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2D24
Asym. Unit
Info
Asym.Unit (155 KB)
Biol.Unit 1 (77 KB)
Biol.Unit 2 (78 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ES COMPLEX OF CATALYTIC-SITE MUTANT XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDIS E-86
Authors
:
R. Suzuki, A. Kuno, Z. Fujimoto, S. Ito, S. I. Kawahara, S. Kaneko, T. Has K. Taira
Date
:
02 Sep 05 (Deposition) - 10 Oct 06 (Release) - 15 Feb 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Tim-Barrel, Retaining Enzyme, Catalytic-Site Mutant, Chemical Rescue, Michaelis Complex, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Suzuki, Z. Fujimoto, S. Ito, S. Kawahara, S. Kaneko, K. Taira, T. Hasegawa, A. Kuno
Crystallographic Snapshots Of An Entire Reaction Cycle For Retaining Xylanase From Streptomyces Olivaceoviridis E-86
J. Biochem. V. 146 61 2009
(for further references see the
PDB file header
)
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Hetero Components
(3, 23)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
3a: XYLOPYRANOSE (XYSa)
3b: XYLOPYRANOSE (XYSb)
3c: XYLOPYRANOSE (XYSc)
3d: XYLOPYRANOSE (XYSd)
3e: XYLOPYRANOSE (XYSe)
3f: XYLOPYRANOSE (XYSf)
3g: XYLOPYRANOSE (XYSg)
3h: XYLOPYRANOSE (XYSh)
3i: XYLOPYRANOSE (XYSi)
3j: XYLOPYRANOSE (XYSj)
3k: XYLOPYRANOSE (XYSk)
3l: XYLOPYRANOSE (XYSl)
3m: XYLOPYRANOSE (XYSm)
3n: XYLOPYRANOSE (XYSn)
3o: XYLOPYRANOSE (XYSo)
3p: XYLOPYRANOSE (XYSp)
3q: XYLOPYRANOSE (XYSq)
3r: XYLOPYRANOSE (XYSr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
3
Ligand/Ion
GLYCEROL
2
SO4
2
Ligand/Ion
SULFATE ION
3
XYS
18
Ligand/Ion
XYLOPYRANOSE
[
close Hetero Component info
]
Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:132 , ASN A:173 , GLY A:211 , XYS A:454 , HOH A:1048
BINDING SITE FOR RESIDUE XYS A 455
02
AC2
SOFTWARE
TYR A:172 , ASN A:173 , ASN A:209 , SER A:212 , ARG A:275 , XYS A:453 , XYS A:455 , HOH A:1026 , HOH A:1164
BINDING SITE FOR RESIDUE XYS A 454
03
AC3
SOFTWARE
HIS A:128 , GLN A:205 , TRP A:274 , XYS A:452 , XYS A:454 , HOH A:1073 , HOH A:1128 , HOH A:1154
BINDING SITE FOR RESIDUE XYS A 453
04
AC4
SOFTWARE
LYS A:48 , HIS A:81 , HIS A:128 , GLN A:205 , HIS A:207 , GLU A:236 , TRP A:266 , XYS A:451 , XYS A:453
BINDING SITE FOR RESIDUE XYS A 452
05
AC5
SOFTWARE
GLU A:44 , ASN A:45 , LYS A:48 , GLN A:88 , TRP A:266 , TRP A:274 , XYS A:452 , HOH A:1035 , HOH A:1084 , HOH A:1128
BINDING SITE FOR RESIDUE XYS A 451
06
AC6
SOFTWARE
ALA A:51 , ALA A:63 , GLY A:411 , GLN A:421 , TYR A:423 , XYS A:458
BINDING SITE FOR RESIDUE XYS A 459
07
AC7
SOFTWARE
GLY A:23 , ASP A:408 , ALA A:409 , VAL A:410 , GLY A:411 , GLY A:412 , GLN A:421 , TYR A:423 , ASN A:430 , XYS A:457 , XYS A:459 , HOH A:1098 , HOH A:1272
BINDING SITE FOR RESIDUE XYS A 458
08
AC8
SOFTWARE
LYS A:24 , TYR A:423 , XYS A:456 , XYS A:458 , HOH A:1214
BINDING SITE FOR RESIDUE XYS A 457
09
AC9
SOFTWARE
CYS A:425 , SER A:426 , XYS A:457
BINDING SITE FOR RESIDUE XYS A 456
10
BC1
SOFTWARE
ASP B:632 , ASN B:673 , XYS B:954 , HOH B:1261 , HOH B:1269
BINDING SITE FOR RESIDUE XYS B 955
11
BC2
SOFTWARE
TYR B:672 , ASN B:673 , ASN B:709 , SER B:712 , ARG B:775 , XYS B:953 , XYS B:955 , HOH B:1006 , HOH B:1159
BINDING SITE FOR RESIDUE XYS B 954
12
BC3
SOFTWARE
HIS B:628 , GLN B:705 , TRP B:774 , XYS B:952 , XYS B:954 , HOH B:1101 , HOH B:1126 , HOH B:1151 , HOH B:1181
BINDING SITE FOR RESIDUE XYS B 953
13
BC4
SOFTWARE
LYS B:548 , HIS B:581 , TRP B:585 , HIS B:628 , GLN B:705 , HIS B:707 , GLU B:736 , TRP B:766 , XYS B:951 , XYS B:953
BINDING SITE FOR RESIDUE XYS B 952
14
BC5
SOFTWARE
GLU B:544 , ASN B:545 , LYS B:548 , GLN B:588 , TRP B:766 , TRP B:774 , XYS B:952 , HOH B:1133 , HOH B:1151
BINDING SITE FOR RESIDUE XYS B 951
15
BC6
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 , XYS A:956
BINDING SITE FOR RESIDUE XYS A 957
16
BC7
SOFTWARE
ASP A:191 , ASN A:328 , GLN A:338 , XYS A:957
BINDING SITE FOR RESIDUE XYS A 956
17
BC8
SOFTWARE
ASP B:908 , ALA B:909 , GLY B:911 , GLN B:921 , TYR B:923 , ASN B:930 , XYS B:958
BINDING SITE FOR RESIDUE XYS B 959
18
BC9
SOFTWARE
VAL B:910 , GLY B:911 , XYS B:959
BINDING SITE FOR RESIDUE XYS B 958
19
CC1
SOFTWARE
ARG A:322
BINDING SITE FOR RESIDUE SO4 A 970
20
CC2
SOFTWARE
LYS A:289 , ARG A:391 , HOH A:1027 , HOH A:1256
BINDING SITE FOR RESIDUE SO4 A 971
21
CC3
SOFTWARE
LYS B:789 , TYR B:793 , THR B:794 , ARG B:891 , ASN B:893 , HOH B:1258
BINDING SITE FOR RESIDUE GOL B 980
22
CC4
SOFTWARE
ASP B:825 , VAL B:826 , PRO B:827 , ASN B:828 , GLN B:838 , TYR B:840 , ASN B:847
BINDING SITE FOR RESIDUE GOL B 981
23
CC5
SOFTWARE
GLN A:77 , GLY A:118 , ILE A:120 , ALA A:164 , HOH A:988 , HOH A:1017 , ASP B:565 , ASN B:569 , HOH B:1132
BINDING SITE FOR RESIDUE GOL B 982
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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:
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[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_d2d24a2 (A:322-436)
1b: SCOP_d2d24b2 (B:822-936)
2a: SCOP_d2d24a1 (A:1-301)
2b: SCOP_d2d24b1 (B:501-801)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
beta-Trefoil
(385)
Superfamily
:
Ricin B-like lectins
(91)
Family
:
automated matches
(21)
Protein domain
:
automated matches
(21)
Streptomyces olivaceoviridis [TaxId: 1921]
(5)
1a
d2d24a2
A:322-436
1b
d2d24b2
B:822-936
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
(Trans)glycosidases
(1191)
Family
:
beta-glycanases
(284)
Protein domain
:
automated matches
(49)
Streptomyces olivaceoviridis [TaxId: 1921]
(8)
2a
d2d24a1
A:1-301
2b
d2d24b1
B:501-801
[
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]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2d24A01 (A:1-300)
1b: CATH_2d24B01 (B:501-800)
2a: CATH_2d24A02 (A:313-434)
2b: CATH_2d24B02 (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. Strain: e-86.
(13)
1a
2d24A01
A:1-300
1b
2d24B01
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. Strain: e-86.
(11)
2a
2d24A02
A:313-434
2b
2d24B02
B:813-934
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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