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.
2WYF
Asym. Unit
Info
Asym.Unit (169 KB)
Biol.Unit 1 (44 KB)
Biol.Unit 2 (44 KB)
Biol.Unit 3 (44 KB)
Biol.Unit 4 (44 KB)
Biol.Unit 5 (83 KB)
Biol.Unit 6 (83 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 PA-IL LECTIN COMPLEXED WITH AGAL12BGAL-O-MET AT 2.4 A RESOLUTION
Authors
:
A. Nurisso, B. Blanchard, A. Varrot, A. Imberty
Date
:
16 Nov 09 (Deposition) - 21 Apr 10 (Release) - 03 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Biol. Unit 5: E,F,G,H (1x)
Biol. Unit 6: A,B,C,D (1x)
Keywords
:
Sugar Binding Protein, Lectin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Nurisso, B. Blanchard, A. Audfray, L. Rydner, S. Oscarson, A. Varrot, A. Imberty
Role Of Water Molecules In Structure And Energetics Of Pseudomonas Aeruginosa Lectin I Interacting With Disaccharides.
J. Biol. Chem. V. 285 20316 2010
[
close entry info
]
Hetero Components
(3, 22)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
2a: ALPHA D-GALACTOSE (GLAa)
2b: ALPHA D-GALACTOSE (GLAb)
2c: ALPHA D-GALACTOSE (GLAc)
2d: ALPHA D-GALACTOSE (GLAd)
2e: ALPHA D-GALACTOSE (GLAe)
2f: ALPHA D-GALACTOSE (GLAf)
2g: ALPHA D-GALACTOSE (GLAg)
2h: ALPHA D-GALACTOSE (GLAh)
3a: METHYL-BETA-GALACTOSE (MBGa)
3b: METHYL-BETA-GALACTOSE (MBGb)
3c: METHYL-BETA-GALACTOSE (MBGc)
3d: METHYL-BETA-GALACTOSE (MBGd)
3e: METHYL-BETA-GALACTOSE (MBGe)
3f: METHYL-BETA-GALACTOSE (MBGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
8
Ligand/Ion
CALCIUM ION
2
GLA
8
Ligand/Ion
ALPHA D-GALACTOSE
3
MBG
6
Ligand/Ion
METHYL-BETA-GALACTOSE
[
close Hetero Component info
]
Sites
(22, 22)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:36 , ASP A:100 , THR A:104 , ASN A:107 , ASN A:108 , GLA A:201
BINDING SITE FOR RESIDUE CA A 200
02
AC2
SOFTWARE
TYR A:36 , HIS A:50 , GLN A:53 , ASP A:100 , THR A:104 , ASN A:107 , CA A:200 , MBG A:202 , HOH A:2086 , HOH A:2087
BINDING SITE FOR RESIDUE GLA A 201
03
AC3
SOFTWARE
HIS A:50 , GLN A:53 , GLA A:201 , HOH A:2089 , HOH A:2090 , HOH A:2091 , THR D:39
BINDING SITE FOR RESIDUE MBG A 202
04
AC4
SOFTWARE
TYR B:36 , ASP B:100 , THR B:104 , ASN B:107 , ASN B:108 , GLA B:201
BINDING SITE FOR RESIDUE CA B 200
05
AC5
SOFTWARE
TYR B:36 , HIS B:50 , GLN B:53 , ASP B:100 , THR B:104 , ASN B:107 , CA B:200 , HOH B:2073 , HOH B:2074 , HOH B:2075
BINDING SITE FOR RESIDUE GLA B 201
06
AC6
SOFTWARE
TYR C:36 , ASP C:100 , THR C:104 , ASN C:107 , ASN C:108 , GLA C:201
BINDING SITE FOR RESIDUE CA C 200
07
AC7
SOFTWARE
TYR C:36 , HIS C:50 , GLN C:53 , ASP C:100 , THR C:104 , ASN C:107 , CA C:200 , MBG C:202 , HOH C:2082
BINDING SITE FOR RESIDUE GLA C 201
08
AC8
SOFTWARE
HIS C:50 , GLN C:53 , GLA C:201 , HOH C:2084
BINDING SITE FOR RESIDUE MBG C 202
09
AC9
SOFTWARE
TYR D:36 , ASP D:100 , THR D:104 , ASN D:107 , ASN D:108 , GLA D:201
BINDING SITE FOR RESIDUE CA D 200
10
BC1
SOFTWARE
TYR D:36 , HIS D:50 , GLN D:53 , ASP D:100 , VAL D:101 , THR D:104 , ASN D:107 , CA D:200 , MBG D:202 , HOH D:2085 , HOH D:2086 , HOH D:2087
BINDING SITE FOR RESIDUE GLA D 201
11
BC2
SOFTWARE
HIS D:50 , GLN D:53 , GLA D:201 , HOH D:2088
BINDING SITE FOR RESIDUE MBG D 202
12
BC3
SOFTWARE
TYR E:36 , ASP E:100 , THR E:104 , ASN E:107 , ASN E:108 , GLA E:201
BINDING SITE FOR RESIDUE CA E 200
13
BC4
SOFTWARE
TYR E:36 , HIS E:50 , GLN E:53 , ASP E:100 , VAL E:101 , THR E:104 , ASN E:107 , CA E:200 , HOH E:2076
BINDING SITE FOR RESIDUE GLA E 201
14
BC5
SOFTWARE
TYR F:36 , ASP F:100 , THR F:104 , ASN F:107 , ASN F:108 , GLA F:201
BINDING SITE FOR RESIDUE CA F 200
15
BC6
SOFTWARE
TYR F:36 , HIS F:50 , GLN F:53 , ASP F:100 , VAL F:101 , THR F:104 , ASN F:107 , CA F:200 , MBG F:202 , HOH F:2068
BINDING SITE FOR RESIDUE GLA F 201
16
BC7
SOFTWARE
GLN F:53 , GLA F:201
BINDING SITE FOR RESIDUE MBG F 202
17
BC8
SOFTWARE
TYR G:36 , ASP G:100 , THR G:104 , ASN G:107 , ASN G:108 , GLA G:201
BINDING SITE FOR RESIDUE CA G 200
18
BC9
SOFTWARE
TYR G:36 , HIS G:50 , GLN G:53 , ASP G:100 , VAL G:101 , THR G:104 , ASN G:107 , CA G:200 , MBG G:202 , HOH G:2083 , HOH G:2084 , HOH G:2085
BINDING SITE FOR RESIDUE GLA G 201
19
CC1
SOFTWARE
HIS G:50 , GLN G:53 , GLA G:201 , HOH G:2086 , HOH G:2087 , HOH G:2088
BINDING SITE FOR RESIDUE MBG G 202
20
CC2
SOFTWARE
TYR H:36 , ASP H:100 , THR H:104 , ASN H:107 , ASN H:108 , GLA H:201
BINDING SITE FOR RESIDUE CA H 200
21
CC3
SOFTWARE
TYR H:36 , HIS H:50 , GLN H:53 , ASP H:100 , THR H:104 , ASN H:107 , CA H:200 , MBG H:202 , HOH H:2033 , HOH H:2073 , HOH H:2074
BINDING SITE FOR RESIDUE GLA H 201
22
CC4
SOFTWARE
HIS H:50 , GLN H:53 , GLA H:201
BINDING SITE FOR RESIDUE MBG H 202
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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, 8)
Info
All SCOP Domains
1a: SCOP_d2wyfa_ (A:)
1b: SCOP_d2wyfb_ (B:)
1c: SCOP_d2wyfc_ (C:)
1d: SCOP_d2wyfd_ (D:)
1e: SCOP_d2wyfe_ (E:)
1f: SCOP_d2wyff_ (F:)
1g: SCOP_d2wyfg_ (G:)
1h: SCOP_d2wyfh_ (H:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Galactose-binding domain-like
(314)
Superfamily
:
Galactose-binding domain-like
(314)
Family
:
PA-IL, galactose-binding lectin 1
(12)
Protein domain
:
PA-IL, galactose-binding lectin 1
(12)
Pseudomonas aeruginosa [TaxId: 287]
(12)
1a
d2wyfa_
A:
1b
d2wyfb_
B:
1c
d2wyfc_
C:
1d
d2wyfd_
D:
1e
d2wyfe_
E:
1f
d2wyff_
F:
1g
d2wyfg_
G:
1h
d2wyfh_
H:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_2wyfA00 (A:1-121)
1b: CATH_2wyfC00 (C:1-121)
1c: CATH_2wyfD00 (D:1-121)
1d: CATH_2wyfE00 (E:1-121)
1e: CATH_2wyfF00 (F:1-121)
1f: CATH_2wyfG00 (G:1-121)
1g: CATH_2wyfH00 (H:1-121)
1h: CATH_2wyfB00 (B:1-121)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
Galactose-binding lectin
(5)
Pseudomonas aeruginosa. Organism_taxid: 208964. Strain: pao1.
(2)
1a
2wyfA00
A:1-121
1b
2wyfC00
C:1-121
1c
2wyfD00
D:1-121
1d
2wyfE00
E:1-121
1e
2wyfF00
F:1-121
1f
2wyfG00
G:1-121
1g
2wyfH00
H:1-121
1h
2wyfB00
B:1-121
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_PA_IL_2wyfH01 (H:1-121)
1b: PFAM_PA_IL_2wyfH02 (H:1-121)
1c: PFAM_PA_IL_2wyfH03 (H:1-121)
1d: PFAM_PA_IL_2wyfH04 (H:1-121)
1e: PFAM_PA_IL_2wyfH05 (H:1-121)
1f: PFAM_PA_IL_2wyfH06 (H:1-121)
1g: PFAM_PA_IL_2wyfH07 (H:1-121)
1h: PFAM_PA_IL_2wyfH08 (H:1-121)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GBD
(153)
Family
:
PA-IL
(5)
Pseudomonas aeruginosa
(5)
1a
PA-IL-2wyfH01
H:1-121
1b
PA-IL-2wyfH02
H:1-121
1c
PA-IL-2wyfH03
H:1-121
1d
PA-IL-2wyfH04
H:1-121
1e
PA-IL-2wyfH05
H:1-121
1f
PA-IL-2wyfH06
H:1-121
1g
PA-IL-2wyfH07
H:1-121
1h
PA-IL-2wyfH08
H:1-121
[
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
Chain E
Chain F
Chain G
Chain H
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 (169 KB)
Header - Asym.Unit
Biol.Unit 1 (44 KB)
Header - Biol.Unit 1
Biol.Unit 2 (44 KB)
Header - Biol.Unit 2
Biol.Unit 3 (44 KB)
Header - Biol.Unit 3
Biol.Unit 4 (44 KB)
Header - Biol.Unit 4
Biol.Unit 5 (83 KB)
Header - Biol.Unit 5
Biol.Unit 6 (83 KB)
Header - Biol.Unit 6
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
2WYF
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
