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2VQT
Biol. Unit 1
Info
Asym.Unit (309 KB)
Biol.Unit 1 (155 KB)
Biol.Unit 2 (154 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
:
18 Mar 08 (Deposition) - 08 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Linear Free Energy Relationship, Transition State Mimic, Hydrolase, 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, 20)
Info
All Hetero Components
1a: (2Z,3R,4S,5R,6R)-2-[(2-AMINOETHYL)... (15Aa)
1b: (2Z,3R,4S,5R,6R)-2-[(2-AMINOETHYL)... (15Ab)
2a: BROMIDE ION (BRa)
2b: BROMIDE ION (BRb)
2c: BROMIDE ION (BRc)
2d: BROMIDE ION (BRd)
2e: BROMIDE ION (BRe)
2f: BROMIDE ION (BRf)
2g: BROMIDE ION (BRg)
2h: BROMIDE ION (BRh)
2i: BROMIDE ION (BRi)
2j: BROMIDE ION (BRj)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
3e: CHLORIDE ION (CLe)
3f: CHLORIDE ION (CLf)
3g: CHLORIDE ION (CLg)
3h: CHLORIDE ION (CLh)
3i: CHLORIDE ION (CLi)
3j: CHLORIDE ION (CLj)
3k: CHLORIDE ION (CLk)
3l: CHLORIDE ION (CLl)
3m: CHLORIDE ION (CLm)
4a: 1,2-ETHANEDIOL (EDOa)
4aa: 1,2-ETHANEDIOL (EDOaa)
4ab: 1,2-ETHANEDIOL (EDOab)
4ac: 1,2-ETHANEDIOL (EDOac)
4ad: 1,2-ETHANEDIOL (EDOad)
4ae: 1,2-ETHANEDIOL (EDOae)
4af: 1,2-ETHANEDIOL (EDOaf)
4ag: 1,2-ETHANEDIOL (EDOag)
4ah: 1,2-ETHANEDIOL (EDOah)
4ai: 1,2-ETHANEDIOL (EDOai)
4aj: 1,2-ETHANEDIOL (EDOaj)
4ak: 1,2-ETHANEDIOL (EDOak)
4al: 1,2-ETHANEDIOL (EDOal)
4am: 1,2-ETHANEDIOL (EDOam)
4an: 1,2-ETHANEDIOL (EDOan)
4ao: 1,2-ETHANEDIOL (EDOao)
4ap: 1,2-ETHANEDIOL (EDOap)
4aq: 1,2-ETHANEDIOL (EDOaq)
4ar: 1,2-ETHANEDIOL (EDOar)
4as: 1,2-ETHANEDIOL (EDOas)
4b: 1,2-ETHANEDIOL (EDOb)
4c: 1,2-ETHANEDIOL (EDOc)
4d: 1,2-ETHANEDIOL (EDOd)
4e: 1,2-ETHANEDIOL (EDOe)
4f: 1,2-ETHANEDIOL (EDOf)
4g: 1,2-ETHANEDIOL (EDOg)
4h: 1,2-ETHANEDIOL (EDOh)
4i: 1,2-ETHANEDIOL (EDOi)
4j: 1,2-ETHANEDIOL (EDOj)
4k: 1,2-ETHANEDIOL (EDOk)
4l: 1,2-ETHANEDIOL (EDOl)
4m: 1,2-ETHANEDIOL (EDOm)
4n: 1,2-ETHANEDIOL (EDOn)
4o: 1,2-ETHANEDIOL (EDOo)
4p: 1,2-ETHANEDIOL (EDOp)
4q: 1,2-ETHANEDIOL (EDOq)
4r: 1,2-ETHANEDIOL (EDOr)
4s: 1,2-ETHANEDIOL (EDOs)
4t: 1,2-ETHANEDIOL (EDOt)
4u: 1,2-ETHANEDIOL (EDOu)
4v: 1,2-ETHANEDIOL (EDOv)
4w: 1,2-ETHANEDIOL (EDOw)
4x: 1,2-ETHANEDIOL (EDOx)
4y: 1,2-ETHANEDIOL (EDOy)
4z: 1,2-ETHANEDIOL (EDOz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
15A
1
Ligand/Ion
(2Z,3R,4S,5R,6R)-2-[(2-AMINOETHYL)IMINO]-6-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL
2
BR
-1
Ligand/Ion
BROMIDE ION
3
CL
-1
Ligand/Ion
CHLORIDE ION
4
EDO
19
Ligand/Ion
1,2-ETHANEDIOL
[
close Hetero Component info
]
Sites
(34, 34)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC3 (SOFTWARE)
10: BC4 (SOFTWARE)
11: BC5 (SOFTWARE)
12: BC6 (SOFTWARE)
13: CC1 (SOFTWARE)
14: CC3 (SOFTWARE)
15: CC4 (SOFTWARE)
16: CC9 (SOFTWARE)
17: DC3 (SOFTWARE)
18: DC6 (SOFTWARE)
19: DC8 (SOFTWARE)
20: DC9 (SOFTWARE)
21: EC2 (SOFTWARE)
22: EC3 (SOFTWARE)
23: EC5 (SOFTWARE)
24: EC7 (SOFTWARE)
25: FC1 (SOFTWARE)
26: FC2 (SOFTWARE)
27: FC6 (SOFTWARE)
28: GC1 (SOFTWARE)
29: GC3 (SOFTWARE)
30: GC4 (SOFTWARE)
31: GC5 (SOFTWARE)
32: GC9 (SOFTWARE)
33: HC2 (SOFTWARE)
34: HC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
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 , HOH A:2471
BINDING SITE FOR RESIDUE 15A A1865
02
AC3
SOFTWARE
GLN A:365 , ASN A:648 , ASP A:649 , ILE A:659 , ASP A:660 , HOH A:2223
BINDING SITE FOR RESIDUE EDO A1866
03
AC5
SOFTWARE
TRP A:525 , SER A:530 , ASN A:532 , ASP A:548 , LEU A:549 , PRO A:550 , MET A:553 , HOH A:2316
BINDING SITE FOR RESIDUE EDO A1867
04
AC6
SOFTWARE
ILE A:328 , GLY A:329 , ARG A:449 , ASN A:450 , HIS A:451 , ALA A:452 , ARG A:507 , HOH A:2137
BINDING SITE FOR RESIDUE EDO A1868
05
AC7
SOFTWARE
ARG A:331 , ASP A:506 , ARG A:507 , HOH A:2472 , HOH A:2473
BINDING SITE FOR RESIDUE EDO A1869
06
AC8
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
AC9
SOFTWARE
ARG A:597 , PRO A:607 , GLU A:608 , SER A:609 , PHE A:610 , PHE A:613 , HOH A:2342
BINDING SITE FOR RESIDUE EDO A1871
08
BC1
SOFTWARE
ASN A:337 , HIS A:511 , TYR A:515 , HOH A:2209 , HOH A:2474
BINDING SITE FOR RESIDUE EDO A1872
09
BC3
SOFTWARE
HIS A:157 , ASP B:88 , HIS B:157 , ARG B:161 , GLN B:162 , HOH B:2447
BINDING SITE FOR RESIDUE EDO B1870
10
BC4
SOFTWARE
GLN A:623 , ARG A:626 , HIS A:774 , PHE A:775 , HOH A:2438 , HOH A:2475
BINDING SITE FOR RESIDUE EDO A1873
11
BC5
SOFTWARE
THR A:432 , HOH A:2262 , LEU B:126 , LYS B:129
BINDING SITE FOR RESIDUE EDO B1871
12
BC6
SOFTWARE
ARG A:446 , HOH A:2061 , HOH A:2265
BINDING SITE FOR RESIDUE EDO A1874
13
CC1
SOFTWARE
TYR A:824 , SER A:825 , ILE A:840 , THR A:842 , HOH A:2228 , HOH A:2455
BINDING SITE FOR RESIDUE EDO A1875
14
CC3
SOFTWARE
SER A:43 , GLN A:44 , GLY A:46 , THR A:47 , GLU A:48 , GLU A:90
BINDING SITE FOR RESIDUE EDO A1876
15
CC4
SOFTWARE
SER A:224 , ILE A:245 , ARG A:446
BINDING SITE FOR RESIDUE EDO A1877
16
CC9
SOFTWARE
HIS A:326 , ARG A:327 , ASN A:450 , HIS A:451 , HOH A:2272
BINDING SITE FOR RESIDUE EDO A1878
17
DC3
SOFTWARE
ARG A:161 , GLN A:162 , ASP B:119 , TYR B:121 , TYR B:155 , HIS B:157
BINDING SITE FOR RESIDUE EDO A1879
18
DC6
SOFTWARE
ASP A:603 , TYR A:604 , LYS A:778 , THR A:779
BINDING SITE FOR RESIDUE EDO A1880
19
DC8
SOFTWARE
SER A:43 , GLN A:44 , THR A:47 , LYS A:49
BINDING SITE FOR RESIDUE EDO A1881
20
DC9
SOFTWARE
ILE A:107 , LYS A:142
BINDING SITE FOR RESIDUE BR A1882
21
EC2
SOFTWARE
HIS A:284
BINDING SITE FOR RESIDUE BR A1883
22
EC3
SOFTWARE
HOH A:2474
BINDING SITE FOR RESIDUE BR A1896
23
EC5
SOFTWARE
GLN A:108
BINDING SITE FOR RESIDUE BR A1884
24
EC7
SOFTWARE
ASP A:688
BINDING SITE FOR RESIDUE BR A1885
25
FC1
SOFTWARE
ILE A:684 , GLN A:685 , HIS A:774 , HOH A:2396
BINDING SITE FOR RESIDUE CL A1886
26
FC2
SOFTWARE
ASN A:402 , HOH A:2017
BINDING SITE FOR RESIDUE CL A1887
27
FC6
SOFTWARE
PHE A:346 , ARG A:551 , HOH A:2377
BINDING SITE FOR RESIDUE CL A1888
28
GC1
SOFTWARE
ASN A:337
BINDING SITE FOR RESIDUE CL A1889
29
GC3
SOFTWARE
ASN A:300 , TRP A:302 , PHE A:356 , ASN A:390 , ASP A:697 , HOH A:2212
BINDING SITE FOR RESIDUE EDO A1890
30
GC4
SOFTWARE
GLU A:502
BINDING SITE FOR RESIDUE EDO A1891
31
GC5
SOFTWARE
THR A:477
BINDING SITE FOR RESIDUE CL A1892
32
GC9
SOFTWARE
GLU A:708 , LYS A:710 , ILE A:760
BINDING SITE FOR RESIDUE EDO A1893
33
HC2
SOFTWARE
LYS A:129 , HIS A:157 , LYS B:129 , HIS B:157
BINDING SITE FOR RESIDUE BR A1894
34
HC4
SOFTWARE
ARG A:634 , TYR A:693 , HOH A:2125 , HOH A:2375
BINDING SITE FOR RESIDUE CL A1895
[
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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_d2vqta4 (A:28-219)
1b: SCOP_d2vqtb4 (B:28-219)
2a: SCOP_d2vqta1 (A:220-330)
2b: SCOP_d2vqta2 (A:784-864)
2c: SCOP_d2vqta3 (A:679-783)
2d: SCOP_d2vqtb1 (B:220-330)
2e: SCOP_d2vqtb2 (B:784-866)
2f: SCOP_d2vqtb3 (B:679-783)
3a: SCOP_d2vqta5 (A:331-678)
3b: SCOP_d2vqtb5 (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: 818]
(1)
1a
d2vqta4
A:28-219
1b
d2vqtb4
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: 818]
(1)
2a
d2vqta1
A:220-330
2b
d2vqta2
A:784-864
2c
d2vqta3
A:679-783
2d
d2vqtb1
B:220-330
2e
d2vqtb2
B:784-866
2f
d2vqtb3
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: 818]
(1)
3a
d2vqta5
A:331-678
3b
d2vqtb5
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_2vqtB01 (B:28-219)
1b: PFAM_Glyco_hydro_2_N_2vqtB02 (B:28-219)
2a: PFAM_Glyco_hydro_2_C_2vqtB03 (B:345-478)
2b: PFAM_Glyco_hydro_2_C_2vqtB04 (B:345-478)
3a: PFAM_Glyco_hydro_2_2vqtB05 (B:221-331)
3b: PFAM_Glyco_hydro_2_2vqtB06 (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-2vqtB01
B:28-219
1b
Glyco_hydro_2_N-2vqtB02
B:28-219
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_2_C
(27)
Bacteroides thetaiotaomicron
(9)
2a
Glyco_hydro_2_C-2vqtB03
B:345-478
2b
Glyco_hydro_2_C-2vqtB04
B:345-478
Clan
:
no clan defined [family: Glyco_hydro_2]
(31)
Family
:
Glyco_hydro_2
(31)
Bacteroides thetaiotaomicron
(9)
3a
Glyco_hydro_2-2vqtB05
B:221-331
3b
Glyco_hydro_2-2vqtB06
B:221-331
[
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]
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