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2VQU
Biol. Unit 1
Info
Asym.Unit (317 KB)
Biol.Unit 1 (159 KB)
Biol.Unit 2 (157 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) - 01 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Linear Free Energy Relationship, Transition State Mimic, Mannosidase, Glycoside Hydrolase, 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)
1i: BROMIDE ION (BRi)
1j: BROMIDE ION (BRj)
1k: BROMIDE ION (BRk)
1l: BROMIDE ION (BRl)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
2h: CHLORIDE ION (CLh)
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)
3ba: 1,2-ETHANEDIOL (EDOba)
3bb: 1,2-ETHANEDIOL (EDObb)
3bc: 1,2-ETHANEDIOL (EDObc)
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: (2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIP... (NOYa)
4b: (2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIP... (NOYb)
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
NOY
1
Ligand/Ion
(2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-2,3,4-TRIOL
[
close Hetero Component info
]
Sites
(41, 41)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC4 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC5 (SOFTWARE)
11: BC7 (SOFTWARE)
12: BC8 (SOFTWARE)
13: BC9 (SOFTWARE)
14: CC1 (SOFTWARE)
15: CC3 (SOFTWARE)
16: CC4 (SOFTWARE)
17: CC6 (SOFTWARE)
18: DC2 (SOFTWARE)
19: DC3 (SOFTWARE)
20: DC5 (SOFTWARE)
21: EC1 (SOFTWARE)
22: EC2 (SOFTWARE)
23: EC3 (SOFTWARE)
24: EC5 (SOFTWARE)
25: EC7 (SOFTWARE)
26: EC9 (SOFTWARE)
27: FC1 (SOFTWARE)
28: FC2 (SOFTWARE)
29: FC3 (SOFTWARE)
30: FC4 (SOFTWARE)
31: FC5 (SOFTWARE)
32: GC2 (SOFTWARE)
33: GC4 (SOFTWARE)
34: GC7 (SOFTWARE)
35: GC8 (SOFTWARE)
36: HC3 (SOFTWARE)
37: HC4 (SOFTWARE)
38: HC6 (SOFTWARE)
39: HC7 (SOFTWARE)
40: HC9 (SOFTWARE)
41: IC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:636 , MET A:640 , HOH A:2577
BINDING SITE FOR RESIDUE EDO A1865
02
AC3
SOFTWARE
TRP A:198 , ASP A:199 , TRP A:200 , TRP A:395 , ASN A:461 , GLU A:462 , TRP A:533 , TYR A:537 , GLU A:555 , TRP A:656 , HOH A:2470 , HOH A:2578
BINDING SITE FOR RESIDUE NOY A1866
03
AC4
SOFTWARE
ASN A:293 , PRO A:294 , GLY B:266 , THR B:267
BINDING SITE FOR RESIDUE EDO A1867
04
AC7
SOFTWARE
GLN A:365 , ASN A:648 , ASP A:649 , ILE A:659 , ASP A:660
BINDING SITE FOR RESIDUE EDO A1868
05
AC9
SOFTWARE
TRP A:525 , SER A:530 , ASN A:532 , ASP A:548 , LEU A:549 , PRO A:550 , MET A:553 , HOH A:2580
BINDING SITE FOR RESIDUE EDO A1869
06
BC1
SOFTWARE
ILE A:328 , GLY A:329 , ARG A:449 , ASN A:450 , HIS A:451 , ALA A:452 , ARG A:507 , HOH A:2186
BINDING SITE FOR RESIDUE EDO A1870
07
BC2
SOFTWARE
GLN A:230 , ARG A:331 , ASP A:506 , ARG A:507 , HOH A:2268 , HOH A:2581 , HOH A:2582
BINDING SITE FOR RESIDUE EDO A1871
08
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 A1872
09
BC4
SOFTWARE
ILE A:578 , PRO A:607 , PHE A:613 , HOH A:2583
BINDING SITE FOR RESIDUE EDO A1873
10
BC5
SOFTWARE
ASN A:337 , HIS A:511 , TYR A:515 , HOH A:2584 , HOH A:2585
BINDING SITE FOR RESIDUE EDO A1874
11
BC7
SOFTWARE
HIS A:157 , EDO A:1887 , ASP B:88 , HIS B:157 , ARG B:161 , GLN B:162 , EDO B:1887
BINDING SITE FOR RESIDUE EDO B1874
12
BC8
SOFTWARE
GLN A:623 , ARG A:626 , HIS A:774 , PHE A:775 , HOH A:2533 , HOH A:2586 , HOH A:2587
BINDING SITE FOR RESIDUE EDO A1875
13
BC9
SOFTWARE
THR A:432 , ARG A:436 , EDO A:1894 , LEU B:126
BINDING SITE FOR RESIDUE EDO B1875
14
CC1
SOFTWARE
TYR A:443 , ARG A:446 , HOH A:2343 , HOH A:2588
BINDING SITE FOR RESIDUE EDO A1876
15
CC3
SOFTWARE
TYR A:117 , ALA A:118 , ASP A:119 , LYS A:129 , ALA A:130 , HIS A:157 , EDO A:1894 , EDO A:1901 , HOH A:2590 , LYS B:129
BINDING SITE FOR RESIDUE EDO A1877
16
CC4
SOFTWARE
SER A:825 , ILE A:840 , THR A:842 , HOH A:2307
BINDING SITE FOR RESIDUE EDO A1878
17
CC6
SOFTWARE
SER A:43 , GLN A:44 , GLY A:46 , THR A:47 , GLU A:48 , GLU A:90
BINDING SITE FOR RESIDUE EDO A1879
18
DC2
SOFTWARE
ARG A:674 , SER A:772 , VAL A:773 , HOH A:2591 , HOH A:2592
BINDING SITE FOR RESIDUE EDO A1880
19
DC3
SOFTWARE
ASP A:603 , TYR A:604 , GLN A:623 , LYS A:778 , THR A:779
BINDING SITE FOR RESIDUE EDO A1881
20
DC5
SOFTWARE
SER A:43 , GLN A:44 , THR A:47 , LYS A:49 , MET A:51 , LEU A:68 , HOH A:2594
BINDING SITE FOR RESIDUE EDO A1882
21
EC1
SOFTWARE
ASP A:119 , TYR A:121 , TYR A:155 , ARG B:161 , GLN B:162 , PRO B:165 , EDO B:1874
BINDING SITE FOR RESIDUE EDO B1887
22
EC2
SOFTWARE
VAL A:372 , THR A:374 , TYR A:377 , ASN A:402 , HOH A:2595
BINDING SITE FOR RESIDUE EDO A1883
23
EC3
SOFTWARE
ILE A:107 , LYS A:142
BINDING SITE FOR RESIDUE BR A1884
24
EC5
SOFTWARE
HIS A:284
BINDING SITE FOR RESIDUE BR A1885
25
EC7
SOFTWARE
ASP A:88 , HIS A:157 , ARG A:161 , HOH A:2596 , EDO B:1874
BINDING SITE FOR RESIDUE EDO A1887
26
EC9
SOFTWARE
HIS A:627 , ILE A:684 , GLN A:685 , HOH A:2487
BINDING SITE FOR RESIDUE CL A1888
27
FC1
SOFTWARE
TRP A:519 , TYR A:537 , HOH A:2355 , HOH A:2597 , HOH A:2601
BINDING SITE FOR RESIDUE EDO A1889
28
FC2
SOFTWARE
PRO A:72 , PHE A:73 , TYR A:74 , GLY A:75 , MET A:76 , GLU A:78 , ALA A:585 , HIS A:586 , TRP A:651
BINDING SITE FOR RESIDUE EDO A1904
29
FC3
SOFTWARE
ASN A:402 , HOH A:2056 , HOH A:2070
BINDING SITE FOR RESIDUE BR A1891
30
FC4
SOFTWARE
ASN A:300 , ASN A:390
BINDING SITE FOR RESIDUE BR A1895
31
FC5
SOFTWARE
PHE A:476 , THR A:477
BINDING SITE FOR RESIDUE CL A1892
32
GC2
SOFTWARE
TYR A:117 , ASP A:131 , GLN A:162 , ARG A:436 , EDO A:1877 , HOH A:2598 , LEU B:126 , LYS B:129 , EDO B:1875
BINDING SITE FOR RESIDUE EDO A1894
33
GC4
SOFTWARE
GLN A:108
BINDING SITE FOR RESIDUE BR A1896
34
GC7
SOFTWARE
GLN A:685 , ASP A:688
BINDING SITE FOR RESIDUE BR A1897
35
GC8
SOFTWARE
ASN A:337 , LYS A:339
BINDING SITE FOR RESIDUE EDO B1900
36
HC3
SOFTWARE
HIS A:326 , HIS A:451 , HOH A:2264 , HOH A:2351
BINDING SITE FOR RESIDUE CL A1898
37
HC4
SOFTWARE
LYS A:540 , ASP A:548 , HOH A:2599 , HOH A:2600 , ASP B:340 , LYS B:341 , HOH B:2268
BINDING SITE FOR RESIDUE EDO A1899
38
HC6
SOFTWARE
TYR A:469 , ASN A:518 , TRP A:519 , GLY A:520 , HOH A:2601
BINDING SITE FOR RESIDUE EDO A1900
39
HC7
SOFTWARE
LYS A:129 , HIS A:157 , GLN A:162 , EDO A:1877 , HOH A:2602 , ASP B:119 , LYS B:129 , HIS B:157 , GLN B:162
BINDING SITE FOR RESIDUE EDO A1901
40
HC9
SOFTWARE
PRO A:786 , THR A:787 , HIS A:858 , ARG A:860
BINDING SITE FOR RESIDUE EDO A1902
41
IC3
SOFTWARE
HOH A:2579 , TRP B:519 , TRP B:533 , HOH B:2603
BINDING SITE FOR RESIDUE EDO A1903
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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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
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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_d2vqua4 (A:28-219)
1b: SCOP_d2vqub4 (B:28-219)
2a: SCOP_d2vqua1 (A:679-783)
2b: SCOP_d2vqub2 (B:220-330)
2c: SCOP_d2vqub3 (B:784-867)
2d: SCOP_d2vqua2 (A:220-330)
2e: SCOP_d2vqua3 (A:784-864)
2f: SCOP_d2vqub1 (B:679-783)
3a: SCOP_d2vqua5 (A:331-678)
3b: SCOP_d2vqub5 (B:331-678)
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(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Galactose-binding domain-like
(314)
Superfamily
:
Galactose-binding domain-like
(314)
Family
:
beta-Galactosidase/glucuronidase, N-terminal domain
(49)
Protein domain
:
Beta-mannosidase
(2)
Bacteroides thetaiotaomicron [TaxId: 818]
(2)
1a
d2vqua4
A:28-219
1b
d2vqub4
B:28-219
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
beta-Galactosidase/glucuronidase domain
(79)
Family
:
beta-Galactosidase/glucuronidase domain
(49)
Protein domain
:
Beta-mannosidase, domains 2, 4 and 5
(2)
Bacteroides thetaiotaomicron [TaxId: 818]
(2)
2a
d2vqua1
A:679-783
2b
d2vqub2
B:220-330
2c
d2vqub3
B:784-867
2d
d2vqua2
A:220-330
2e
d2vqua3
A:784-864
2f
d2vqub1
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
:
Five-domain beta-mannosidase, domain 3
(2)
Bacteroides thetaiotaomicron [TaxId: 818]
(2)
3a
d2vqua5
A:331-678
3b
d2vqub5
B:331-678
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
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Sorry, no Info available
[
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_2_N_2vquB01 (B:28-219)
1b: PFAM_Glyco_hydro_2_N_2vquB02 (B:28-219)
2a: PFAM_Glyco_hydro_2_C_2vquB03 (B:345-478)
2b: PFAM_Glyco_hydro_2_C_2vquB04 (B:345-478)
3a: PFAM_Glyco_hydro_2_2vquB05 (B:221-331)
3b: PFAM_Glyco_hydro_2_2vquB06 (B:221-331)
View:
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Clans
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Families
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(
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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-2vquB01
B:28-219
1b
Glyco_hydro_2_N-2vquB02
B:28-219
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_2_C
(27)
Bacteroides thetaiotaomicron
(9)
2a
Glyco_hydro_2_C-2vquB03
B:345-478
2b
Glyco_hydro_2_C-2vquB04
B:345-478
Clan
:
no clan defined [family: Glyco_hydro_2]
(31)
Family
:
Glyco_hydro_2
(31)
Bacteroides thetaiotaomicron
(9)
3a
Glyco_hydro_2-2vquB05
B:221-331
3b
Glyco_hydro_2-2vquB06
B:221-331
[
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]
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