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.
2WDA
Asym. Unit
Info
Asym.Unit (136 KB)
Biol.Unit 1 (130 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE X-RAY STRUCTURE OF THE STREPTOMYCES COELICOLOR A3 CHONDROITIN AC LYASE IN COMPLEX WITH CHONDROITIN SULPHATE
Authors
:
Z. H. Elmabrouk, E. J. Taylor, F. Vincent, N. L. Smith, J. P. Turkenburg, G. J. Davies, G. W. Black
Date
:
23 Mar 09 (Deposition) - 21 Apr 10 (Release) - 16 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Lyase, Hyaluronate Lyase, Chondroitin Lyase, Family 8
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. H. Elmabrouk, F. Vincent, M. Zhang, N. L. Smith, J. P. Turkenburg, S. J. Charnock, G. W. Black, E. J. Taylor
Crystal Structures Of A Family 8 Polysaccharide Lyase Reveal Open And Highly Occluded Substrate- Binding Cleft Conformations.
Proteins V. 79 965 2011
[
close entry info
]
Hetero Components
(5, 19)
Info
All Hetero Components
1a: FORMIC ACID (FMTa)
1b: FORMIC ACID (FMTb)
1c: FORMIC ACID (FMTc)
1d: FORMIC ACID (FMTd)
1e: FORMIC ACID (FMTe)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
3a: 2-(ACETYLAMINO)-2-DEOXY-3-O-(4-DEO... (L42a)
4a: MAGNESIUM ION (MGa)
5a: DI(HYDROXYETHYL)ETHER (PEGa)
5b: DI(HYDROXYETHYL)ETHER (PEGb)
5c: DI(HYDROXYETHYL)ETHER (PEGc)
5d: DI(HYDROXYETHYL)ETHER (PEGd)
5e: DI(HYDROXYETHYL)ETHER (PEGe)
5f: DI(HYDROXYETHYL)ETHER (PEGf)
5g: DI(HYDROXYETHYL)ETHER (PEGg)
5h: DI(HYDROXYETHYL)ETHER (PEGh)
5i: DI(HYDROXYETHYL)ETHER (PEGi)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FMT
5
Ligand/Ion
FORMIC ACID
2
GOL
3
Ligand/Ion
GLYCEROL
3
L42
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-3-O-(4-DEOXY-ALPHA-L-THREO-HEX-4-ENOPYRANURONOSYL)-4-O-SULFO-BETA-D-GALACTOPYRANOSE
4
MG
1
Ligand/Ion
MAGNESIUM ION
5
PEG
9
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
close Hetero Component info
]
Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:140 , ASN A:194 , HIS A:244 , TYR A:253 , GOL A:1773 , L42 A:1784
BINDING SITE FOR RESIDUE FMT A1766
02
AC2
SOFTWARE
ASP A:153 , HOH A:2483
BINDING SITE FOR RESIDUE FMT A1767
03
AC3
SOFTWARE
ARG A:53 , THR A:57 , GLU A:99 , GLN A:103 , PRO A:374 , VAL A:375 , HOH A:2237
BINDING SITE FOR RESIDUE FMT A1768
04
AC4
SOFTWARE
ASP A:456 , ASP A:460 , ASN A:557
BINDING SITE FOR RESIDUE FMT A1769
05
AC5
SOFTWARE
ARG A:406 , MET A:420 , ALA A:426 , HIS A:427 , THR A:441 , GLY A:442 , HOH A:2484 , HOH A:2485
BINDING SITE FOR RESIDUE FMT A1770
06
AC6
SOFTWARE
HIS A:427 , PRO A:494 , ASP A:495 , LYS A:515 , GLY A:516 , SER A:519 , HOH A:2486
BINDING SITE FOR RESIDUE GOL A1771
07
AC7
SOFTWARE
LEU A:400 , CYS A:755 , THR A:756 , THR A:757
BINDING SITE FOR RESIDUE GOL A1772
08
AC8
SOFTWARE
ASN A:139 , TRP A:140 , TRP A:141 , ASN A:432 , ARG A:743 , FMT A:1766 , L42 A:1784 , HOH A:2487
BINDING SITE FOR RESIDUE GOL A1773
09
AC9
SOFTWARE
ASP A:175 , PRO A:179 , ASP A:180 , LYS A:214 , HOH A:2488
BINDING SITE FOR RESIDUE PEG A1774
10
BC1
SOFTWARE
TRP A:141 , ARG A:149 , ASP A:197 , GLN A:255 , VAL A:256 , ASP A:259 , L42 A:1784 , HOH A:2489
BINDING SITE FOR RESIDUE PEG A1775
11
BC2
SOFTWARE
HIS A:574 , GLY A:577 , GLY A:638 , ALA A:639 , HOH A:2490
BINDING SITE FOR RESIDUE PEG A1776
12
BC3
SOFTWARE
ASP A:467 , TYR A:469 , ARG A:470 , VAL A:476 , THR A:478 , ARG A:480 , GLU A:550 , PEG A:1782 , HOH A:2341
BINDING SITE FOR RESIDUE PEG A1777
13
BC4
SOFTWARE
VAL A:466 , ASP A:467 , TRP A:468 , ARG A:595 , HOH A:2270
BINDING SITE FOR RESIDUE PEG A1778
14
BC5
SOFTWARE
THR A:230 , GLY A:232 , TYR A:236 , ALA A:403 , ARG A:424 , VAL A:754 , HOH A:2451 , HOH A:2491 , HOH A:2492 , HOH A:2493
BINDING SITE FOR RESIDUE PEG A1779
15
BC6
SOFTWARE
ARG A:589 , THR A:590 , LEU A:591 , PEG A:1781 , HOH A:2364
BINDING SITE FOR RESIDUE PEG A1780
16
BC7
SOFTWARE
ALA A:565 , LEU A:566 , THR A:590 , LEU A:591 , ARG A:592 , GLN A:616 , PEG A:1780
BINDING SITE FOR RESIDUE PEG A1781
17
BC8
SOFTWARE
VAL A:466 , ASP A:467 , ARG A:470 , ASN A:555 , GLU A:593 , ARG A:595 , TRP A:615 , THR A:617 , PEG A:1777 , HOH A:2367
BINDING SITE FOR RESIDUE PEG A1782
18
BC9
SOFTWARE
TRP A:653 , VAL A:668 , PRO A:669 , SER A:670 , HOH A:2417
BINDING SITE FOR RESIDUE MG A1783
19
CC1
SOFTWARE
TRP A:141 , GLU A:142 , ARG A:149 , TYR A:253 , ARG A:307 , ARG A:311 , GLU A:434 , FMT A:1766 , GOL A:1773 , PEG A:1775 , HOH A:2194 , HOH A:2206 , HOH A:2494 , HOH A:2495 , HOH A:2496 , HOH A:2497 , HOH A:2498 , HOH A:2499
BINDING SITE FOR RESIDUE L42 A1784
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2wdaA01 (A:24-394)
2a: CATH_2wdaA02 (A:395-650)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Alpha/alpha barrel
(251)
Topology
:
Glycosyltransferase
(233)
Homologous Superfamily
:
[code=1.50.10.100, no name defined]
(43)
Streptomyces violaceoruber. Organism_taxid: 1935. Strain: a3(2).
(1)
1a
2wdaA01
A:24-394
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Beta-galactosidase; Chain A, domain 5
(250)
Homologous Superfamily
:
[code=2.70.98.10, no name defined]
(116)
Streptomyces violaceoruber. Organism_taxid: 1935. Strain: a3(2).
(1)
2a
2wdaA02
A:395-650
[
close CATH info
]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_Lyase_8_2wdaA01 (A:391-645)
2a: PFAM_Lyase_8_N_2wdaA02 (A:34-357)
3a: PFAM_Lyase_8_C_2wdaA03 (A:654-734)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Gal_mutarotase
(81)
Family
:
Lyase_8
(15)
Streptomyces coelicolor
(3)
1a
Lyase_8-2wdaA01
A:391-645
Clan
:
Hy-ly_N
(15)
Family
:
Lyase_8_N
(15)
Streptomyces coelicolor
(3)
2a
Lyase_8_N-2wdaA02
A:34-357
Clan
:
no clan defined [family: Lyase_8_C]
(15)
Family
:
Lyase_8_C
(15)
Streptomyces coelicolor
(3)
3a
Lyase_8_C-2wdaA03
A:654-734
[
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
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 (136 KB)
Header - Asym.Unit
Biol.Unit 1 (130 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
2WDA
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help