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2VO5
Biol. Unit 2
Info
Asym.Unit (306 KB)
Biol.Unit 1 (152 KB)
Biol.Unit 2 (153 KB)
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(1)
Title
:
STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA-MANNOSIDASES
Authors
:
L. E. Tailford, W. A. Offen, N. L. Smith, C. Dumon, C. Moreland, J. Gratien, M. P. Heck, R. V. Stick, Y. Bleriot, A. Vasella, H. J. Gilbert, G. J. Davies
Date
:
08 Feb 08 (Deposition) - 01 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Glycoside, Hydrolase, Mannosidase, Transition State Mimic, Linear Free Energy Relationship
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. E. Tailford, W. A. Offen, N. L. Smith, C. Dumon, C. Morland, J. Gratien, M. P. Heck, R. V. Stick, Y. Bleriot, A. Vasella, H. J. Gilbert, G. J. Davies
Structural And Biochemical Evidence For A Boat-Like Transition State In Beta-Mannosidases.
Nat. Chem. Biol. V. 4 306 2008
[
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Hetero Components
(2, 20)
Info
All Hetero Components
1a: BROMIDE ION (BRa)
1b: BROMIDE ION (BRb)
1c: BROMIDE ION (BRc)
1d: BROMIDE ION (BRd)
1e: BROMIDE ION (BRe)
1f: BROMIDE ION (BRf)
1g: BROMIDE ION (BRg)
1h: BROMIDE ION (BRh)
1i: BROMIDE ION (BRi)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
3a: 1,2-ETHANEDIOL (EDOa)
3aa: 1,2-ETHANEDIOL (EDOaa)
3ab: 1,2-ETHANEDIOL (EDOab)
3ac: 1,2-ETHANEDIOL (EDOac)
3ad: 1,2-ETHANEDIOL (EDOad)
3ae: 1,2-ETHANEDIOL (EDOae)
3af: 1,2-ETHANEDIOL (EDOaf)
3ag: 1,2-ETHANEDIOL (EDOag)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
3r: 1,2-ETHANEDIOL (EDOr)
3s: 1,2-ETHANEDIOL (EDOs)
3t: 1,2-ETHANEDIOL (EDOt)
3u: 1,2-ETHANEDIOL (EDOu)
3v: 1,2-ETHANEDIOL (EDOv)
3w: 1,2-ETHANEDIOL (EDOw)
3x: 1,2-ETHANEDIOL (EDOx)
3y: 1,2-ETHANEDIOL (EDOy)
3z: 1,2-ETHANEDIOL (EDOz)
4a: (1R,4R,5R,7R,8R)-2-BENZYL-5-HYDROX... (VBZa)
4b: (1R,4R,5R,7R,8R)-2-BENZYL-5-HYDROX... (VBZb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BR
-1
Ligand/Ion
BROMIDE ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
EDO
19
Ligand/Ion
1,2-ETHANEDIOL
4
VBZ
1
Ligand/Ion
(1R,4R,5R,7R,8R)-2-BENZYL-5-HYDROXYMETHYL-2-AZA-BICYCLO[2.2.2]OCTANE-4,7,8-TRIOL
[
close Hetero Component info
]
Sites
(28, 28)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC8 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC6 (SOFTWARE)
10: BC8 (SOFTWARE)
11: BC9 (SOFTWARE)
12: CC1 (SOFTWARE)
13: CC2 (SOFTWARE)
14: CC3 (SOFTWARE)
15: CC4 (SOFTWARE)
16: CC6 (SOFTWARE)
17: DC1 (SOFTWARE)
18: DC2 (SOFTWARE)
19: DC3 (SOFTWARE)
20: DC4 (SOFTWARE)
21: DC6 (SOFTWARE)
22: DC8 (SOFTWARE)
23: EC1 (SOFTWARE)
24: EC2 (SOFTWARE)
25: EC4 (SOFTWARE)
26: EC5 (SOFTWARE)
27: EC6 (SOFTWARE)
28: EC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
TRP B:198 , ASP B:199 , TRP B:200 , TRP B:395 , CYS B:424 , ASN B:461 , GLU B:462 , TRP B:470 , TRP B:533 , TYR B:537 , GLU B:555 , TRP B:645 , TRP B:656 , EDO B:1869
BINDING SITE FOR RESIDUE VBZ B1868
02
AC3
SOFTWARE
TRP B:519 , VBZ B:1868 , HOH B:2280 , HOH B:2475
BINDING SITE FOR RESIDUE EDO B1869
03
AC6
SOFTWARE
GLN B:230 , ARG B:331 , HOH B:2205 , HOH B:2476
BINDING SITE FOR RESIDUE EDO B1870
04
AC8
SOFTWARE
ARG B:376 , TYR B:661
BINDING SITE FOR RESIDUE EDO B1871
05
AC9
SOFTWARE
ILE B:328 , GLY B:329 , ARG B:331 , ASN B:450 , HIS B:451 , ALA B:452
BINDING SITE FOR RESIDUE EDO B1872
06
BC1
SOFTWARE
TYR B:347 , HOH B:2328
BINDING SITE FOR RESIDUE EDO B1873
07
BC2
SOFTWARE
GLN B:365 , ASN B:648 , ASP B:649 , ILE B:659 , ASP B:660 , HOH B:2223
BINDING SITE FOR RESIDUE EDO B1874
08
BC4
SOFTWARE
THR A:432 , LEU B:126 , HOH B:2478
BINDING SITE FOR RESIDUE EDO B1875
09
BC6
SOFTWARE
HIS B:326 , ARG B:327 , ASN B:450 , HIS B:451 , HOH B:2201 , HOH B:2257 , HOH B:2479
BINDING SITE FOR RESIDUE EDO B1876
10
BC8
SOFTWARE
LEU B:164 , HIS B:181 , LYS B:183 , HOH B:2043
BINDING SITE FOR RESIDUE EDO B1877
11
BC9
SOFTWARE
TRP B:519 , TRP B:525 , ASN B:532 , ASP B:548 , MET B:553 , HOH B:2314
BINDING SITE FOR RESIDUE EDO B1878
12
CC1
SOFTWARE
SER B:43 , GLN B:44 , SER B:45 , GLY B:46 , GLU B:48 , GLU B:90
BINDING SITE FOR RESIDUE EDO B1879
13
CC2
SOFTWARE
GLU B:465 , LYS B:468 , TYR B:469 , PRO B:514 , LEU B:516 , ALA B:517 , ASN B:518
BINDING SITE FOR RESIDUE EDO B1880
14
CC3
SOFTWARE
PHE B:42 , SER B:43 , GLN B:44 , LYS B:49 , MET B:51 , HOH B:2012
BINDING SITE FOR RESIDUE EDO B1881
15
CC4
SOFTWARE
ARG B:626 , PRO B:683 , SER B:772 , VAL B:773 , HIS B:774 , HOH B:2361 , HOH B:2384 , HOH B:2427
BINDING SITE FOR RESIDUE EDO B1882
16
CC6
SOFTWARE
ASN B:337 , HIS B:511 , TYR B:515 , HOH B:2480
BINDING SITE FOR RESIDUE EDO B1883
17
DC1
SOFTWARE
ILE B:107 , LYS B:142
BINDING SITE FOR RESIDUE BR B1884
18
DC2
SOFTWARE
HOH B:2294
BINDING SITE FOR RESIDUE BR A1895
19
DC3
SOFTWARE
GLN B:685 , ASP B:688
BINDING SITE FOR RESIDUE BR B1885
20
DC4
SOFTWARE
GLN B:108
BINDING SITE FOR RESIDUE CL B1886
21
DC6
SOFTWARE
GLN B:685 , HIS B:774 , HOH B:2384
BINDING SITE FOR RESIDUE CL B1887
22
DC8
SOFTWARE
PHE B:476 , THR B:477 , VAL B:480
BINDING SITE FOR RESIDUE CL B1888
23
EC1
SOFTWARE
HOH B:2275
BINDING SITE FOR RESIDUE CL B1896
24
EC2
SOFTWARE
GLN B:577 , ILE B:578 , ARG B:597
BINDING SITE FOR RESIDUE EDO B1889
25
EC4
SOFTWARE
TYR B:863 , LYS B:864
BINDING SITE FOR RESIDUE EDO B1890
26
EC5
SOFTWARE
GLU B:48 , TRP B:50 , ARG B:92 , HOH B:2481
BINDING SITE FOR RESIDUE EDO B1891
27
EC6
SOFTWARE
PHE B:356 , ARG B:633 , ARG B:636 , ILE B:695 , SER B:696 , ASP B:697 , THR B:734
BINDING SITE FOR RESIDUE EDO B1892
28
EC9
SOFTWARE
ASN B:300 , ASN B:390
BINDING SITE FOR RESIDUE BR B1893
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 10)
Info
All SCOP Domains
1a: SCOP_d2vo5a4 (A:28-219)
1b: SCOP_d2vo5b4 (B:27-219)
2a: SCOP_d2vo5a1 (A:220-330)
2b: SCOP_d2vo5a2 (A:784-864)
2c: SCOP_d2vo5a3 (A:679-783)
2d: SCOP_d2vo5b1 (B:220-330)
2e: SCOP_d2vo5b2 (B:784-867)
2f: SCOP_d2vo5b3 (B:679-783)
3a: SCOP_d2vo5a5 (A:331-678)
3b: SCOP_d2vo5b5 (B:331-678)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Galactose-binding domain-like
(314)
Superfamily
:
Galactose-binding domain-like
(314)
Family
:
automated matches
(85)
Protein domain
:
automated matches
(85)
Bacteroides thetaiotaomicron [TaxId: 226186]
(7)
1a
d2vo5a4
A:28-219
1b
d2vo5b4
B:27-219
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
beta-Galactosidase/glucuronidase domain
(79)
Family
:
automated matches
(30)
Protein domain
:
automated matches
(30)
Bacteroides thetaiotaomicron [TaxId: 226186]
(7)
2a
d2vo5a1
A:220-330
2b
d2vo5a2
A:784-864
2c
d2vo5a3
A:679-783
2d
d2vo5b1
B:220-330
2e
d2vo5b2
B:784-867
2f
d2vo5b3
B:679-783
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)
Bacteroides thetaiotaomicron [TaxId: 226186]
(7)
3a
d2vo5a5
A:331-678
3b
d2vo5b5
B:331-678
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_2_N_2vo5B01 (B:28-219)
1b: PFAM_Glyco_hydro_2_N_2vo5B02 (B:28-219)
2a: PFAM_Glyco_hydro_2_C_2vo5B03 (B:345-478)
2b: PFAM_Glyco_hydro_2_C_2vo5B04 (B:345-478)
3a: PFAM_Glyco_hydro_2_2vo5B05 (B:221-331)
3b: PFAM_Glyco_hydro_2_2vo5B06 (B:221-331)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GBD
(153)
Family
:
Glyco_hydro_2_N
(32)
Bacteroides thetaiotaomicron
(9)
1a
Glyco_hydro_2_N-2vo5B01
B:28-219
1b
Glyco_hydro_2_N-2vo5B02
B:28-219
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_2_C
(27)
Bacteroides thetaiotaomicron
(9)
2a
Glyco_hydro_2_C-2vo5B03
B:345-478
2b
Glyco_hydro_2_C-2vo5B04
B:345-478
Clan
:
no clan defined [family: Glyco_hydro_2]
(31)
Family
:
Glyco_hydro_2
(31)
Bacteroides thetaiotaomicron
(9)
3a
Glyco_hydro_2-2vo5B05
B:221-331
3b
Glyco_hydro_2-2vo5B06
B:221-331
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]
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Chain B
Asymmetric Unit 1
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Asym.Unit (306 KB)
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Biol.Unit 1 (152 KB)
Header - Biol.Unit 1
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Header - Biol.Unit 2
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