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2VL4
Biol. Unit 1
Info
Asym.Unit (318 KB)
Biol.Unit 1 (158 KB)
Biol.Unit 2 (159 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
:
08 Jan 08 (Deposition) - 01 Apr 08 (Release) - 17 Nov 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, 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, 16)
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)
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)
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: (2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-H... (MNMa)
4b: (2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-H... (MNMb)
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
15
Ligand/Ion
1,2-ETHANEDIOL
4
MNM
1
Ligand/Ion
(2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-HYDROXYMETHYL-PIPERIDINE
[
close Hetero Component info
]
Sites
(28, 28)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC8 (SOFTWARE)
04: AC9 (SOFTWARE)
05: BC3 (SOFTWARE)
06: BC6 (SOFTWARE)
07: BC7 (SOFTWARE)
08: CC1 (SOFTWARE)
09: CC2 (SOFTWARE)
10: CC4 (SOFTWARE)
11: CC5 (SOFTWARE)
12: CC8 (SOFTWARE)
13: DC1 (SOFTWARE)
14: DC2 (SOFTWARE)
15: DC3 (SOFTWARE)
16: DC4 (SOFTWARE)
17: DC6 (SOFTWARE)
18: DC8 (SOFTWARE)
19: EC1 (SOFTWARE)
20: EC2 (SOFTWARE)
21: EC4 (SOFTWARE)
22: EC5 (SOFTWARE)
23: EC6 (SOFTWARE)
24: EC7 (SOFTWARE)
25: FC1 (SOFTWARE)
26: FC2 (SOFTWARE)
27: FC7 (SOFTWARE)
28: FC9 (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 , EDO A:1866
BINDING SITE FOR RESIDUE MNM A1865
02
AC3
SOFTWARE
ASN A:178 , ASP A:199 , CYS A:424 , GLU A:462 , TRP A:470 , MNM A:1865
BINDING SITE FOR RESIDUE EDO A1866
03
AC8
SOFTWARE
ILE A:328 , GLY A:329 , ARG A:449 , ASN A:450 , HIS A:451 , ALA A:452 , ARG A:507 , HOH A:2693
BINDING SITE FOR RESIDUE EDO A1867
04
AC9
SOFTWARE
GLN A:365 , ASN A:648 , ASP A:649 , ILE A:659 , ASP A:660
BINDING SITE FOR RESIDUE EDO A1868
05
BC3
SOFTWARE
SER A:43 , GLN A:44 , THR A:47 , LYS A:49 , HOH A:2689
BINDING SITE FOR RESIDUE EDO A1869
06
BC6
SOFTWARE
ARG A:597 , PRO A:607 , GLU A:608 , HOH A:2690
BINDING SITE FOR RESIDUE EDO A1870
07
BC7
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 A1871
08
CC1
SOFTWARE
TRP A:525 , SER A:530 , ASN A:532 , ASP A:548 , LEU A:549 , PRO A:550 , MET A:553 , HOH A:2473
BINDING SITE FOR RESIDUE EDO A1872
09
CC2
SOFTWARE
ARG A:331 , ARG A:507 , HOH A:2691 , HOH A:2692 , HOH A:2693
BINDING SITE FOR RESIDUE EDO A1873
10
CC4
SOFTWARE
HIS A:157 , ARG A:161 , ASP B:88 , HIS B:157 , GLN B:162 , HOH B:2751
BINDING SITE FOR RESIDUE EDO B1880
11
CC5
SOFTWARE
SER A:43 , GLN A:44 , SER A:45 , GLY A:46 , THR A:47 , GLU A:48 , GLU A:90
BINDING SITE FOR RESIDUE EDO A1874
12
CC8
SOFTWARE
GLN A:685 , PHE A:775 , PHE A:776 , ARG A:777 , LYS A:778 , HOH A:2694
BINDING SITE FOR RESIDUE EDO A1875
13
DC1
SOFTWARE
ASN A:300 , TRP A:302 , PHE A:356 , ASN A:390 , ASP A:697 , HOH A:2345 , HOH A:2609
BINDING SITE FOR RESIDUE EDO A1876
14
DC2
SOFTWARE
HIS A:326 , ARG A:327 , ASN A:450 , HIS A:451 , HOH A:2318 , HOH A:2418
BINDING SITE FOR RESIDUE EDO A1877
15
DC3
SOFTWARE
ILE A:107 , LYS A:142
BINDING SITE FOR RESIDUE BR A1878
16
DC4
SOFTWARE
HIS A:284
BINDING SITE FOR RESIDUE BR A1879
17
DC6
SOFTWARE
HIS A:627 , ILE A:684 , GLN A:685 , HIS A:774 , HOH A:2579
BINDING SITE FOR RESIDUE BR A1880
18
DC8
SOFTWARE
HOH A:2458
BINDING SITE FOR RESIDUE BR A1881
19
EC1
SOFTWARE
GLN A:108
BINDING SITE FOR RESIDUE BR A1882
20
EC2
SOFTWARE
GLN A:685 , ASP A:688
BINDING SITE FOR RESIDUE BR A1883
21
EC4
SOFTWARE
TRP A:519 , HOH A:2695 , HOH A:2696 , HOH A:2697
BINDING SITE FOR RESIDUE EDO A1884
22
EC5
SOFTWARE
ASN A:77 , HOH A:2044
BINDING SITE FOR RESIDUE CL A1889
23
EC6
SOFTWARE
ALA A:168 , ARG B:92 , TYR B:153 , HOH B:2753 , HOH B:2754
BINDING SITE FOR RESIDUE EDO B1888
24
EC7
SOFTWARE
ASN A:402 , HOH A:2041
BINDING SITE FOR RESIDUE CL A1885
25
FC1
SOFTWARE
PHE A:476 , THR A:477 , HOH A:2430
BINDING SITE FOR RESIDUE BR A1886
26
FC2
SOFTWARE
ASN A:293 , HOH A:2224 , HOH A:2698 , GLY B:266 , THR B:267
BINDING SITE FOR RESIDUE EDO A1887
27
FC7
SOFTWARE
HIS A:774 , PHE A:775 , HOH A:2634 , HOH A:2699 , HOH A:2700
BINDING SITE FOR RESIDUE EDO A1888
28
FC9
SOFTWARE
HOH A:2353 , ASP B:797
BINDING SITE FOR RESIDUE CL B1896
[
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_d2vl4a4 (A:28-219)
1b: SCOP_d2vl4b4 (B:27-219)
2a: SCOP_d2vl4a1 (A:220-330)
2b: SCOP_d2vl4a2 (A:784-864)
2c: SCOP_d2vl4a3 (A:679-783)
2d: SCOP_d2vl4b1 (B:220-330)
2e: SCOP_d2vl4b2 (B:784-867)
2f: SCOP_d2vl4b3 (B:679-783)
3a: SCOP_d2vl4a5 (A:331-678)
3b: SCOP_d2vl4b5 (B:331-678)
View:
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Label:
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
d2vl4a4
A:28-219
1b
d2vl4b4
B:27-219
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
d2vl4a1
A:220-330
2b
d2vl4a2
A:784-864
2c
d2vl4a3
A:679-783
2d
d2vl4b1
B:220-330
2e
d2vl4b2
B:784-867
2f
d2vl4b3
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
d2vl4a5
A:331-678
3b
d2vl4b5
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_2vl4B01 (B:28-219)
1b: PFAM_Glyco_hydro_2_N_2vl4B02 (B:28-219)
2a: PFAM_Glyco_hydro_2_C_2vl4B03 (B:345-478)
2b: PFAM_Glyco_hydro_2_C_2vl4B04 (B:345-478)
3a: PFAM_Glyco_hydro_2_2vl4B05 (B:221-331)
3b: PFAM_Glyco_hydro_2_2vl4B06 (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-2vl4B01
B:28-219
1b
Glyco_hydro_2_N-2vl4B02
B:28-219
Clan
:
Glyco_hydro_tim
(488)
Family
:
Glyco_hydro_2_C
(27)
Bacteroides thetaiotaomicron
(9)
2a
Glyco_hydro_2_C-2vl4B03
B:345-478
2b
Glyco_hydro_2_C-2vl4B04
B:345-478
Clan
:
no clan defined [family: Glyco_hydro_2]
(31)
Family
:
Glyco_hydro_2
(31)
Bacteroides thetaiotaomicron
(9)
3a
Glyco_hydro_2-2vl4B05
B:221-331
3b
Glyco_hydro_2-2vl4B06
B:221-331
[
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]
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Asym.Unit (318 KB)
Header - Asym.Unit
Biol.Unit 1 (158 KB)
Header - Biol.Unit 1
Biol.Unit 2 (159 KB)
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