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2ZML
Asym. Unit
Info
Asym.Unit (166 KB)
Biol.Unit 1 (82 KB)
Biol.Unit 2 (80 KB)
Biol.Unit 3 (43 KB)
Biol.Unit 4 (44 KB)
Biol.Unit 5 (43 KB)
Biol.Unit 6 (42 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BASIC WINGED BEAN LECTIN IN COMPLEX WITH GAL-ALPHA 1,4 GAL
Authors
:
K. A. Kulkarni, S. Katiyar, A. Surolia, M. Vijayan, K. Suguna
Date
:
19 Apr 08 (Deposition) - 29 Jul 08 (Release) - 08 Feb 17 (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)
Biol. Unit 3: A (1x)
Biol. Unit 4: B (1x)
Biol. Unit 5: C (1x)
Biol. Unit 6: D (1x)
Keywords
:
Legume Lectin, Sugar Specificity, Winged Bean Lectin, Sugar Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. A. Kulkarni, S. Katiyar, A. Surolia, M. Vijayan, K. Suguna
Structure And Sugar-Specificity Of Basic Winged-Bean Lectin Structures Of New Disaccharide Complexes And A Comparative Study With Other Known Disaccharide Complexes Of The Lectin
Acta Crystallogr. , Sect. D V. 64 730 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 30)
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 D-GALACTOSE (GLAa)
3b: ALPHA D-GALACTOSE (GLAb)
3c: ALPHA D-GALACTOSE (GLAc)
3d: ALPHA D-GALACTOSE (GLAd)
3e: ALPHA D-GALACTOSE (GLAe)
3f: ALPHA D-GALACTOSE (GLAf)
3g: ALPHA D-GALACTOSE (GLAg)
3h: ALPHA D-GALACTOSE (GLAh)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
FUC
4
Ligand/Ion
ALPHA-L-FUCOSE
3
GLA
8
Ligand/Ion
ALPHA D-GALACTOSE
4
MN
4
Ligand/Ion
MANGANESE (II) ION
5
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(26, 26)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC6 (SOFTWARE)
06: AC7 (SOFTWARE)
07: AC8 (SOFTWARE)
08: AC9 (SOFTWARE)
09: BC3 (SOFTWARE)
10: BC4 (SOFTWARE)
11: BC6 (SOFTWARE)
12: BC7 (SOFTWARE)
13: BC8 (SOFTWARE)
14: CC1 (SOFTWARE)
15: CC2 (SOFTWARE)
16: CC3 (SOFTWARE)
17: CC4 (SOFTWARE)
18: CC5 (SOFTWARE)
19: CC6 (SOFTWARE)
20: CC7 (SOFTWARE)
21: CC8 (SOFTWARE)
22: CC9 (SOFTWARE)
23: DC1 (SOFTWARE)
24: DC2 (SOFTWARE)
25: DC3 (SOFTWARE)
26: DC4 (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
BINDING SITE FOR RESIDUE GLA A 400
02
AC2
SOFTWARE
PHE A:126 , SER A:214
BINDING SITE FOR RESIDUE GLA A 401
03
AC3
SOFTWARE
ARG A:82 , PRO A:83 , GLN A:217 , ASN A:219
BINDING SITE FOR RESIDUE NAG A 501
04
AC4
SOFTWARE
ASN D:8 , GLN D:9
BINDING SITE FOR RESIDUE FUC A 502
05
AC6
SOFTWARE
ASN A:44 , SER D:60
BINDING SITE FOR RESIDUE NAG A 601
06
AC7
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
BINDING SITE FOR RESIDUE GLA B 400
07
AC8
SOFTWARE
SER B:214
BINDING SITE FOR RESIDUE GLA B 401
08
AC9
SOFTWARE
ARG B:82 , PRO B:83 , ASN B:219
BINDING SITE FOR RESIDUE NAG B 501
09
BC3
SOFTWARE
ASN B:44
BINDING SITE FOR RESIDUE NAG B 601
10
BC4
SOFTWARE
LEU D:113 , SER D:114
BINDING SITE FOR RESIDUE FUC B 602
11
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 , ALA C:220
BINDING SITE FOR RESIDUE GLA C 400
12
BC7
SOFTWARE
PHE C:126 , SER C:214
BINDING SITE FOR RESIDUE GLA C 401
13
BC8
SOFTWARE
PHE C:80 , PRO C:83 , GLN C:217 , ASN C:219
BINDING SITE FOR RESIDUE NAG C 501
14
CC1
SOFTWARE
SER B:181 , GLU B:200 , ARG C:82
BINDING SITE FOR RESIDUE NAG C 503
15
CC2
SOFTWARE
ASN C:44 , PRO C:213
BINDING SITE FOR RESIDUE NAG C 601
16
CC3
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 , ALA D:220
BINDING SITE FOR RESIDUE GLA D 400
17
CC4
SOFTWARE
ARG D:82 , SER D:214
BINDING SITE FOR RESIDUE GLA D 401
18
CC5
SOFTWARE
ARG D:21 , ASN D:44
BINDING SITE FOR RESIDUE NAG D 601
19
CC6
SOFTWARE
GLU A:122 , ASP A:124 , ASP A:131 , HIS A:136
BINDING SITE FOR RESIDUE MN A 300
20
CC7
SOFTWARE
ASP A:124 , PHE A:126 , ASN A:128 , ASP A:131
BINDING SITE FOR RESIDUE CA A 303
21
CC8
SOFTWARE
GLU B:122 , ASP B:124 , ASP B:131 , HIS B:136
BINDING SITE FOR RESIDUE MN B 300
22
CC9
SOFTWARE
ASP B:124 , PHE B:126 , ASN B:128 , ASP B:131
BINDING SITE FOR RESIDUE CA B 303
23
DC1
SOFTWARE
GLU C:122 , ASP C:124 , ASP C:131 , HIS C:136
BINDING SITE FOR RESIDUE MN C 300
24
DC2
SOFTWARE
ASP C:124 , PHE C:126 , ASN C:128 , ASP C:131
BINDING SITE FOR RESIDUE CA C 303
25
DC3
SOFTWARE
GLU D:122 , ASP D:124 , ASP D:131 , HIS D:136
BINDING SITE FOR RESIDUE MN D 300
26
DC4
SOFTWARE
ASP D:124 , PHE D:126 , ASN D:128 , ASP D:131
BINDING SITE FOR RESIDUE CA D 303
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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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
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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_d2zmla_ (A:)
1b: SCOP_d2zmlb_ (B:)
1c: SCOP_d2zmlc_ (C:)
1d: SCOP_d2zmld_ (D:)
View:
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)
(
)
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(
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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
d2zmla_
A:
1b
d2zmlb_
B:
1c
d2zmlc_
C:
1d
d2zmld_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2zmlA00 (A:1-237)
1b: CATH_2zmlB00 (B:1-237)
1c: CATH_2zmlC00 (C:1-237)
1d: CATH_2zmlD00 (D:1-237)
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(
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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)
Goa bean (Psophocarpus tetragonolobus)
(3)
1a
2zmlA00
A:1-237
1b
2zmlB00
B:1-237
1c
2zmlC00
C:1-237
1d
2zmlD00
D:1-237
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Lectin_legB_2zmlD01 (D:1-232)
1b: PFAM_Lectin_legB_2zmlD02 (D:1-232)
1c: PFAM_Lectin_legB_2zmlD03 (D:1-232)
1d: PFAM_Lectin_legB_2zmlD04 (D:1-232)
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Clans
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(
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Organisms
(
)
(
)
Clan
:
Concanavalin
(293)
Family
:
Lectin_legB
(93)
Psophocarpus tetragonolobus (Winged bean) (Dolichos tetragonolobus)
(5)
1a
Lectin_legB-2zmlD01
D:1-232
1b
Lectin_legB-2zmlD02
D:1-232
1c
Lectin_legB-2zmlD03
D:1-232
1d
Lectin_legB-2zmlD04
D:1-232
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