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2VJX
Biol. Unit 1
Info
Asym.Unit (314 KB)
Biol.Unit 1 (158 KB)
Biol.Unit 2 (156 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
:
14 Dec 07 (Deposition) - 01 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
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. Moreland, 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, 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)
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)
2i: CHLORIDE ION (CLi)
2j: CHLORIDE ION (CLj)
2k: CHLORIDE ION (CLk)
2l: CHLORIDE ION (CLl)
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)
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: (3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROX... (IFLa)
4b: (3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROX... (IFLb)
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
IFL
1
Ligand/Ion
(3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-2-ONE
[
close Hetero Component info
]
Sites
(40, 40)
Info
All Sites
01: AC1 (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: BC7 (SOFTWARE)
14: BC9 (SOFTWARE)
15: CC2 (SOFTWARE)
16: CC4 (SOFTWARE)
17: CC5 (SOFTWARE)
18: CC9 (SOFTWARE)
19: DC1 (SOFTWARE)
20: DC2 (SOFTWARE)
21: DC3 (SOFTWARE)
22: DC5 (SOFTWARE)
23: DC6 (SOFTWARE)
24: DC7 (SOFTWARE)
25: DC9 (SOFTWARE)
26: EC3 (SOFTWARE)
27: EC6 (SOFTWARE)
28: EC8 (SOFTWARE)
29: EC9 (SOFTWARE)
30: FC1 (SOFTWARE)
31: FC3 (SOFTWARE)
32: FC4 (SOFTWARE)
33: FC5 (SOFTWARE)
34: FC9 (SOFTWARE)
35: GC1 (SOFTWARE)
36: GC2 (SOFTWARE)
37: GC6 (SOFTWARE)
38: GC7 (SOFTWARE)
39: GC8 (SOFTWARE)
40: HC3 (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:533 , TYR A:537 , GLU A:555 , TRP A:645 , TRP A:656 , EDO A:1879
BINDING SITE FOR RESIDUE IFL A1865
02
AC3
SOFTWARE
GLN A:365 , ASN A:648 , ASP A:649 , ILE A:659 , ASP A:660
BINDING SITE FOR RESIDUE EDO A1866
03
AC5
SOFTWARE
TRP A:519 , TRP A:525 , SER A:530 , ASN A:532 , ASP A:548 , LEU A:549 , PRO A:550 , MET A:553 , HOH A:2618
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:2619
BINDING SITE FOR RESIDUE EDO A1868
05
AC7
SOFTWARE
ARG A:331 , ARG A:507 , HOH A:2267 , HOH A:2619 , HOH A:2620
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:613 , HOH A:2621 , HOH A:2622
BINDING SITE FOR RESIDUE EDO A1871
08
BC1
SOFTWARE
ASN A:337 , TYR A:515 , HOH A:2623 , HOH A:2624
BINDING SITE FOR RESIDUE EDO A1872
09
BC3
SOFTWARE
TYR A:155 , HIS A:157 , ASP B:88 , HIS B:157 , GLN B:162 , EDO B:1885
BINDING SITE FOR RESIDUE EDO B1870
10
BC4
SOFTWARE
GLN A:623 , ARG A:626 , HIS A:774 , PHE A:775 , HOH A:2556 , HOH A:2625 , HOH A:2626
BINDING SITE FOR RESIDUE EDO A1873
11
BC5
SOFTWARE
THR A:432 , HOH A:2093 , LEU B:126 , LEU B:127 , LYS B:129
BINDING SITE FOR RESIDUE EDO B1871
12
BC6
SOFTWARE
ARG A:634 , ASN A:635 , TYR A:693 , HOH A:2627
BINDING SITE FOR RESIDUE EDO A1874
13
BC7
SOFTWARE
VAL A:442 , ARG A:446 , HOH A:2342
BINDING SITE FOR RESIDUE EDO A1875
14
BC9
SOFTWARE
TYR A:117 , ALA A:118 , ASP A:119 , LYS A:129 , ALA A:130 , HIS A:157 , BR A:1893 , HOH A:2628 , HOH A:2629 , LYS B:129
BINDING SITE FOR RESIDUE EDO A1876
15
CC2
SOFTWARE
ARG A:382 , ILE A:840 , HOH A:2305 , HOH A:2599
BINDING SITE FOR RESIDUE EDO A1877
16
CC4
SOFTWARE
SER A:43 , GLN A:44 , GLY A:46 , THR A:47 , GLU A:48 , GLU A:90
BINDING SITE FOR RESIDUE EDO A1878
17
CC5
SOFTWARE
ASN A:178 , ASP A:199 , CYS A:424 , GLU A:462 , TRP A:470 , IFL A:1865
BINDING SITE FOR RESIDUE EDO A1879
18
CC9
SOFTWARE
ASP A:88 , HIS A:157 , GLN A:162 , EDO A:1888 , TYR B:155 , HIS B:157
BINDING SITE FOR RESIDUE EDO A1880
19
DC1
SOFTWARE
PHE A:775 , ARG A:777 , CL A:1896
BINDING SITE FOR RESIDUE EDO A1881
20
DC2
SOFTWARE
HIS A:326 , ARG A:327 , ASN A:450 , HIS A:451 , HOH A:2262 , HOH A:2349
BINDING SITE FOR RESIDUE EDO A1882
21
DC3
SOFTWARE
TYR A:74 , ALA A:568 , ALA A:571 , ALA A:572 , PRO A:573 , TYR A:576
BINDING SITE FOR RESIDUE EDO A1883
22
DC5
SOFTWARE
ARG A:626 , GLN A:671 , ARG A:674 , SER A:772 , VAL A:773
BINDING SITE FOR RESIDUE EDO A1884
23
DC6
SOFTWARE
ARG A:211 , PRO A:212 , ASN A:402 , HOH A:2077 , HOH A:2168 , HOH A:2631
BINDING SITE FOR RESIDUE EDO A1885
24
DC7
SOFTWARE
ASP A:603 , TYR A:604 , LYS A:778 , THR A:779 , EDO A:1890
BINDING SITE FOR RESIDUE EDO A1886
25
DC9
SOFTWARE
PHE A:42 , SER A:43 , GLN A:44 , THR A:47 , LYS A:49 , MET A:51 , LEU A:63
BINDING SITE FOR RESIDUE EDO A1887
26
EC3
SOFTWARE
ARG A:161 , GLN A:162 , PRO A:165 , EDO A:1880 , ASP B:119 , TYR B:121 , TYR B:155
BINDING SITE FOR RESIDUE EDO A1888
27
EC6
SOFTWARE
ARG A:376 , TYR A:661 , TYR A:662 , HOH A:2633
BINDING SITE FOR RESIDUE EDO A1889
28
EC8
SOFTWARE
PHE A:542 , GLU A:543 , ASP A:603 , GLY A:624 , EDO A:1886 , HOH A:2481
BINDING SITE FOR RESIDUE EDO A1890
29
EC9
SOFTWARE
ASP A:119 , TYR A:121 , TYR A:155 , ARG B:161 , GLN B:162 , PRO B:165 , EDO B:1870
BINDING SITE FOR RESIDUE EDO B1885
30
FC1
SOFTWARE
ILE A:107 , LYS A:142 , HOH A:2068
BINDING SITE FOR RESIDUE BR A1891
31
FC3
SOFTWARE
HIS A:284
BINDING SITE FOR RESIDUE BR A1892
32
FC4
SOFTWARE
LYS A:129 , HIS A:157 , EDO A:1876 , LYS B:129 , HIS B:157 , GLN B:162
BINDING SITE FOR RESIDUE BR A1893
33
FC5
SOFTWARE
HOH A:2624
BINDING SITE FOR RESIDUE BR A1894
34
FC9
SOFTWARE
GLN A:108 , HOH A:2210
BINDING SITE FOR RESIDUE CL A1895
35
GC1
SOFTWARE
HIS A:627 , ILE A:684 , GLN A:685 , EDO A:1881 , HOH A:2516
BINDING SITE FOR RESIDUE CL A1896
36
GC2
SOFTWARE
GLN A:685 , ASP A:688
BINDING SITE FOR RESIDUE CL A1897
37
GC6
SOFTWARE
ASN A:337
BINDING SITE FOR RESIDUE CL A1901
38
GC7
SOFTWARE
PRO A:786 , THR A:787 , GLU A:861 , HOH A:2613
BINDING SITE FOR RESIDUE CL A1898
39
GC8
SOFTWARE
ASN A:300 , ASN A:390
BINDING SITE FOR RESIDUE BR A1899
40
HC3
SOFTWARE
PHE A:476 , THR A:477
BINDING SITE FOR RESIDUE CL A1900
[
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
[
close SNP/Variant info
]
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:
Select:
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 10)
Info
All SCOP Domains
1a: SCOP_d2vjxa4 (A:28-219)
1b: SCOP_d2vjxb4 (B:28-219)
2a: SCOP_d2vjxa1 (A:220-330)
2b: SCOP_d2vjxa2 (A:784-864)
2c: SCOP_d2vjxa3 (A:679-783)
2d: SCOP_d2vjxb1 (B:220-330)
2e: SCOP_d2vjxb2 (B:784-866)
2f: SCOP_d2vjxb3 (B:679-783)
3a: SCOP_d2vjxa5 (A:331-678)
3b: SCOP_d2vjxb5 (B:331-678)
View:
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Classes
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)
(
)
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
d2vjxa4
A:28-219
1b
d2vjxb4
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
d2vjxa1
A:220-330
2b
d2vjxa2
A:784-864
2c
d2vjxa3
A:679-783
2d
d2vjxb1
B:220-330
2e
d2vjxb2
B:784-866
2f
d2vjxb3
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
d2vjxa5
A:331-678
3b
d2vjxb5
B:331-678
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_2_N_2vjxB01 (B:28-219)
1b: PFAM_Glyco_hydro_2_N_2vjxB02 (B:28-219)
2a: PFAM_Glyco_hydro_2_C_2vjxB03 (B:345-478)
2b: PFAM_Glyco_hydro_2_C_2vjxB04 (B:345-478)
3a: PFAM_Glyco_hydro_2_2vjxB05 (B:221-331)
3b: PFAM_Glyco_hydro_2_2vjxB06 (B:221-331)
View:
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Clans
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Families
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(
)
Organisms
(
)
(
)
Clan
:
GBD
(153)
Family
:
Glyco_hydro_2_N
(32)
Bacteroides thetaiotaomicron
(9)
1a
Glyco_hydro_2_N-2vjxB01
B:28-219
1b
Glyco_hydro_2_N-2vjxB02
B:28-219
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_2_C
(27)
Bacteroides thetaiotaomicron
(9)
2a
Glyco_hydro_2_C-2vjxB03
B:345-478
2b
Glyco_hydro_2_C-2vjxB04
B:345-478
Clan
:
no clan defined [family: Glyco_hydro_2]
(31)
Family
:
Glyco_hydro_2
(31)
Bacteroides thetaiotaomicron
(9)
3a
Glyco_hydro_2-2vjxB05
B:221-331
3b
Glyco_hydro_2-2vjxB06
B:221-331
[
close Pfam info
]
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