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2VOT
Biol. Unit 1
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
[
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Hetero Components
(2, 26)
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
25
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
(33, 33)
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: DC2 (SOFTWARE)
27: DC3 (SOFTWARE)
28: EC9 (SOFTWARE)
29: GC1 (SOFTWARE)
30: GC5 (SOFTWARE)
31: GC6 (SOFTWARE)
32: GC9 (SOFTWARE)
33: HC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:198 , ASP A:199 , TRP A:200 , TRP A:395 , 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:1878 , HOH A:2533
BINDING SITE FOR RESIDUE NHV A1865
02
AC2
SOFTWARE
GLN A:365 , ASN A:648 , ASP A:649 , ILE A:659 , ASP A:660 , HOH A:2259
BINDING SITE FOR RESIDUE EDO A1866
03
AC3
SOFTWARE
TRP A:525 , SER A:530 , ASN A:532 , ASP A:548 , MET A:553 , HOH A:2368
BINDING SITE FOR RESIDUE EDO A1867
04
AC4
SOFTWARE
ILE A:328 , GLY A:329 , ARG A:449 , ASN A:450 , HIS A:451 , ALA A:452 , ARG A:507 , HOH A:2534
BINDING SITE FOR RESIDUE EDO A1868
05
AC5
SOFTWARE
ARG A:331 , ARG A:507 , HOH A:2534 , HOH A:2535 , HOH A:2536
BINDING SITE FOR RESIDUE EDO A1869
06
AC6
SOFTWARE
GLU A:465 , LYS A:468 , TYR A:469 , PRO A:514 , LEU A:516 , ALA A:517 , ASN A:518
BINDING SITE FOR RESIDUE EDO A1870
07
AC7
SOFTWARE
ILE A:578 , ARG A:597 , PRO A:607 , GLU A:608 , PHE A:613 , HOH A:2389
BINDING SITE FOR RESIDUE EDO A1871
08
AC8
SOFTWARE
ASN A:337 , VAL A:510 , TYR A:515 , EDO A:1892 , HOH A:2537 , HOH A:2538
BINDING SITE FOR RESIDUE EDO A1872
09
AC9
SOFTWARE
GLN A:623 , ARG A:626 , PHE A:775 , HOH A:2539 , HOH A:2540
BINDING SITE FOR RESIDUE EDO A1873
10
BC1
SOFTWARE
ARG A:634 , GLN A:686 , TYR A:693 , HOH A:2424 , HOH A:2541
BINDING SITE FOR RESIDUE EDO A1874
11
BC2
SOFTWARE
VAL A:442 , ARG A:446 , HOH A:2314 , HOH A:2542
BINDING SITE FOR RESIDUE EDO A1875
12
BC3
SOFTWARE
TYR A:824 , SER A:825 , ILE A:840 , HOH A:2278
BINDING SITE FOR RESIDUE EDO A1876
13
BC4
SOFTWARE
SER A:43 , GLN A:44 , GLY A:46 , THR A:47 , GLU A:48 , GLU A:90
BINDING SITE FOR RESIDUE EDO A1877
14
BC5
SOFTWARE
ASN A:178 , TRP A:198 , ASP A:199 , CYS A:424 , GLU A:462 , NHV A:1865
BINDING SITE FOR RESIDUE EDO A1878
15
BC6
SOFTWARE
GLU A:543 , GLN A:623 , GLY A:624
BINDING SITE FOR RESIDUE EDO A1879
16
BC7
SOFTWARE
ASP A:88 , HIS A:157 , ARG A:161 , EDO A:1884 , EDO B:1871
BINDING SITE FOR RESIDUE EDO A1880
17
BC8
SOFTWARE
HIS A:326 , ARG A:327 , ASN A:450 , HIS A:451 , HOH A:2236 , HOH A:2321
BINDING SITE FOR RESIDUE EDO A1881
18
BC9
SOFTWARE
PRO A:212 , ASN A:402 , EDO A:1891 , HOH A:2290 , HOH A:2543
BINDING SITE FOR RESIDUE EDO A1882
19
CC1
SOFTWARE
SER A:43 , GLN A:44 , THR A:47 , LYS A:49 , MET A:51 , LEU A:68
BINDING SITE FOR RESIDUE EDO A1883
20
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
21
CC3
SOFTWARE
TRP A:470 , ASN A:518 , TRP A:519
BINDING SITE FOR RESIDUE EDO A1885
22
CC4
SOFTWARE
ILE A:107
BINDING SITE FOR RESIDUE BR A1886
23
CC5
SOFTWARE
HIS A:284
BINDING SITE FOR RESIDUE BR A1887
24
CC6
SOFTWARE
GLN A:108 , HOH A:2175
BINDING SITE FOR RESIDUE BR A1888
25
CC7
SOFTWARE
GLN A:685 , ASP A:688
BINDING SITE FOR RESIDUE BR A1889
26
DC2
SOFTWARE
EDO A:1880 , ASP B:88 , HIS B:157 , GLN B:162 , EDO B:1887
BINDING SITE FOR RESIDUE EDO B1871
27
DC3
SOFTWARE
THR A:432 , HOH A:2069 , LEU B:126 , HOH B:2086
BINDING SITE FOR RESIDUE EDO B1872
28
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
29
GC1
SOFTWARE
ASN A:300 , TRP A:302 , PHE A:356 , LYS A:358 , ASN A:390 , ASP A:697 , HOH A:2258 , HOH A:2474
BINDING SITE FOR RESIDUE EDO A1890
30
GC5
SOFTWARE
PRO A:370 , VAL A:372 , ASN A:402 , LEU A:404 , EDO A:1882 , HOH A:2544
BINDING SITE FOR RESIDUE EDO A1891
31
GC6
SOFTWARE
ASN A:337 , LYS A:339 , GLU A:344 , EDO A:1872
BINDING SITE FOR RESIDUE EDO A1892
32
GC9
SOFTWARE
GLU A:243 , LEU A:244 , ILE A:245 , HIS A:284 , ILE A:285 , THR A:286 , HOH A:2545
BINDING SITE FOR RESIDUE EDO A1893
33
HC2
SOFTWARE
GLU A:708 , LYS A:710 , LYS A:758 , ILE A:760
BINDING SITE FOR RESIDUE EDO A1894
[
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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
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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)
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
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
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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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