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2VO5
Biol. Unit 1
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
[
close entry info
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Hetero Components
(2, 15)
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
14
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
(22, 22)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC7 (SOFTWARE)
05: BC3 (SOFTWARE)
06: BC4 (SOFTWARE)
07: BC5 (SOFTWARE)
08: BC7 (SOFTWARE)
09: CC5 (SOFTWARE)
10: CC7 (SOFTWARE)
11: CC8 (SOFTWARE)
12: CC9 (SOFTWARE)
13: DC5 (SOFTWARE)
14: DC7 (SOFTWARE)
15: DC9 (SOFTWARE)
16: EC3 (SOFTWARE)
17: EC7 (SOFTWARE)
18: EC8 (SOFTWARE)
19: FC1 (SOFTWARE)
20: FC2 (SOFTWARE)
21: FC3 (SOFTWARE)
22: FC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:198 , ASP A:199 , TRP A:200 , TRP A:395 , CYS A:424 , ASN A:461 , GLU A:462 , TRP A:470 , TRP A:533 , TYR A:537 , GLU A:555 , TRP A:645 , TRP A:656 , EDO A:1872
BINDING SITE FOR RESIDUE VBZ A1865
02
AC4
SOFTWARE
ARG A:597 , PRO A:607 , GLU A:608 , PHE A:610 , PHE A:613 , HOH A:2459 , HOH A:2460
BINDING SITE FOR RESIDUE EDO A1866
03
AC5
SOFTWARE
PHE A:42 , GLN A:44 , LYS A:49 , MET A:51
BINDING SITE FOR RESIDUE EDO A1867
04
AC7
SOFTWARE
ILE A:328 , GLY A:329 , ARG A:449 , ASN A:450 , HIS A:451 , ALA A:452 , ARG A:507
BINDING SITE FOR RESIDUE EDO A1868
05
BC3
SOFTWARE
GLU A:465 , LYS A:468 , TYR A:469 , PRO A:514 , LEU A:516 , ALA A:517
BINDING SITE FOR RESIDUE EDO A1869
06
BC4
SOFTWARE
THR A:432 , LEU B:126 , HOH B:2478
BINDING SITE FOR RESIDUE EDO B1875
07
BC5
SOFTWARE
TRP A:525 , SER A:530 , ASN A:532 , ASP A:548 , LEU A:549 , PRO A:550 , MET A:553 , HOH A:2461
BINDING SITE FOR RESIDUE EDO A1870
08
BC7
SOFTWARE
GLU A:563 , MET A:564 , GLU A:611 , TYR A:615 , PHE A:814 , GLU A:816 , LYS A:857
BINDING SITE FOR RESIDUE EDO A1871
09
CC5
SOFTWARE
TRP A:519 , TRP A:533 , VBZ A:1865 , HOH A:2280
BINDING SITE FOR RESIDUE EDO A1872
10
CC7
SOFTWARE
ARG A:626 , VAL A:773 , HIS A:774 , PHE A:775 , HOH A:2422 , HOH A:2450
BINDING SITE FOR RESIDUE EDO A1873
11
CC8
SOFTWARE
ILE A:107 , LYS A:142
BINDING SITE FOR RESIDUE BR A1874
12
CC9
SOFTWARE
HIS A:284
BINDING SITE FOR RESIDUE BR A1875
13
DC5
SOFTWARE
GLN A:685 , ASP A:688
BINDING SITE FOR RESIDUE CL A1876
14
DC7
SOFTWARE
GLN A:685 , HIS A:774 , HOH A:2392
BINDING SITE FOR RESIDUE CL A1877
15
DC9
SOFTWARE
ASN A:337 , VAL A:510 , HIS A:511 , TYR A:515 , HOH A:2216 , HOH A:2463
BINDING SITE FOR RESIDUE EDO A1878
16
EC3
SOFTWARE
LEU A:244 , HIS A:284 , ILE A:285 , THR A:286 , HOH A:2464
BINDING SITE FOR RESIDUE EDO A1879
17
EC7
SOFTWARE
PRO A:70 , ASN A:71 , TYR A:74 , ASN A:77
BINDING SITE FOR RESIDUE EDO A1880
18
EC8
SOFTWARE
ASN A:518 , TRP A:519 , HOH A:2466
BINDING SITE FOR RESIDUE EDO A1881
19
FC1
SOFTWARE
THR A:477
BINDING SITE FOR RESIDUE BR A1882
20
FC2
SOFTWARE
HIS A:326 , ARG A:327 , ASN A:450 , HIS A:451 , HOH A:2467 , HOH A:2468
BINDING SITE FOR RESIDUE EDO A1883
21
FC3
SOFTWARE
GLN A:108
BINDING SITE FOR RESIDUE BR A1884
22
FC4
SOFTWARE
TYR A:74 , ALA A:568 , ALA A:571 , ALA A:572 , PRO A:573 , TYR A:576
BINDING SITE FOR RESIDUE EDO A1885
[
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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
[
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
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
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)
(
)
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
[
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]
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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Asym.Unit (306 KB)
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