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2VOT
Biol. Unit 2
Info
Asym.Unit (317 KB)
Biol.Unit 1 (159 KB)
Biol.Unit 2 (158 KB)
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(1)
Title
:
STRUCTURAL AND BIOCHEMICAL EVIDENCE FOR A BOAT-LIKE TRANSITION STATE IN BETA-MANNOSIDASES
Authors
:
L. N. Tailford, W. A. Offen, N. Smith, C. Dumon, C. Moreland, J. Gratien, M. -P. Heck, R. V. Stick, Y. Bleriot, A. Vasella, H. J. Gilbert, G. J. Davies
Date
:
20 Feb 08 (Deposition) - 01 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Linear Free Energy Relationship, Hydrolase, Transition State Mimic, Mannosidase, Glycoside Hydrolase
(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
(2, 28)
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)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
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)
3ah: 1,2-ETHANEDIOL (EDOah)
3ai: 1,2-ETHANEDIOL (EDOai)
3aj: 1,2-ETHANEDIOL (EDOaj)
3ak: 1,2-ETHANEDIOL (EDOak)
3al: 1,2-ETHANEDIOL (EDOal)
3am: 1,2-ETHANEDIOL (EDOam)
3an: 1,2-ETHANEDIOL (EDOan)
3ao: 1,2-ETHANEDIOL (EDOao)
3ap: 1,2-ETHANEDIOL (EDOap)
3aq: 1,2-ETHANEDIOL (EDOaq)
3ar: 1,2-ETHANEDIOL (EDOar)
3as: 1,2-ETHANEDIOL (EDOas)
3at: 1,2-ETHANEDIOL (EDOat)
3au: 1,2-ETHANEDIOL (EDOau)
3av: 1,2-ETHANEDIOL (EDOav)
3aw: 1,2-ETHANEDIOL (EDOaw)
3ax: 1,2-ETHANEDIOL (EDOax)
3ay: 1,2-ETHANEDIOL (EDOay)
3az: 1,2-ETHANEDIOL (EDOaz)
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: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (NHVa)
4b: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (NHVb)
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
27
Ligand/Ion
1,2-ETHANEDIOL
4
NHV
1
Ligand/Ion
(5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(HYDROXYMETHYL)-2-[(PHENYLAMINO)METHYL]-5,6,7,8-TETRAHYDRO-1H-IMIDAZO[1,2-A]PYRIDIN-4-IUM
[
close Hetero Component info
]
Sites
(37, 37)
Info
All Sites
01: BC7 (SOFTWARE)
02: CC2 (SOFTWARE)
03: CC8 (SOFTWARE)
04: CC9 (SOFTWARE)
05: DC1 (SOFTWARE)
06: DC2 (SOFTWARE)
07: DC3 (SOFTWARE)
08: DC4 (SOFTWARE)
09: DC5 (SOFTWARE)
10: DC6 (SOFTWARE)
11: DC7 (SOFTWARE)
12: DC8 (SOFTWARE)
13: DC9 (SOFTWARE)
14: EC1 (SOFTWARE)
15: EC2 (SOFTWARE)
16: EC3 (SOFTWARE)
17: EC4 (SOFTWARE)
18: EC5 (SOFTWARE)
19: EC6 (SOFTWARE)
20: EC7 (SOFTWARE)
21: EC8 (SOFTWARE)
22: EC9 (SOFTWARE)
23: FC1 (SOFTWARE)
24: FC2 (SOFTWARE)
25: FC3 (SOFTWARE)
26: FC4 (SOFTWARE)
27: FC5 (SOFTWARE)
28: FC6 (SOFTWARE)
29: FC7 (SOFTWARE)
30: FC8 (SOFTWARE)
31: FC9 (SOFTWARE)
32: GC2 (SOFTWARE)
33: GC3 (SOFTWARE)
34: GC4 (SOFTWARE)
35: GC7 (SOFTWARE)
36: GC8 (SOFTWARE)
37: HC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC7
SOFTWARE
ASP A:88 , HIS A:157 , ARG A:161 , EDO A:1884 , EDO B:1871
BINDING SITE FOR RESIDUE EDO A1880
02
CC2
SOFTWARE
ARG A:161 , GLN A:162 , PRO A:165 , EDO A:1880 , ASP B:119 , TYR B:121 , TYR B:155 , HIS B:157
BINDING SITE FOR RESIDUE EDO A1884
03
CC8
SOFTWARE
TRP B:198 , ASP B:199 , TRP B:200 , TRP B:395 , 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:1877 , EDO B:1879
BINDING SITE FOR RESIDUE NHV B1868
04
CC9
SOFTWARE
TRP B:525 , SER B:530 , ASN B:532 , ASP B:548 , PRO B:550 , MET B:553 , HOH B:2591
BINDING SITE FOR RESIDUE EDO B1869
05
DC1
SOFTWARE
ASN B:337 , HIS B:511 , TYR B:515 , EDO B:1902 , HOH B:2376 , HOH B:2592 , HOH B:2593
BINDING SITE FOR RESIDUE EDO B1870
06
DC2
SOFTWARE
EDO A:1880 , ASP B:88 , HIS B:157 , GLN B:162 , EDO B:1887
BINDING SITE FOR RESIDUE EDO B1871
07
DC3
SOFTWARE
THR A:432 , HOH A:2069 , LEU B:126 , HOH B:2086
BINDING SITE FOR RESIDUE EDO B1872
08
DC4
SOFTWARE
SER B:43 , GLN B:44 , GLY B:46 , THR B:47 , GLU B:48 , GLU B:90
BINDING SITE FOR RESIDUE EDO B1873
09
DC5
SOFTWARE
ARG B:376 , TYR B:661
BINDING SITE FOR RESIDUE EDO B1874
10
DC6
SOFTWARE
ARG B:331 , ASP B:506 , ARG B:507 , HOH B:2269 , HOH B:2594
BINDING SITE FOR RESIDUE EDO B1875
11
DC7
SOFTWARE
GLN B:365 , ASN B:648 , ASP B:649 , ILE B:659 , ASP B:660
BINDING SITE FOR RESIDUE EDO B1876
12
DC8
SOFTWARE
ASN B:178 , ASP B:199 , CYS B:424 , GLU B:462 , NHV B:1868
BINDING SITE FOR RESIDUE EDO B1877
13
DC9
SOFTWARE
GLN B:623 , ARG B:626 , HIS B:774 , PHE B:775 , EDO B:1882 , HOH B:2456 , HOH B:2457 , HOH B:2538
BINDING SITE FOR RESIDUE EDO B1878
14
EC1
SOFTWARE
GLU B:465 , TRP B:519 , NHV B:1868 , EDO B:1886
BINDING SITE FOR RESIDUE EDO B1879
15
EC2
SOFTWARE
PHE B:356 , ARG B:633 , ARG B:636 , ILE B:695 , SER B:696 , ASP B:697 , ASN B:733 , THR B:734
BINDING SITE FOR RESIDUE EDO B1880
16
EC3
SOFTWARE
ILE B:328 , GLY B:329 , ARG B:449 , ASN B:450 , HIS B:451 , ALA B:452 , ARG B:507
BINDING SITE FOR RESIDUE EDO B1881
17
EC4
SOFTWARE
GLN B:685 , PHE B:775 , PHE B:776 , ARG B:777 , LYS B:778 , EDO B:1878 , CL B:1894 , HOH B:2595
BINDING SITE FOR RESIDUE EDO B1882
18
EC5
SOFTWARE
PHE B:42 , SER B:43 , GLN B:44 , THR B:47 , LYS B:49 , LEU B:63 , LEU B:68 , HOH B:2014
BINDING SITE FOR RESIDUE EDO B1883
19
EC6
SOFTWARE
ASN B:300 , TRP B:302 , PHE B:356 , ASN B:390 , ASP B:697 , HOH B:2286 , HOH B:2513
BINDING SITE FOR RESIDUE EDO B1884
20
EC7
SOFTWARE
ARG B:382 , ARG B:823 , SER B:825 , ILE B:840 , THR B:842 , HOH B:2599
BINDING SITE FOR RESIDUE EDO B1885
21
EC8
SOFTWARE
GLU B:465 , TRP B:470 , ASN B:518 , TRP B:519 , EDO B:1879
BINDING SITE FOR RESIDUE EDO B1886
22
EC9
SOFTWARE
ASP A:119 , TYR A:121 , TYR A:155 , ARG B:161 , GLN B:162 , PRO B:165 , EDO B:1871
BINDING SITE FOR RESIDUE EDO B1887
23
FC1
SOFTWARE
HIS B:326 , ARG B:327 , ASN B:450 , HIS B:451 , HOH B:2264 , HOH B:2353 , HOH B:2596
BINDING SITE FOR RESIDUE EDO B1888
24
FC2
SOFTWARE
ARG B:602 , LYS B:778 , HOH B:2597
BINDING SITE FOR RESIDUE EDO B1889
25
FC3
SOFTWARE
ILE B:107 , LYS B:142 , HOH B:2066
BINDING SITE FOR RESIDUE BR B1890
26
FC4
SOFTWARE
GLN B:685 , ASP B:688
BINDING SITE FOR RESIDUE BR B1891
27
FC5
SOFTWARE
HOH B:2378
BINDING SITE FOR RESIDUE BR B1892
28
FC6
SOFTWARE
GLN B:108
BINDING SITE FOR RESIDUE CL B1893
29
FC7
SOFTWARE
ILE B:684 , GLN B:685 , HIS B:774 , EDO B:1882 , HOH B:2489
BINDING SITE FOR RESIDUE CL B1894
30
FC8
SOFTWARE
TYR B:347 , EDO B:1900 , HOH B:2276 , HOH B:2466 , HOH B:2468
BINDING SITE FOR RESIDUE EDO B1895
31
FC9
SOFTWARE
GLN B:230 , HOH B:2185 , HOH B:2190
BINDING SITE FOR RESIDUE CL B1896
32
GC2
SOFTWARE
TRP B:665 , TYR B:670 , ARG B:823 , TYR B:824 , HOH B:2480 , HOH B:2599
BINDING SITE FOR RESIDUE EDO B1897
33
GC3
SOFTWARE
TYR B:194 , GLY B:197 , TRP B:198 , TRP B:200 , GLY B:201 , ILE B:202 , SER B:650 , HOH B:2600
BINDING SITE FOR RESIDUE EDO B1898
34
GC4
SOFTWARE
MET B:298 , TRP B:302 , ASN B:351
BINDING SITE FOR RESIDUE CL B1899
35
GC7
SOFTWARE
ASP B:340 , LYS B:341 , ASP B:342 , PRO B:637 , EDO B:1895
BINDING SITE FOR RESIDUE EDO B1900
36
GC8
SOFTWARE
ARG B:376 , LEU B:380 , ASP B:383 , GLY B:663 , HOH B:2288 , HOH B:2602
BINDING SITE FOR RESIDUE EDO B1901
37
HC1
SOFTWARE
ASN B:337 , LYS B:339 , GLU B:344 , EDO B:1870 , HOH B:2603
BINDING SITE FOR RESIDUE EDO B1902
[
close Site info
]
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:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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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_d2vota4 (A:28-219)
1b: SCOP_d2votb4 (B:28-219)
2a: SCOP_d2vota1 (A:220-330)
2b: SCOP_d2vota2 (A:784-864)
2c: SCOP_d2vota3 (A:679-783)
2d: SCOP_d2votb1 (B:220-330)
2e: SCOP_d2votb2 (B:784-867)
2f: SCOP_d2votb3 (B:679-783)
3a: SCOP_d2vota5 (A:331-678)
3b: SCOP_d2votb5 (B:331-678)
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)
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)
Folds
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Superfamilies
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)
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)
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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
d2vota4
A:28-219
1b
d2votb4
B:28-219
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
d2vota1
A:220-330
2b
d2vota2
A:784-864
2c
d2vota3
A:679-783
2d
d2votb1
B:220-330
2e
d2votb2
B:784-867
2f
d2votb3
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
d2vota5
A:331-678
3b
d2votb5
B:331-678
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_2_N_2votB01 (B:28-219)
1b: PFAM_Glyco_hydro_2_N_2votB02 (B:28-219)
2a: PFAM_Glyco_hydro_2_C_2votB03 (B:345-478)
2b: PFAM_Glyco_hydro_2_C_2votB04 (B:345-478)
3a: PFAM_Glyco_hydro_2_2votB05 (B:221-331)
3b: PFAM_Glyco_hydro_2_2votB06 (B:221-331)
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Clans
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Organisms
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Clan
:
GBD
(153)
Family
:
Glyco_hydro_2_N
(32)
Bacteroides thetaiotaomicron
(9)
1a
Glyco_hydro_2_N-2votB01
B:28-219
1b
Glyco_hydro_2_N-2votB02
B:28-219
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_2_C
(27)
Bacteroides thetaiotaomicron
(9)
2a
Glyco_hydro_2_C-2votB03
B:345-478
2b
Glyco_hydro_2_C-2votB04
B:345-478
Clan
:
no clan defined [family: Glyco_hydro_2]
(31)
Family
:
Glyco_hydro_2
(31)
Bacteroides thetaiotaomicron
(9)
3a
Glyco_hydro_2-2votB05
B:221-331
3b
Glyco_hydro_2-2votB06
B:221-331
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