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1V6W
Asym. Unit
Info
Asym.Unit (159 KB)
Biol.Unit 1 (155 KB)
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Title
:
CRYSTAL STRUCTURE OF XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDIS E-86 COMPLEXED WITH 2(2)-4-O-METHYL-ALPHA-D-GLUCURONOSYL-XYLOBIOSE
Authors
:
Z. Fujimoto, S. Kaneko, A. Kuno, H. Kobayashi, I. Kusakabe, H. Mizuno
Date
:
04 Dec 03 (Deposition) - 27 Apr 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Alpha-Beta Barrel, Protein-Sugar Complex, Carbohydrate Binding Module, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Fujimoto, S. Kaneko, A. Kuno, H. Kobayashi, I. Kusakabe, H. Mizuno
Crystal Structures Of Decorated Xylooligosaccharides Bound To A Family 10 Xylanase From Streptomyces Olivaceoviridis E-86
J. Biol. Chem. V. 279 9606 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 10)
Info
All Hetero Components
1a: 4-O-METHYL-ALPHA-D-GLUCURONIC ACID (GCVa)
1b: 4-O-METHYL-ALPHA-D-GLUCURONIC ACID (GCVb)
2a: BETA-D-XYLOPYRANOSE (XYPa)
2b: BETA-D-XYLOPYRANOSE (XYPb)
2c: BETA-D-XYLOPYRANOSE (XYPc)
2d: BETA-D-XYLOPYRANOSE (XYPd)
2e: BETA-D-XYLOPYRANOSE (XYPe)
2f: BETA-D-XYLOPYRANOSE (XYPf)
2g: BETA-D-XYLOPYRANOSE (XYPg)
2h: BETA-D-XYLOPYRANOSE (XYPh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GCV
2
Ligand/Ion
4-O-METHYL-ALPHA-D-GLUCURONIC ACID
2
XYP
8
Ligand/Ion
BETA-D-XYLOPYRANOSE
[
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Sites
(10, 10)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:195 , XYP A:460 , XYP A:461
BINDING SITE FOR RESIDUE GCV A 459
02
AC2
SOFTWARE
TYR A:340 , HIS A:343 , GCV A:459 , XYP A:461
BINDING SITE FOR RESIDUE XYP A 460
03
AC3
SOFTWARE
ASP A:325 , VAL A:326 , PRO A:327 , ASN A:328 , GLN A:338 , TYR A:340 , HIS A:343 , ASN A:347 , GCV A:459 , XYP A:460 , HOH A:906
BINDING SITE FOR RESIDUE XYP A 461
04
AC4
SOFTWARE
ALA A:21 , LYS A:24 , GLU A:44 , ASN A:45 , ASP A:272 , XYP A:470 , XYP A:471 , HOH A:547 , HOH A:758 , HOH A:794 , HOH A:858 , HOH A:907
BINDING SITE FOR RESIDUE GCV A 469
05
AC5
SOFTWARE
TYR A:423 , SER A:424 , SER A:426 , GCV A:469 , XYP A:471 , HOH A:858
BINDING SITE FOR RESIDUE XYP A 470
06
AC6
SOFTWARE
ASP A:408 , ALA A:409 , GLY A:411 , GLY A:412 , GLN A:421 , TYR A:423 , ASN A:430 , GCV A:469 , XYP A:470 , HOH A:494 , HOH A:786
BINDING SITE FOR RESIDUE XYP A 471
07
AC7
SOFTWARE
GLN B:588 , XYP B:951 , HOH B:1409
BINDING SITE FOR RESIDUE XYP B 950
08
AC8
SOFTWARE
GLU B:544 , ASN B:545 , LYS B:548 , GLN B:588 , TRP B:766 , TRP B:774 , XYP B:950 , HOH B:1038 , HOH B:1179 , HOH B:1182
BINDING SITE FOR RESIDUE XYP B 951
09
AC9
SOFTWARE
ASP B:825 , VAL B:826 , PRO B:827 , ASN B:828 , TYR B:840 , HIS B:843 , ASN B:847 , HOH B:1420
BINDING SITE FOR RESIDUE XYP B 961
10
BC1
SOFTWARE
ASP B:908 , ALA B:909 , GLY B:911 , GLY B:912 , GLN B:921 , TYR B:923 , ASN B:930 , HOH B:1384
BINDING SITE FOR RESIDUE XYP B 971
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1v6wa1 (A:304-436)
1b: SCOP_d1v6wb1 (B:804-936)
2a: SCOP_d1v6wa2 (A:1-303)
2b: SCOP_d1v6wb2 (B:501-803)
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Classes
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Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
beta-Trefoil
(385)
Superfamily
:
Ricin B-like lectins
(91)
Family
:
Ricin B-like
(65)
Protein domain
:
Xylan binding domain, CBM13 (Endo-1,4-beta-xylanase C-terminal domain)
(14)
Streptomyces olivaceoviridis [TaxId: 1921]
(11)
1a
d1v6wa1
A:304-436
1b
d1v6wb1
B:804-936
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
beta-glycanases
(284)
Protein domain
:
Xylanase A, catalytic core
(61)
Streptomyces olivaceoviridis [TaxId: 1921]
(12)
2a
d1v6wa2
A:1-303
2b
d1v6wb2
B:501-803
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1v6wA02 (A:1-300)
1b: CATH_1v6wB02 (B:501-800)
2a: CATH_1v6wA01 (A:313-434)
2b: CATH_1v6wB01 (B:813-934)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Streptomyces olivaceoviridis. Organism_taxid: 1921.
(4)
1a
1v6wA02
A:1-300
1b
1v6wB02
B:501-800
Class
:
Mainly Beta
(13760)
Architecture
:
Trefoil
(289)
Topology
:
Trefoil (Acidic Fibroblast Growth Factor, subunit A)
(289)
Homologous Superfamily
:
[code=2.80.10.50, no name defined]
(289)
Streptomyces olivaceoviridis. Organism_taxid: 1921.
(4)
2a
1v6wA01
A:313-434
2b
1v6wB01
B:813-934
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_10_1v6wB01 (B:504-800)
1b: PFAM_Glyco_hydro_10_1v6wB02 (B:504-800)
2a: PFAM_Ricin_B_lectin_1v6wB03 (B:811-933)
2b: PFAM_Ricin_B_lectin_1v6wB04 (B:811-933)
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Clans
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(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_10
(42)
Streptomyces olivaceoviridis (Streptomyces corchorusii)
(4)
1a
Glyco_hydro_10-1v6wB01
B:504-800
1b
Glyco_hydro_10-1v6wB02
B:504-800
Clan
:
Trefoil
(131)
Family
:
Ricin_B_lectin
(25)
Streptomyces olivaceoviridis (Streptomyces corchorusii)
(3)
2a
Ricin_B_lectin-1v6wB03
B:811-933
2b
Ricin_B_lectin-1v6wB04
B:811-933
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Asymmetric Unit 1
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Asym.Unit (159 KB)
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