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2VO5
Asym. Unit
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
]
Hetero Components
(4, 50)
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
9
Ligand/Ion
BROMIDE ION
2
CL
6
Ligand/Ion
CHLORIDE ION
3
EDO
33
Ligand/Ion
1,2-ETHANEDIOL
4
VBZ
2
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
(49, 49)
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)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: 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
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
03
AC3
SOFTWARE
TRP B:519 , VBZ B:1868 , HOH B:2280 , HOH B:2475
BINDING SITE FOR RESIDUE EDO B1869
04
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
05
AC5
SOFTWARE
PHE A:42 , GLN A:44 , LYS A:49 , MET A:51
BINDING SITE FOR RESIDUE EDO A1867
06
AC6
SOFTWARE
GLN B:230 , ARG B:331 , HOH B:2205 , HOH B:2476
BINDING SITE FOR RESIDUE EDO B1870
07
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
08
AC8
SOFTWARE
ARG B:376 , TYR B:661
BINDING SITE FOR RESIDUE EDO B1871
09
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
10
BC1
SOFTWARE
TYR B:347 , HOH B:2328
BINDING SITE FOR RESIDUE EDO B1873
11
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
12
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
13
BC4
SOFTWARE
THR A:432 , LEU B:126 , HOH B:2478
BINDING SITE FOR RESIDUE EDO B1875
14
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
15
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
16
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
17
BC8
SOFTWARE
LEU B:164 , HIS B:181 , LYS B:183 , HOH B:2043
BINDING SITE FOR RESIDUE EDO B1877
18
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
19
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
20
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
21
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
22
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
23
CC5
SOFTWARE
TRP A:519 , TRP A:533 , VBZ A:1865 , HOH A:2280
BINDING SITE FOR RESIDUE EDO A1872
24
CC6
SOFTWARE
ASN B:337 , HIS B:511 , TYR B:515 , HOH B:2480
BINDING SITE FOR RESIDUE EDO B1883
25
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
26
CC8
SOFTWARE
ILE A:107 , LYS A:142
BINDING SITE FOR RESIDUE BR A1874
27
CC9
SOFTWARE
HIS A:284
BINDING SITE FOR RESIDUE BR A1875
28
DC1
SOFTWARE
ILE B:107 , LYS B:142
BINDING SITE FOR RESIDUE BR B1884
29
DC2
SOFTWARE
HOH B:2294
BINDING SITE FOR RESIDUE BR A1895
30
DC3
SOFTWARE
GLN B:685 , ASP B:688
BINDING SITE FOR RESIDUE BR B1885
31
DC4
SOFTWARE
GLN B:108
BINDING SITE FOR RESIDUE CL B1886
32
DC5
SOFTWARE
GLN A:685 , ASP A:688
BINDING SITE FOR RESIDUE CL A1876
33
DC6
SOFTWARE
GLN B:685 , HIS B:774 , HOH B:2384
BINDING SITE FOR RESIDUE CL B1887
34
DC7
SOFTWARE
GLN A:685 , HIS A:774 , HOH A:2392
BINDING SITE FOR RESIDUE CL A1877
35
DC8
SOFTWARE
PHE B:476 , THR B:477 , VAL B:480
BINDING SITE FOR RESIDUE CL B1888
36
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
37
EC1
SOFTWARE
HOH B:2275
BINDING SITE FOR RESIDUE CL B1896
38
EC2
SOFTWARE
GLN B:577 , ILE B:578 , ARG B:597
BINDING SITE FOR RESIDUE EDO B1889
39
EC3
SOFTWARE
LEU A:244 , HIS A:284 , ILE A:285 , THR A:286 , HOH A:2464
BINDING SITE FOR RESIDUE EDO A1879
40
EC4
SOFTWARE
TYR B:863 , LYS B:864
BINDING SITE FOR RESIDUE EDO B1890
41
EC5
SOFTWARE
GLU B:48 , TRP B:50 , ARG B:92 , HOH B:2481
BINDING SITE FOR RESIDUE EDO B1891
42
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
43
EC7
SOFTWARE
PRO A:70 , ASN A:71 , TYR A:74 , ASN A:77
BINDING SITE FOR RESIDUE EDO A1880
44
EC8
SOFTWARE
ASN A:518 , TRP A:519 , HOH A:2466
BINDING SITE FOR RESIDUE EDO A1881
45
EC9
SOFTWARE
ASN B:300 , ASN B:390
BINDING SITE FOR RESIDUE BR B1893
46
FC1
SOFTWARE
THR A:477
BINDING SITE FOR RESIDUE BR A1882
47
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
48
FC3
SOFTWARE
GLN A:108
BINDING SITE FOR RESIDUE BR A1884
49
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
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
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.
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
(
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(
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Superfamilies
(
)
(
)
Families
(
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(
)
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
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(
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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
[
close Pfam info
]
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