALPHA-METHYL-N-ACETYL-D-GALACTOSAM... (MGCa)
3b: ALPHA-METHYL-N-ACETYL-D-GALACTOSAM... (MGCb)
3c: ALPHA-METHYL-N-ACETYL-D-GALACTOSAM... (MGCc)
3d: ALPHA-METHYL-N-ACETYL-D-GALACTOSAM... (MGCd)
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)
5m: N-ACETYL-D-GLUCOSAMINE (NAGm)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
FUC
3
Ligand/Ion
ALPHA-L-FUCOSE
3
MGC
2
Ligand/Ion
ALPHA-METHYL-N-ACETYL-D-GALACTOSAMINE
4
MN
-1
Ligand/Ion
MANGANESE (II) ION
5
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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]
Sites
(17, 17)
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: BC7 (SOFTWARE)
14: CC4 (SOFTWARE)
15: CC5 (SOFTWARE)
16: CC6 (SOFTWARE)
17: CC7 (SOFTWARE)
View:
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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 MGC 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 , HOH A:1459 , HIS D:11 , LYS D:53
BINDING SITE FOR RESIDUE NAG A 503
05
AC5
SOFTWARE
ASN A:44 , SER D:60
BINDING SITE FOR RESIDUE NAG A 601
06
AC6
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:2440
BINDING SITE FOR RESIDUE MGC B 2401
07
AC7
SOFTWARE
ARG B:82 , ASN B:219 , FUC B:502 , NAG B:503
BINDING SITE FOR RESIDUE NAG B 501
08
AC8
SOFTWARE
NAG B:501 , NAG B:503 , HOH B:2449
BINDING SITE FOR RESIDUE FUC B 502
09
AC9
SOFTWARE
NAG B:501 , FUC B:502 , HOH B:2449
BINDING SITE FOR RESIDUE NAG B 503
10
BC1
SOFTWARE
ASN B:44 , FUC B:602 , NAG B:603
BINDING SITE FOR RESIDUE NAG B 601
11
BC2
SOFTWARE
NAG B:601 , NAG B:603 , LEU D:113 , SER D:114 , PRO D:115
BINDING SITE FOR RESIDUE FUC B 602
12
BC3
SOFTWARE
NAG B:601 , FUC B:602
BINDING SITE FOR RESIDUE NAG B 603
13
BC7
SOFTWARE
SER B:181 , GLU B:200 , NAG C:501 , FUC C:502
BINDING SITE FOR RESIDUE NAG C 503
14
CC4
SOFTWARE
ASP A:124 , PHE A:126 , ASN A:128 , ASP A:131 , HOH A:1404
BINDING SITE FOR RESIDUE CA A 1303
15
CC5
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
16
CC6
SOFTWARE
ASP B:124 , PHE B:126 , ASN B:128 , ASP B:131 , HOH B:2404
BINDING SITE FOR RESIDUE CA B 2303
17
CC7
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
[
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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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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: LECTIN_LEGUME_BETA (A:119-125,B: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
A:119-125
B: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_d2du1a_ (A:)
1b: SCOP_d2du1b_ (B:)
1c: SCOP_d2du1c_ (C:)
1d: SCOP_d2du1d_ (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
d2du1a_
A:
1b
d2du1b_
B:
1c
d2du1c_
C:
1d
d2du1d_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2du1A00 (A:1-237)
1b: CATH_2du1B00 (B:1-237)
1c: CATH_2du1C00 (C:1-237)
1d: CATH_2du1D00 (D:1-237)
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(
)
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
2du1A00
A:1-237
1b
2du1B00
B:1-237
1c
2du1C00
C:1-237
1d
2du1D00
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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Asymmetric Unit 1
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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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Asym.Unit (170 KB)
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Header - Biol.Unit 1
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