PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2P34
Asym. Unit
Info
Asym.Unit (162 KB)
Biol.Unit 1 (152 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF A LECTIN FROM CANAVALIA MARITIMA SEEDS (CML) IN COMPLEX WITH MAN1-4MAN-OME
Authors
:
F. B. M. B. Moreno, G. A. Bezerra, T. M. Oliveira, E. P. Souza, B. A. M. Rocha, R. G. Benevides, P. Delatorre, B. S. Cavada, W. De Azevedo Jr.
Date
:
08 Mar 07 (Deposition) - 22 Jan 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,O
#
,P
#
,Q
#
,R
#
Biol. Unit 1: A,B,C,D (1x)
(
#
: chains that contain no standard or modified protein/DNA/RNA residue)
Keywords
:
Canavalia Maritima Lectin, Dimannoside, Plant Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. A. Bezerra, T. M. Oliveira, F. B. M. B. Moreno, E. P. De Souza, B. A. M. Da Rocha, R. G. Benevides, P. Delatorre, W. F. De Azevedo Jr. , B. S. Cavada
Structural Analysis Of Canavalia Maritima And Canavalia Gladiata Lectins Complexed With Different Dimannosides: New Insights Into The Understanding Of The Structure-Biological Activity Relationship In Legume Lectins.
J. Struct. Biol. V. 160 168 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 16)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
2c: ALPHA-D-MANNOSE (MANc)
2d: ALPHA-D-MANNOSE (MANd)
3a: O1-METHYL-MANNOSE (MMAa)
3b: O1-METHYL-MANNOSE (MMAb)
3c: O1-METHYL-MANNOSE (MMAc)
3d: O1-METHYL-MANNOSE (MMAd)
4a: MANGANESE (II) ION (MNa)
4b: MANGANESE (II) ION (MNb)
4c: MANGANESE (II) ION (MNc)
4d: MANGANESE (II) ION (MNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
3
MMA
4
Ligand/Ion
O1-METHYL-MANNOSE
4
MN
4
Ligand/Ion
MANGANESE (II) ION
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU D:99 , MAN O:1
BINDING SITE FOR RESIDUE MMA O 2
02
AC2
SOFTWARE
TYR D:12 , ASN D:14 , GLY D:98 , LEU D:99 , TYR D:100 , ALA D:207 , ASP D:208 , GLY D:227 , ARG D:228 , MMA O:2
BINDING SITE FOR RESIDUE MAN O 1
03
AC3
SOFTWARE
TYR A:12 , VAL B:57 , GLY B:58 , ASP B:78 , ARG D:60 , THR D:74 , SER D:76 , HOH D:312 , MAN P:1 , HOH P:3
BINDING SITE FOR RESIDUE MMA P 2
04
AC4
SOFTWARE
TYR A:12 , ASN A:14 , GLY A:98 , LEU A:99 , TYR A:100 , ALA A:207 , ASP A:208 , GLY A:227 , ARG A:228 , HOH B:368 , MMA P:2 , HOH P:4
BINDING SITE FOR RESIDUE MAN P 1
05
AC5
SOFTWARE
VAL A:57 , GLY A:58 , ASP A:78 , LEU B:99 , ARG C:60 , THR C:74 , SER C:76 , MAN Q:1 , HOH Q:3
BINDING SITE FOR RESIDUE MMA Q 2
06
AC6
SOFTWARE
HOH A:345 , TYR B:12 , ASN B:14 , GLY B:98 , LEU B:99 , TYR B:100 , ALA B:207 , ASP B:208 , GLY B:227 , ARG B:228 , MMA Q:2 , HOH Q:4
BINDING SITE FOR RESIDUE MAN Q 1
07
AC7
SOFTWARE
LEU C:99 , PRO D:68 , MAN R:1
BINDING SITE FOR RESIDUE MMA R 2
08
AC8
SOFTWARE
TYR C:12 , ASN C:14 , GLY C:98 , LEU C:99 , TYR C:100 , ALA C:207 , ASP C:208 , GLY C:227 , ARG C:228 , MMA R:2
BINDING SITE FOR RESIDUE MAN R 1
09
AC9
SOFTWARE
GLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:328 , HOH A:350
BINDING SITE FOR RESIDUE MN A 238
10
BC1
SOFTWARE
ASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:245 , HOH A:253
BINDING SITE FOR RESIDUE CA A 239
11
BC2
SOFTWARE
GLU B:8 , ASP B:10 , ASP B:19 , HIS B:24 , HOH B:290 , HOH B:343
BINDING SITE FOR RESIDUE MN B 238
12
BC3
SOFTWARE
ASP B:10 , TYR B:12 , ASN B:14 , ASP B:19 , HOH B:242 , HOH B:250
BINDING SITE FOR RESIDUE CA B 239
13
BC4
SOFTWARE
GLU C:8 , ASP C:10 , ASP C:19 , HIS C:24 , HOH C:266 , HOH C:313
BINDING SITE FOR RESIDUE MN C 238
14
BC5
SOFTWARE
ASP C:10 , TYR C:12 , ASN C:14 , ASP C:19 , HOH C:242 , HOH C:270
BINDING SITE FOR RESIDUE CA C 239
15
BC6
SOFTWARE
GLU D:8 , ASP D:10 , ASP D:19 , HIS D:24 , HOH D:268
BINDING SITE FOR RESIDUE MN D 238
16
BC7
SOFTWARE
ASP D:10 , TYR D:12 , ASN D:14 , ASP D:19 , HOH D:240 , HOH D:276
BINDING SITE FOR RESIDUE CA D 239
[
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
(2, 8)
Info
All PROSITE Patterns/Profiles
1: LECTIN_LEGUME_BETA (A:5-11,B:5-11,C:5-11,D:5-11)
2: LECTIN_LEGUME_ALPHA (A:85-94,B:85-94,C:85-94,D:85-94)
;
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.
CONA_CANRO
5-11
4
A:5-11
B:5-11
C:5-11
D:5-11
2
LECTIN_LEGUME_ALPHA
PS00308
Legume lectins alpha-chain signature.
CONA_CANRO
84-93
4
A:85-94
B:85-94
C:85-94
D:85-94
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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_d2p34a_ (A:)
1b: SCOP_d2p34d_ (D:)
1c: SCOP_d2p34b_ (B:)
1d: SCOP_d2p34c_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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
:
automated matches
(63)
Canavalia maritima [TaxId: 3825]
(6)
1a
d2p34a_
A:
1b
d2p34d_
D:
1c
d2p34b_
B:
1d
d2p34c_
C:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2p34A00 (A:1-237)
1b: CATH_2p34B00 (B:1-237)
1c: CATH_2p34C00 (C:1-237)
1d: CATH_2p34D00 (D:1-237)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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)
Canavalia maritima. Organism_taxid: 3825.
(6)
1a
2p34A00
A:1-237
1b
2p34B00
B:1-237
1c
2p34C00
C:1-237
1d
2p34D00
D:1-237
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Lectin_legB_2p34D01 (D:124-237)
1b: PFAM_Lectin_legB_2p34D02 (D:124-237)
1c: PFAM_Lectin_legB_2p34D03 (D:124-237)
1d: PFAM_Lectin_legB_2p34D04 (D:124-237)
1e: PFAM_Lectin_legB_2p34D05 (D:124-237)
1f: PFAM_Lectin_legB_2p34D06 (D:124-237)
1g: PFAM_Lectin_legB_2p34D07 (D:124-237)
1h: PFAM_Lectin_legB_2p34D08 (D:124-237)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Concanavalin
(293)
Family
:
Lectin_legB
(93)
Canavalia rosea (Beach bean) (Canavalia maritima)
(3)
1a
Lectin_legB-2p34D01
D:124-237
1b
Lectin_legB-2p34D02
D:124-237
1c
Lectin_legB-2p34D03
D:124-237
1d
Lectin_legB-2p34D04
D:124-237
1e
Lectin_legB-2p34D05
D:124-237
1f
Lectin_legB-2p34D06
D:124-237
1g
Lectin_legB-2p34D07
D:124-237
1h
Lectin_legB-2p34D08
D:124-237
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
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)
[
close Script example commands
]
Log
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") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (162 KB)
Header - Asym.Unit
Biol.Unit 1 (152 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2P34
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help