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1V6U
Asym. Unit
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Asym.Unit (155 KB)
Biol.Unit 1 (149 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDIS E-86 COMPLEXED WITH 2(2)-ALPHA-L-ARABINOFURANOSYL-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
:
2.10
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
(3, 17)
Info
All Hetero Components
1a: ALPHA-L-ARABINOFURANOSE (AHRa)
1b: ALPHA-L-ARABINOFURANOSE (AHRb)
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)
2i: BETA-D-XYLOPYRANOSE (XYPi)
2j: BETA-D-XYLOPYRANOSE (XYPj)
2k: BETA-D-XYLOPYRANOSE (XYPk)
2l: BETA-D-XYLOPYRANOSE (XYPl)
2m: BETA-D-XYLOPYRANOSE (XYPm)
2n: BETA-D-XYLOPYRANOSE (XYPn)
3a: XYLOPYRANOSE (XYSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AHR
2
Ligand/Ion
ALPHA-L-ARABINOFURANOSE
2
XYP
14
Ligand/Ion
BETA-D-XYLOPYRANOSE
3
XYS
1
Ligand/Ion
XYLOPYRANOSE
[
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Sites
(17, 17)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:44 , ASN A:45 , LYS A:48 , GLN A:88 , TRP A:266 , TRP A:274 , XYP A:452
BINDING SITE FOR RESIDUE XYP A 451
02
AC2
SOFTWARE
LYS A:48 , HIS A:81 , ASN A:127 , GLU A:128 , GLN A:205 , GLU A:236 , TRP A:266 , TRP A:274 , XYP A:451 , XYP A:456
BINDING SITE FOR RESIDUE XYP A 452
03
AC3
SOFTWARE
TYR A:172 , GLN A:205 , HIS A:207 , TRP A:274 , ARG A:275 , XYP A:452 , XYP A:457 , HOH A:1695
BINDING SITE FOR RESIDUE XYP A 456
04
AC4
SOFTWARE
ASN A:173 , ASN A:209 , GLY A:211 , SER A:212 , ARG A:275 , XYP A:456 , HOH A:1634
BINDING SITE FOR RESIDUE XYP A 457
05
AC5
SOFTWARE
TYR A:340 , HIS A:343 , XYS A:1461
BINDING SITE FOR RESIDUE XYP A 1460
06
AC6
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 , XYP A:1460 , HOH A:1681
BINDING SITE FOR RESIDUE XYS A 1461
07
AC7
SOFTWARE
ASP A:50 , ALA A:51 , XYP A:470
BINDING SITE FOR RESIDUE AHR A 469
08
AC8
SOFTWARE
GLU A:46 , ALA A:51 , ALA A:63 , GLN A:421 , AHR A:469 , XYP A:471
BINDING SITE FOR RESIDUE XYP A 470
09
AC9
SOFTWARE
ASP A:408 , ALA A:409 , VAL A:410 , GLY A:411 , GLY A:412 , GLN A:421 , TYR A:423 , ASN A:430 , XYP A:470 , HOH A:1516 , HOH A:1564
BINDING SITE FOR RESIDUE XYP A 471
10
BC1
SOFTWARE
GLU B:544 , ASP B:772 , XYP B:951 , HOH B:1250
BINDING SITE FOR RESIDUE AHR B 950
11
BC2
SOFTWARE
GLU B:544 , ASN B:545 , LYS B:548 , GLN B:588 , TRP B:766 , TRP B:774 , AHR B:950 , XYP B:952
BINDING SITE FOR RESIDUE XYP B 951
12
BC3
SOFTWARE
LYS B:548 , HIS B:581 , TRP B:585 , ASN B:627 , GLU B:628 , GLN B:705 , GLU B:736 , TRP B:766 , TRP B:774 , XYP B:951 , XYP B:956 , HOH B:1262
BINDING SITE FOR RESIDUE XYP B 952
13
BC4
SOFTWARE
GLU B:628 , TYR B:672 , ARG B:775 , XYP B:952 , XYP B:957 , HOH B:1080 , HOH B:1262
BINDING SITE FOR RESIDUE XYP B 956
14
BC5
SOFTWARE
ASN B:673 , ASN B:709 , GLY B:711 , SER B:712 , ARG B:775 , XYP B:956
BINDING SITE FOR RESIDUE XYP B 957
15
BC6
SOFTWARE
ASP B:825 , VAL B:826 , PRO B:827 , ASN B:828 , GLN B:838 , TYR B:840 , HIS B:843 , ASN B:847
BINDING SITE FOR RESIDUE XYP B 961
16
BC7
SOFTWARE
GLY B:911 , XYP B:971
BINDING SITE FOR RESIDUE XYP B 970
17
BC8
SOFTWARE
ASP B:908 , ALA B:909 , VAL B:910 , GLY B:911 , GLY B:912 , GLN B:921 , TYR B:923 , ASN B:930 , XYP B:970
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)
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Exons
(0, 0)
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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_d1v6ua1 (A:304-436)
1b: SCOP_d1v6ub1 (B:804-936)
2a: SCOP_d1v6ua2 (A:1-303)
2b: SCOP_d1v6ub2 (B:501-803)
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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
d1v6ua1
A:304-436
1b
d1v6ub1
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
d1v6ua2
A:1-303
2b
d1v6ub2
B:501-803
[
close SCOP info
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1v6uA02 (A:1-300)
1b: CATH_1v6uB02 (B:501-800)
2a: CATH_1v6uA01 (A:313-434)
2b: CATH_1v6uB01 (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
1v6uA02
A:1-300
1b
1v6uB02
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
1v6uA01
A:313-434
2b
1v6uB01
B:813-934
[
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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