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.
2W5F
Asym. Unit
Info
Asym.Unit (210 KB)
Biol.Unit 1 (101 KB)
Biol.Unit 2 (103 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HIGH RESOLUTION CRYSTALLOGRAPHIC STRUCTURE OF THE CLOSTRIDIUM THERMOCELLUM N-TERMINAL ENDO-1,4-BETA-D-XYLANASE 10B (XYN10B) CBM22-1-GH10 MODULES COMPLEXED WITH XYLOHEXAOSE
Authors
:
S. Najmudin, B. A. Pinheiro, M. J. Romao, J. A. M. Prates, C. M. G. A. Fonte
Date
:
10 Dec 08 (Deposition) - 19 Jan 10 (Release) - 18 Jan 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Cellulosome, Glycosidase, Xylan Degradation, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Najmudin, B. A. Pinheiro, J. A. M. Prates, H. J. Gilbert, M. J. Romao, C. M. G. A. Fontes
Putting An N-Terminal End To The Clostridium Thermocellum Xylanase Xyn10B Story: Crystal Structure Of The Cbm22-1-Gh10 Modules Complexed With Xylohexaose.
J. Struct. Biol. V. 172 353 2010
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 28)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
1h: ACETATE ION (ACTh)
1i: ACETATE ION (ACTi)
2a: CADMIUM ION (CDa)
2b: CADMIUM ION (CDb)
2c: CADMIUM ION (CDc)
2d: CADMIUM ION (CDd)
2e: CADMIUM ION (CDe)
2f: CADMIUM ION (CDf)
2g: CADMIUM ION (CDg)
2h: CADMIUM ION (CDh)
2i: CADMIUM ION (CDi)
2j: CADMIUM ION (CDj)
2k: CADMIUM ION (CDk)
2l: CADMIUM ION (CDl)
2m: CADMIUM ION (CDm)
3a: BETA-D-XYLOPYRANOSE (XYPa)
3b: BETA-D-XYLOPYRANOSE (XYPb)
3c: BETA-D-XYLOPYRANOSE (XYPc)
3d: BETA-D-XYLOPYRANOSE (XYPd)
3e: BETA-D-XYLOPYRANOSE (XYPe)
3f: BETA-D-XYLOPYRANOSE (XYPf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
9
Ligand/Ion
ACETATE ION
2
CD
13
Ligand/Ion
CADMIUM ION
3
XYP
6
Ligand/Ion
BETA-D-XYLOPYRANOSE
[
close Hetero Component info
]
Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:75 , ARG A:76 , ASP A:169 , ACT A:1553 , CD A:1558 , HOH A:2742 , THR B:167 , ASP B:169 , HOH B:2295
BINDING SITE FOR RESIDUE ACT A1552
02
AC2
SOFTWARE
THR A:167 , ASP A:169 , ACT A:1552 , CD A:1558 , HOH A:2742 , ASN B:75 , ARG B:76 , ASP B:169 , HOH B:2295
BINDING SITE FOR RESIDUE ACT A1553
03
AC3
SOFTWARE
GLU A:35 , HIS A:38 , CD A:1560 , HOH A:2004
BINDING SITE FOR RESIDUE ACT A1554
04
AC4
SOFTWARE
TYR A:202 , LYS A:497 , VAL A:498 , HOH A:2743
BINDING SITE FOR RESIDUE ACT A1555
05
AC5
SOFTWARE
GLU A:126 , CD A:1564 , HOH A:2744 , HOH A:2745 , GLU B:127
BINDING SITE FOR RESIDUE ACT A1556
06
AC6
SOFTWARE
THR A:346 , CYS A:406 , SER A:409 , CD A:1561 , HOH A:2520 , HOH A:2581 , HOH A:2747
BINDING SITE FOR RESIDUE ACT A1557
07
AC7
SOFTWARE
ASP A:169 , ACT A:1552 , ACT A:1553 , ASP B:169
BINDING SITE FOR RESIDUE CD A1558
08
AC8
SOFTWARE
GLU A:42 , THR A:68 , ARG A:69 , ASP A:173 , HOH A:2014 , HOH A:2298
BINDING SITE FOR RESIDUE CD A1559
09
AC9
SOFTWARE
GLU A:35 , HIS A:38 , ACT A:1554 , HOH A:2004
BINDING SITE FOR RESIDUE CD A1560
10
BC1
SOFTWARE
CYS A:406 , ACT A:1557 , HOH A:2520 , HOH A:2526 , HOH A:2747
BINDING SITE FOR RESIDUE CD A1561
11
BC2
SOFTWARE
GLU A:127 , CD A:1563 , GLU B:126
BINDING SITE FOR RESIDUE CD A1562
12
BC3
SOFTWARE
GLU A:127 , CD A:1562 , GLU B:126
BINDING SITE FOR RESIDUE CD A1563
13
BC4
SOFTWARE
GLU A:126 , ACT A:1556 , GLU B:127
BINDING SITE FOR RESIDUE CD A1564
14
BC5
SOFTWARE
ASP A:401 , HOH A:2583 , HOH A:2621 , HOH A:2624
BINDING SITE FOR RESIDUE CD A1565
15
BC6
SOFTWARE
ASP B:405 , CYS B:406 , ACT B:1553 , CD B:1555 , HOH B:2850 , HOH B:2851
BINDING SITE FOR RESIDUE ACT B1552
16
BC7
SOFTWARE
THR B:346 , GLY B:350 , CYS B:406 , ACT B:1552 , CD B:1555 , HOH B:2562 , HOH B:2566 , HOH B:2852 , HOH B:2853
BINDING SITE FOR RESIDUE ACT B1553
17
BC8
SOFTWARE
GLU B:35 , HIS B:38 , CD B:1557 , HOH B:2854
BINDING SITE FOR RESIDUE ACT B1554
18
BC9
SOFTWARE
CYS B:406 , ACT B:1552 , ACT B:1553 , HOH B:2852
BINDING SITE FOR RESIDUE CD B1555
19
CC1
SOFTWARE
THR B:40 , GLU B:42 , THR B:68 , ARG B:69 , ASP B:173 , HOH B:2305
BINDING SITE FOR RESIDUE CD B1556
20
CC2
SOFTWARE
GLU B:35 , HIS B:38 , ACT B:1554 , HOH B:2002
BINDING SITE FOR RESIDUE CD B1557
21
CC3
SOFTWARE
ASP B:401 , HOH B:2645 , HOH B:2646 , HOH B:2651
BINDING SITE FOR RESIDUE CD B1558
22
CC4
SOFTWARE
ASP B:291 , HOH B:2487
BINDING SITE FOR RESIDUE CD B1559
23
CC5
SOFTWARE
GLU A:233 , ASN A:234 , LYS A:237 , HIS A:276 , TRP A:280 , GLN A:283 , ASN A:336 , GLN A:426 , GLU A:460 , TRP A:504 , TRP A:512 , HOH A:2733 , HOH A:2734 , HOH A:2735 , HOH A:2737 , HOH A:2738 , HOH A:2740 , HOH A:2741 , HOH B:2742
BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 1001 TO 1003
24
CC6
SOFTWARE
HOH A:2649 , GLU B:233 , ASN B:234 , LYS B:237 , HIS B:276 , TRP B:280 , GLN B:283 , ASN B:336 , GLN B:426 , GLU B:460 , TRP B:504 , TRP B:512 , HOH B:2470 , HOH B:2842 , HOH B:2844 , HOH B:2846 , HOH B:2847 , HOH B:2848 , HOH B:2849
BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 1001 TO 1003
[
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, 4)
Info
All PROSITE Patterns/Profiles
1: GH10_2 (A:190-538,B:189-538)
2: GH10_1 (A:453-463,B:453-463)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GH10_2
PS51760
Glycosyl hydrolases family 10 (GH10) domain profile.
XYNY_CLOTM
189-538
2
A:190-538
B:189-538
2
GH10_1
PS00591
Glycosyl hydrolases family 10 (GH10) active site.
XYNY_CLOTM
453-463
2
A:453-463
B:453-463
[
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
(1, 2)
Info
all CATH domains
1a: CATH_2w5fA02 (A:191-551)
1b: CATH_2w5fB02 (B:191-551)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Clostridium thermocellum. Organism_taxid: 1515. Strain: ys.
(3)
1a
2w5fA02
A:191-551
1b
2w5fB02
B:191-551
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_CBM_4_9_2w5fB01 (B:35-168)
1b: PFAM_CBM_4_9_2w5fB02 (B:35-168)
2a: PFAM_Glyco_hydro_10_2w5fB03 (B:194-539)
2b: PFAM_Glyco_hydro_10_2w5fB04 (B:194-539)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GBD
(153)
Family
:
CBM_4_9
(7)
Clostridium thermocellum
(3)
1a
CBM_4_9-2w5fB01
B:35-168
1b
CBM_4_9-2w5fB02
B:35-168
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_10
(42)
Clostridium thermocellum
(3)
2a
Glyco_hydro_10-2w5fB03
B:194-539
2b
Glyco_hydro_10-2w5fB04
B:194-539
[
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
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 (210 KB)
Header - Asym.Unit
Biol.Unit 1 (101 KB)
Header - Biol.Unit 1
Biol.Unit 2 (103 KB)
Header - Biol.Unit 2
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
2W5F
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help