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3ZYR
Asym. Unit
Info
Asym.Unit (105 KB)
Biol.Unit 1 (98 KB)
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(1)
Title
:
STRUCTURE OF THE LECTIN FROM PLATYPODIUM ELEGANS IN COMPLEX WITH HEPTASACCHARIDE
Authors
:
R. G. Benevides, G. Ganne, B. S. Cavazza, A. Varrot, A. Imberty
Date
:
24 Aug 11 (Deposition) - 11 Jan 12 (Release) - 08 Aug 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Sugar Binding Protein, N-Glycan, Plant Lectin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. G. Benevides, G. Ganne, R. D. C. Simoes, V. Schubert, M. Niemietz, C. Unverzagt, V. Chazalet, C. Breton, A. Varrot, B. S. Cavada, A. Imberty
A Lectin From Platypodium Elegans With Unusual Specificity And Affinity For Asymmetric Complex N-Glycans.
J. Biol. Chem. V. 287 26352 2012
[
close entry info
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Hetero Components
(8, 25)
Info
All Hetero Components
1a: ASPARAGINE (ASNa)
2a: BETA-D-MANNOSE (BMAa)
2b: BETA-D-MANNOSE (BMAb)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
5a: ALPHA-D-MANNOSE (MANa)
5b: ALPHA-D-MANNOSE (MANb)
5c: ALPHA-D-MANNOSE (MANc)
5d: ALPHA-D-MANNOSE (MANd)
6a: MANGANESE (II) ION (MNa)
6b: MANGANESE (II) ION (MNb)
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)
8a: UREA (UREa)
8b: UREA (UREb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ASN
1
Mod. Amino Acid
ASPARAGINE
2
BMA
2
Ligand/Ion
BETA-D-MANNOSE
3
CA
2
Ligand/Ion
CALCIUM ION
4
GOL
4
Ligand/Ion
GLYCEROL
5
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
6
MN
2
Ligand/Ion
MANGANESE (II) ION
7
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
8
URE
2
Ligand/Ion
UREA
[
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Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
NAG A:300 , HOH A:2280 , ARG B:221
BINDING SITE FOR RESIDUE ASN A 299
02
AC2
SOFTWARE
GLU A:137 , ASP A:139 , ASP A:150 , HIS A:155 , HOH A:2175 , HOH A:2176
BINDING SITE FOR RESIDUE MN A 400
03
AC3
SOFTWARE
ASP A:139 , PHE A:141 , ASN A:147 , ASP A:150 , HOH A:2137 , HOH A:2152
BINDING SITE FOR RESIDUE CA A 401
04
AC4
SOFTWARE
ASP A:10 , SER A:11 , ARG A:66 , TRP A:219 , HOH A:2006 , HOH A:2100 , HOH A:2292 , HOH A:2293 , GLU B:23 , ASN B:25
BINDING SITE FOR RESIDUE GOL A 402
05
AC5
SOFTWARE
TRP A:149 , ARG A:164 , HOH A:2197 , HOH A:2199 , ARG B:174 , LYS B:177
BINDING SITE FOR RESIDUE URE A 403
06
AC6
SOFTWARE
ARG A:58 , THR A:106 , LEU A:119 , ASN A:131 , GLN A:132 , HOH A:2144 , HOH A:2170 , HOH A:2171 , HOH A:2294
BINDING SITE FOR RESIDUE GOL A 405
07
AC7
SOFTWARE
PRO A:109 , GLY A:111 , HOH A:2148 , HOH A:2151 , HOH A:2295
BINDING SITE FOR RESIDUE GOL A 406
08
AC8
SOFTWARE
GLU B:137 , ASP B:139 , ASP B:150 , HIS B:155 , HOH B:2113 , HOH B:2114
BINDING SITE FOR RESIDUE MN B 400
09
AC9
SOFTWARE
ASP B:139 , PHE B:141 , ASN B:147 , ASP B:150 , HOH B:2084 , HOH B:2098
BINDING SITE FOR RESIDUE CA B 401
10
BC1
SOFTWARE
ALA B:143 , GLN B:144 , ASN B:145 , ASN B:152 , MAN B:303 , HOH B:2222 , HOH B:2223
BINDING SITE FOR RESIDUE GOL B 403
11
BC2
SOFTWARE
HOH A:2030 , GLN B:64 , VAL B:65 , ARG B:66 , HOH B:2060
BINDING SITE FOR RESIDUE URE B 404
12
BC3
SOFTWARE
ARG A:53 , SER A:54 , SER A:91 , ASN A:92 , ALA A:94 , ASP A:95 , GLY A:111 , ALA A:113 , GLY A:114 , GLY A:115 , LEU A:116 , PHE A:141 , ALA A:143 , ASN A:145 , SER A:146 , ASN A:147 , GLY A:229 , GLU A:230 , GLN A:231 , ASN A:299 , HOH A:2132 , HOH A:2151 , HOH A:2181 , HOH A:2182 , HOH A:2184 , HOH A:2275 , HOH A:2281 , HOH A:2283 , HOH A:2284 , HOH A:2285 , HOH A:2286 , HOH A:2287 , HOH A:2288 , HOH A:2289 , HOH A:2290 , HOH A:2291
BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 300 TO 306
13
BC4
SOFTWARE
ARG A:203 , GLN A:205 , HOH A:2206 , HOH A:2238 , HOH A:2254 , HOH A:2257 , ARG B:53 , SER B:54 , PRO B:89 , SER B:91 , ASN B:92 , ALA B:94 , ASP B:95 , GLY B:111 , ALA B:113 , GLY B:114 , GLY B:115 , LEU B:116 , PHE B:141 , ALA B:143 , ASN B:145 , SER B:146 , ASN B:147 , GLY B:229 , GLU B:230 , GLN B:231 , GOL B:403 , HOH B:2080 , HOH B:2082 , HOH B:2097 , HOH B:2117 , HOH B:2119 , HOH B:2198 , HOH B:2199 , HOH B:2207 , HOH B:2208 , HOH B:2209 , HOH B:2210 , HOH B:2213 , HOH B:2215 , HOH B:2217 , HOH B:2218 , HOH B:2219 , HOH B:2220 , HOH B:2221
BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 300 TO 306
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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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.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3zyra_ (A:)
1b: SCOP_d3zyrb_ (B:)
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Protein Domains
(
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(
)
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)
Platypodium elegans [TaxId: 115002]
(2)
1a
d3zyra_
A:
1b
d3zyrb_
B:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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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
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
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Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (105 KB)
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