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2ZMK
Asym. Unit
Info
Asym.Unit (168 KB)
Biol.Unit 1 (83 KB)
Biol.Unit 2 (81 KB)
Biol.Unit 3 (44 KB)
Biol.Unit 4 (44 KB)
Biol.Unit 5 (43 KB)
Biol.Unit 6 (43 KB)
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(1)
Title
:
CRYSTL STRUCTURE OF BASIC WINGED BEAN LECTIN IN COMPLEX WITH GAL-ALPHA-1,4-GAL-BETA-ETHYLENE
Authors
:
K. A. Kulkarni, S. Katiyar, A. Surolia, M. Vijayan
Date
:
19 Apr 08 (Deposition) - 29 Jul 08 (Release) - 18 Jun 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
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 Binding Protein, Sugar Specificity, Glycoprotein, Lectin
(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
(7, 34)
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: ETHYL BETA-D-GALACTOPYRANOSIDE (EGAa)
3b: ETHYL BETA-D-GALACTOPYRANOSIDE (EGAb)
3c: ETHYL BETA-D-GALACTOPYRANOSIDE (EGAc)
3d: ETHYL BETA-D-GALACTOPYRANOSIDE (EGAd)
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)
5a: ALPHA D-GALACTOSE (GLAa)
5b: ALPHA D-GALACTOSE (GLAb)
5c: ALPHA D-GALACTOSE (GLAc)
5d: ALPHA D-GALACTOSE (GLAd)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
CA
4
Ligand/Ion
CALCIUM ION
3
EGA
4
Ligand/Ion
ETHYL BETA-D-GALACTOPYRANOSIDE
4
FUC
6
Ligand/Ion
ALPHA-L-FUCOSE
5
GLA
4
Ligand/Ion
ALPHA D-GALACTOSE
6
MN
4
Ligand/Ion
MANGANESE (II) ION
7
NAG
11
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(25, 25)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:122 , ASP A:124 , ASP A:131 , HIS A:136 , HOH A:401 , HOH A:447
BINDING SITE FOR RESIDUE MN A 301
02
AC2
SOFTWARE
ASP A:124 , PHE A:126 , ASN A:128 , ASP A:131 , HOH A:402 , HOH A:403
BINDING SITE FOR RESIDUE CA A 302
03
AC3
SOFTWARE
HIS A:84 , ASP A:87 , GLY A:105 , PHE A:126 , ASN A:128 , GLY A:211 , ASP A:212 , GLY A:215 , ALA A:220 , EGA A:309
BINDING SITE FOR RESIDUE GLA A 308
04
AC4
SOFTWARE
SER A:214 , GLA A:308
BINDING SITE FOR RESIDUE EGA A 309
05
AC5
SOFTWARE
GLU B:122 , ASP B:124 , ASP B:131 , HIS B:136 , HOH B:401 , HOH B:402
BINDING SITE FOR RESIDUE MN B 301
06
AC6
SOFTWARE
ASP B:124 , PHE B:126 , ASN B:128 , ASP B:131 , HOH B:403 , HOH B:404
BINDING SITE FOR RESIDUE CA B 302
07
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 , ALA B:220 , EGA B:308 , HOH B:421
BINDING SITE FOR RESIDUE GLA B 307
08
AC8
SOFTWARE
THR B:129 , SER B:214 , GLY B:215 , GLA B:307
BINDING SITE FOR RESIDUE EGA B 308
09
AC9
SOFTWARE
GLU C:122 , ASP C:124 , ASP C:131 , HIS C:136 , HOH C:401
BINDING SITE FOR RESIDUE MN C 301
10
BC1
SOFTWARE
ASP C:124 , PHE C:126 , ASN C:128 , ASP C:131 , HOH C:402 , HOH C:403
BINDING SITE FOR RESIDUE CA C 302
11
BC2
SOFTWARE
HIS C:84 , ASP C:87 , GLY C:105 , PHE C:126 , ASN C:128 , GLY C:211 , ASP C:212 , EGA C:304 , HOH C:427
BINDING SITE FOR RESIDUE GLA C 303
12
BC3
SOFTWARE
SER C:214 , GLA C:303
BINDING SITE FOR RESIDUE EGA C 304
13
BC4
SOFTWARE
SER B:60 , THR B:61 , GLU B:200
BINDING SITE FOR RESIDUE BMA C 306
14
BC5
SOFTWARE
GLU D:122 , ASP D:124 , ASP D:131 , HIS D:136 , HOH D:401 , HOH D:402
BINDING SITE FOR RESIDUE MN D 301
15
BC6
SOFTWARE
ASP D:124 , PHE D:126 , ASN D:128 , ASP D:131 , HOH D:403
BINDING SITE FOR RESIDUE CA D 302
16
BC7
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 , EGA D:309
BINDING SITE FOR RESIDUE GLA D 308
17
BC8
SOFTWARE
PRO D:81 , ARG D:82 , PRO D:83 , PHE D:126 , THR D:129 , SER D:214 , FUC D:304 , GLA D:308
BINDING SITE FOR RESIDUE EGA D 309
18
BC9
SOFTWARE
ASN A:44 , SER D:60
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 44 RESIDUES 305 TO 307
19
CC1
SOFTWARE
PRO A:83 , GLN A:217 , ASN A:219 , ASN D:8
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 219 RESIDUES 303 TO 304
20
CC2
SOFTWARE
ARG A:24 , ASN B:44
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 44 RESIDUES 305 TO 306
21
CC3
SOFTWARE
PRO B:83 , GLN B:217 , ASN B:219
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 219 RESIDUES 303 TO 304
22
CC4
SOFTWARE
ASN C:44
BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 44 RESIDUES 307 TO 308
23
CC5
SOFTWARE
PHE C:80 , GLN C:217 , ASN C:219
BINDING SITE FOR MONO-SACCHARIDE NAG C 305 BOUND TO ASN C 219
24
CC6
SOFTWARE
HOH C:413 , ARG D:21 , ASN D:44
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 44 RESIDUES 305 TO 307
25
CC7
SOFTWARE
PHE D:80 , SER D:214 , ASN D:219 , EGA D:309
BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 219 RESIDUES 303 TO 304
[
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]
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_d2zmka_ (A:)
1b: SCOP_d2zmkb_ (B:)
1c: SCOP_d2zmkc_ (C:)
1d: SCOP_d2zmkd_ (D:)
View:
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Classes
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(
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(
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(
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(
)
(
)
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)
Winged bean (Psophocarpus tetragonolobus), basic agglutinin [TaxId: 3891]
(13)
1a
d2zmka_
A:
1b
d2zmkb_
B:
1c
d2zmkc_
C:
1d
d2zmkd_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2zmkA00 (A:1-237)
1b: CATH_2zmkB00 (B:1-237)
1c: CATH_2zmkC00 (C:1-237)
1d: CATH_2zmkD00 (D:1-237)
View:
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(
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(
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Architectures
(
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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)
Goa bean (Psophocarpus tetragonolobus)
(3)
1a
2zmkA00
A:1-237
1b
2zmkB00
B:1-237
1c
2zmkC00
C:1-237
1d
2zmkD00
D:1-237
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Lectin_legB_2zmkD01 (D:1-232)
1b: PFAM_Lectin_legB_2zmkD02 (D:1-232)
1c: PFAM_Lectin_legB_2zmkD03 (D:1-232)
1d: PFAM_Lectin_legB_2zmkD04 (D:1-232)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Concanavalin
(293)
Family
:
Lectin_legB
(93)
Psophocarpus tetragonolobus (Winged bean) (Dolichos tetragonolobus)
(5)
1a
Lectin_legB-2zmkD01
D:1-232
1b
Lectin_legB-2zmkD02
D:1-232
1c
Lectin_legB-2zmkD03
D:1-232
1d
Lectin_legB-2zmkD04
D:1-232
[
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]
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select residue range 5 to 10 in chain 'A'
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