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2VQT
Biol. Unit 2
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, 27)
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
26
Ligand/Ion
1,2-ETHANEDIOL
[
close Hetero Component info
]
Sites
(37, 37)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC4 (SOFTWARE)
03: BC2 (SOFTWARE)
04: BC3 (SOFTWARE)
05: BC5 (SOFTWARE)
06: BC7 (SOFTWARE)
07: BC8 (SOFTWARE)
08: BC9 (SOFTWARE)
09: CC2 (SOFTWARE)
10: CC5 (SOFTWARE)
11: CC6 (SOFTWARE)
12: CC7 (SOFTWARE)
13: CC8 (SOFTWARE)
14: DC1 (SOFTWARE)
15: DC2 (SOFTWARE)
16: DC3 (SOFTWARE)
17: DC4 (SOFTWARE)
18: DC5 (SOFTWARE)
19: DC7 (SOFTWARE)
20: EC1 (SOFTWARE)
21: EC4 (SOFTWARE)
22: EC6 (SOFTWARE)
23: EC8 (SOFTWARE)
24: EC9 (SOFTWARE)
25: FC3 (SOFTWARE)
26: FC4 (SOFTWARE)
27: FC5 (SOFTWARE)
28: FC7 (SOFTWARE)
29: FC8 (SOFTWARE)
30: FC9 (SOFTWARE)
31: GC2 (SOFTWARE)
32: GC6 (SOFTWARE)
33: GC7 (SOFTWARE)
34: GC8 (SOFTWARE)
35: HC1 (SOFTWARE)
36: HC2 (SOFTWARE)
37: HC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP B:198 , ASP B:199 , TRP B:200 , TRP B:395 , ASN B:461 , GLU B:462 , TRP B:470 , TRP B:533 , TYR B:537 , GLU B:555 , TRP B:645 , TRP B:656 , HOH B:2442 , HOH B:2443 , HOH B:2444
BINDING SITE FOR RESIDUE 15A B1867
02
AC4
SOFTWARE
TRP B:519 , TRP B:525 , SER B:530 , ASN B:532 , ASP B:548 , PRO B:550 , MET B:553 , HOH B:2445
BINDING SITE FOR RESIDUE EDO B1868
03
BC2
SOFTWARE
ASN B:337 , VAL B:510 , HIS B:511 , TYR B:515 , HOH B:2446
BINDING SITE FOR RESIDUE EDO B1869
04
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
05
BC5
SOFTWARE
THR A:432 , HOH A:2262 , LEU B:126 , LYS B:129
BINDING SITE FOR RESIDUE EDO B1871
06
BC7
SOFTWARE
SER B:43 , GLN B:44 , GLY B:46 , THR B:47 , GLU B:48 , GLU B:90
BINDING SITE FOR RESIDUE EDO B1872
07
BC8
SOFTWARE
HIS B:326 , ARG B:327 , ASN B:450 , HIS B:451 , HOH B:2257 , HOH B:2448
BINDING SITE FOR RESIDUE EDO B1873
08
BC9
SOFTWARE
GLY B:471 , PHE B:472 , GLU B:473 , LYS B:474 , HOH B:2449
BINDING SITE FOR RESIDUE EDO B1874
09
CC2
SOFTWARE
ARG B:331 , ARG B:507 , EDO B:1899 , HOH B:2450
BINDING SITE FOR RESIDUE EDO B1875
10
CC5
SOFTWARE
GLN B:365 , ASN B:648 , ASP B:649 , ILE B:659 , ASP B:660
BINDING SITE FOR RESIDUE EDO B1876
11
CC6
SOFTWARE
GLU B:465 , LYS B:468 , PRO B:514 , LEU B:516 , ALA B:517
BINDING SITE FOR RESIDUE EDO B1877
12
CC7
SOFTWARE
ASN B:300 , TRP B:302 , PHE B:356 , LYS B:358 , ASN B:390 , ASP B:697 , HOH B:2451
BINDING SITE FOR RESIDUE EDO B1878
13
CC8
SOFTWARE
GLN B:623 , ARG B:626 , HIS B:774 , PHE B:775 , EDO B:1882 , HOH B:2343 , HOH B:2345 , HOH B:2452
BINDING SITE FOR RESIDUE EDO B1879
14
DC1
SOFTWARE
PHE B:356 , ARG B:633 , ARG B:636 , ILE B:695 , SER B:696 , ASP B:697 , ASN B:733 , THR B:734
BINDING SITE FOR RESIDUE EDO B1880
15
DC2
SOFTWARE
PHE B:42 , SER B:43 , GLN B:44 , THR B:47 , LYS B:49
BINDING SITE FOR RESIDUE EDO B1881
16
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
17
DC4
SOFTWARE
PHE B:775 , ARG B:777 , LYS B:778 , EDO B:1879 , CL B:1889 , HOH B:2453
BINDING SITE FOR RESIDUE EDO B1882
18
DC5
SOFTWARE
ARG B:382 , ARG B:823 , SER B:825 , ILE B:840 , THR B:842 , HOH B:2454
BINDING SITE FOR RESIDUE EDO B1883
19
DC7
SOFTWARE
ILE B:328 , GLY B:329 , ARG B:449 , ASN B:450 , HIS B:451 , ALA B:452 , ARG B:507
BINDING SITE FOR RESIDUE EDO B1884
20
EC1
SOFTWARE
ILE B:107 , LYS B:142
BINDING SITE FOR RESIDUE BR B1885
21
EC4
SOFTWARE
GLN B:685 , ASP B:688
BINDING SITE FOR RESIDUE BR B1886
22
EC6
SOFTWARE
HOH B:2446
BINDING SITE FOR RESIDUE BR B1887
23
EC8
SOFTWARE
GLN B:108
BINDING SITE FOR RESIDUE CL B1888
24
EC9
SOFTWARE
ILE B:684 , GLN B:685 , HIS B:774 , EDO B:1882 , HOH B:2371
BINDING SITE FOR RESIDUE CL B1889
25
FC3
SOFTWARE
ARG B:845 , GLU B:850
BINDING SITE FOR RESIDUE EDO B1891
26
FC4
SOFTWARE
TYR B:347 , HOH B:2196 , HOH B:2353 , HOH B:2455
BINDING SITE FOR RESIDUE EDO B1892
27
FC5
SOFTWARE
GLU B:112 , GLY B:113 , MET B:133 , PHE B:134 , VAL B:135 , TRP B:210 , ARG B:211 , TYR B:443 , ASN B:444 , ARG B:447 , HOH B:2044 , HOH B:2457
BINDING SITE FOR RESIDUE EDO B1893
28
FC7
SOFTWARE
GLU B:271
BINDING SITE FOR RESIDUE BR B1894
29
FC8
SOFTWARE
TYR B:661 , TYR B:662
BINDING SITE FOR RESIDUE EDO B1895
30
FC9
SOFTWARE
ARG B:376 , LEU B:380 , ASP B:383 , GLY B:663 , HOH B:2205
BINDING SITE FOR RESIDUE EDO B1896
31
GC2
SOFTWARE
LYS B:147
BINDING SITE FOR RESIDUE CL A1898
32
GC6
SOFTWARE
TRP B:470 , ASN B:518 , HOH B:2288
BINDING SITE FOR RESIDUE CL B1898
33
GC7
SOFTWARE
GLN B:230 , THR B:332 , ASP B:506 , EDO B:1875 , HOH B:2458
BINDING SITE FOR RESIDUE EDO B1899
34
GC8
SOFTWARE
PRO B:541 , ARG B:602
BINDING SITE FOR RESIDUE EDO B1900
35
HC1
SOFTWARE
GLU B:708 , LYS B:710 , LYS B:758 , ILE B:760
BINDING SITE FOR RESIDUE EDO B1901
36
HC2
SOFTWARE
LYS A:129 , HIS A:157 , LYS B:129 , HIS B:157
BINDING SITE FOR RESIDUE BR A1894
37
HC3
SOFTWARE
LYS B:79 , LYS B:80 , GLN B:82 , TRP B:83
BINDING SITE FOR RESIDUE EDO B1902
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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)
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)
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Folds
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(
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Superfamilies
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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
:
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
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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_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)
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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-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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