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2WZE
Asym. Unit
Info
Asym.Unit (378 KB)
Biol.Unit 1 (185 KB)
Biol.Unit 2 (186 KB)
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(1)
Title
:
HIGH RESOLUTION CRYSTALLOGRAPHIC STRUCTURE OF THE CLOSTRIDIUM THERMOCELLUM N-TERMINAL ENDO-1,4-BETA-D XYLANAS XYLOHEXAOSE
Authors
:
S. Najmudin, B. A. Pinheiro, M. J. Romao, J. A. M. Prates, C. M. G. A. Fonte
Date
:
27 Nov 09 (Deposition) - 25 Aug 10 (Release) - 18 Jan 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Hydrolase, Xylan Degradation, Cellulosome, Glycosidase
(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
)
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Hetero Components
(5, 40)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
5a: BETA-D-XYLOPYRANOSE (XYPa)
5b: BETA-D-XYLOPYRANOSE (XYPb)
5c: BETA-D-XYLOPYRANOSE (XYPc)
5d: BETA-D-XYLOPYRANOSE (XYPd)
5e: BETA-D-XYLOPYRANOSE (XYPe)
5f: BETA-D-XYLOPYRANOSE (XYPf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
GOL
12
Ligand/Ion
GLYCEROL
3
MSE
18
Mod. Amino Acid
SELENOMETHIONINE
4
PO4
2
Ligand/Ion
PHOSPHATE ION
5
XYP
6
Ligand/Ion
BETA-D-XYLOPYRANOSE
[
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Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:40 , GLU A:42 , THR A:68 , ARG A:69 , ASP A:173
BINDING SITE FOR RESIDUE CA A1552
02
AC2
SOFTWARE
GLY A:435 , PHE A:436 , PO4 A:1562 , HOH A:2411 , HOH A:2412 , HOH A:2413 , LYS B:469 , HOH B:2375 , HOH B:2504
BINDING SITE FOR RESIDUE GOL A1556
03
AC3
SOFTWARE
ASN A:210 , GLU A:233 , ASN A:510 , THR A:511 , TRP A:512 , XYP A:1554 , HOH A:2414
BINDING SITE FOR RESIDUE GOL A1557
04
AC4
SOFTWARE
ASP A:239 , GLN A:283 , TYR A:357 , HOH A:2203 , HOH A:2416 , HOH A:2417
BINDING SITE FOR RESIDUE GOL A1558
05
AC5
SOFTWARE
HIS A:428 , ILE A:429 , ASP A:462 , SER A:464 , LEU A:513 , HOH A:2418 , HOH B:2462
BINDING SITE FOR RESIDUE GOL A1559
06
AC6
SOFTWARE
PRO A:540 , SER A:542 , HOH A:2399 , HOH A:2400 , HOH A:2419 , GLN B:286 , LYS B:290
BINDING SITE FOR RESIDUE GOL A1560
07
AC7
SOFTWARE
VAL A:36 , HIS A:38 , ASP A:39 , LYS A:87 , ASN A:264 , GLN A:268
BINDING SITE FOR RESIDUE GOL A1561
08
AC8
SOFTWARE
ASN A:430 , GLU A:466 , LYS A:469 , GOL A:1556 , HOH A:2413 , HOH A:2418 , HOH A:2420 , HOH A:2421 , HOH A:2422 , ASN B:430 , GLU B:466 , LYS B:469 , HOH B:2504
BINDING SITE FOR RESIDUE PO4 A1562
09
AC9
SOFTWARE
THR B:40 , GLU B:42 , THR B:68 , ARG B:69 , ASP B:173 , HOH B:2136
BINDING SITE FOR RESIDUE CA B1552
10
BC1
SOFTWARE
GLU B:233 , ASN B:510 , THR B:511 , TRP B:512 , XYP B:1554 , HOH B:2493 , HOH B:2496 , HOH B:2497
BINDING SITE FOR RESIDUE GOL B1556
11
BC2
SOFTWARE
HIS B:281 , SER B:282 , GLN B:283 , THR B:284 , TYR B:357 , HOH B:2498 , HOH B:2499 , HOH B:2500
BINDING SITE FOR RESIDUE GOL B1557
12
BC3
SOFTWARE
LYS A:469 , HOH A:2420 , HOH A:2422 , GLY B:435 , PHE B:436 , HOH B:2502 , HOH B:2503 , HOH B:2504
BINDING SITE FOR RESIDUE GOL B1558
13
BC4
SOFTWARE
ARG B:204 , ASN B:328 , ALA B:551 , HOH B:2449 , HOH B:2505 , HOH B:2506
BINDING SITE FOR RESIDUE GOL B1559
14
BC5
SOFTWARE
TYR A:202 , GLN A:484 , ARG A:491 , ILE A:538 , GLU A:543 , HOH A:2359 , HOH A:2398 , PRO B:355 , ARG B:361 , GLN B:366 , HOH B:2507
BINDING SITE FOR RESIDUE GOL B1560
15
BC6
SOFTWARE
ASP B:401 , ARG B:404 , ASN B:441 , HOH B:2356 , HOH B:2508 , HOH B:2509 , HOH B:2510
BINDING SITE FOR RESIDUE GOL B1561
16
BC7
SOFTWARE
THR B:40 , PHE B:41 , GLU B:42 , VAL B:43 , ASN B:44 , ASP B:46 , HOH B:2511 , HOH B:2512
BINDING SITE FOR RESIDUE PO4 B1562
17
BC8
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 , GOL A:1557 , HOH A:2408 , HOH A:2409 , HOH A:2410 , HOH B:2411
BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 1553 TO 1555
18
BC9
SOFTWARE
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 , GOL B:1556 , HOH B:2492 , HOH B:2493 , HOH B:2494 , HOH B:2495
BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 1553 TO 1555
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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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: GH10_2 (A:189-538,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:189-538
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
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
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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
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2wzeA02 (A:191-551)
1b: CATH_2wzeB02 (B:191-551)
View:
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Classes
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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
2wzeA02
A:191-551
1b
2wzeB02
B:191-551
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_CBM_4_9_2wzeB01 (B:35-168)
1b: PFAM_CBM_4_9_2wzeB02 (B:35-168)
2a: PFAM_Glyco_hydro_10_2wzeB03 (B:194-539)
2b: PFAM_Glyco_hydro_10_2wzeB04 (B:194-539)
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Clans
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(
)
Organisms
(
)
(
)
Clan
:
GBD
(153)
Family
:
CBM_4_9
(7)
Clostridium thermocellum
(3)
1a
CBM_4_9-2wzeB01
B:35-168
1b
CBM_4_9-2wzeB02
B:35-168
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_10
(42)
Clostridium thermocellum
(3)
2a
Glyco_hydro_10-2wzeB03
B:194-539
2b
Glyco_hydro_10-2wzeB04
B:194-539
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