PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2VQT
Asym. Unit
Info
Asym.Unit (309 KB)
Biol.Unit 1 (155 KB)
Biol.Unit 2 (154 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(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
[
close entry info
]
Hetero Components
(4, 70)
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
2
Ligand/Ion
(2Z,3R,4S,5R,6R)-2-[(2-AMINOETHYL)IMINO]-6-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL
2
BR
10
Ligand/Ion
BROMIDE ION
3
CL
13
Ligand/Ion
CHLORIDE ION
4
EDO
45
Ligand/Ion
1,2-ETHANEDIOL
[
close Hetero Component info
]
Sites
(67, 67)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (SOFTWARE)
54: FC9 (SOFTWARE)
55: GC1 (SOFTWARE)
56: GC2 (SOFTWARE)
57: GC3 (SOFTWARE)
58: GC4 (SOFTWARE)
59: GC5 (SOFTWARE)
60: GC6 (SOFTWARE)
61: GC7 (SOFTWARE)
62: GC8 (SOFTWARE)
63: GC9 (SOFTWARE)
64: HC1 (SOFTWARE)
65: HC2 (SOFTWARE)
66: HC3 (SOFTWARE)
67: HC4 (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
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
03
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
04
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
05
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
06
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
07
AC7
SOFTWARE
ARG A:331 , ASP A:506 , ARG A:507 , HOH A:2472 , HOH A:2473
BINDING SITE FOR RESIDUE EDO A1869
08
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
09
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
10
BC1
SOFTWARE
ASN A:337 , HIS A:511 , TYR A:515 , HOH A:2209 , HOH A:2474
BINDING SITE FOR RESIDUE EDO A1872
11
BC2
SOFTWARE
ASN B:337 , VAL B:510 , HIS B:511 , TYR B:515 , HOH B:2446
BINDING SITE FOR RESIDUE EDO B1869
12
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
13
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
14
BC5
SOFTWARE
THR A:432 , HOH A:2262 , LEU B:126 , LYS B:129
BINDING SITE FOR RESIDUE EDO B1871
15
BC6
SOFTWARE
ARG A:446 , HOH A:2061 , HOH A:2265
BINDING SITE FOR RESIDUE EDO A1874
16
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
17
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
18
BC9
SOFTWARE
GLY B:471 , PHE B:472 , GLU B:473 , LYS B:474 , HOH B:2449
BINDING SITE FOR RESIDUE EDO B1874
19
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
20
CC2
SOFTWARE
ARG B:331 , ARG B:507 , EDO B:1899 , HOH B:2450
BINDING SITE FOR RESIDUE EDO B1875
21
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
22
CC4
SOFTWARE
SER A:224 , ILE A:245 , ARG A:446
BINDING SITE FOR RESIDUE EDO A1877
23
CC5
SOFTWARE
GLN B:365 , ASN B:648 , ASP B:649 , ILE B:659 , ASP B:660
BINDING SITE FOR RESIDUE EDO B1876
24
CC6
SOFTWARE
GLU B:465 , LYS B:468 , PRO B:514 , LEU B:516 , ALA B:517
BINDING SITE FOR RESIDUE EDO B1877
25
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
26
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
27
CC9
SOFTWARE
HIS A:326 , ARG A:327 , ASN A:450 , HIS A:451 , HOH A:2272
BINDING SITE FOR RESIDUE EDO A1878
28
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
29
DC2
SOFTWARE
PHE B:42 , SER B:43 , GLN B:44 , THR B:47 , LYS B:49
BINDING SITE FOR RESIDUE EDO B1881
30
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
31
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
32
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
33
DC6
SOFTWARE
ASP A:603 , TYR A:604 , LYS A:778 , THR A:779
BINDING SITE FOR RESIDUE EDO A1880
34
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
35
DC8
SOFTWARE
SER A:43 , GLN A:44 , THR A:47 , LYS A:49
BINDING SITE FOR RESIDUE EDO A1881
36
DC9
SOFTWARE
ILE A:107 , LYS A:142
BINDING SITE FOR RESIDUE BR A1882
37
EC1
SOFTWARE
ILE B:107 , LYS B:142
BINDING SITE FOR RESIDUE BR B1885
38
EC2
SOFTWARE
HIS A:284
BINDING SITE FOR RESIDUE BR A1883
39
EC3
SOFTWARE
HOH A:2474
BINDING SITE FOR RESIDUE BR A1896
40
EC4
SOFTWARE
GLN B:685 , ASP B:688
BINDING SITE FOR RESIDUE BR B1886
41
EC5
SOFTWARE
GLN A:108
BINDING SITE FOR RESIDUE BR A1884
42
EC6
SOFTWARE
HOH B:2446
BINDING SITE FOR RESIDUE BR B1887
43
EC7
SOFTWARE
ASP A:688
BINDING SITE FOR RESIDUE BR A1885
44
EC8
SOFTWARE
GLN B:108
BINDING SITE FOR RESIDUE CL B1888
45
EC9
SOFTWARE
ILE B:684 , GLN B:685 , HIS B:774 , EDO B:1882 , HOH B:2371
BINDING SITE FOR RESIDUE CL B1889
46
FC1
SOFTWARE
ILE A:684 , GLN A:685 , HIS A:774 , HOH A:2396
BINDING SITE FOR RESIDUE CL A1886
47
FC2
SOFTWARE
ASN A:402 , HOH A:2017
BINDING SITE FOR RESIDUE CL A1887
48
FC3
SOFTWARE
ARG B:845 , GLU B:850
BINDING SITE FOR RESIDUE EDO B1891
49
FC4
SOFTWARE
TYR B:347 , HOH B:2196 , HOH B:2353 , HOH B:2455
BINDING SITE FOR RESIDUE EDO B1892
50
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
51
FC6
SOFTWARE
PHE A:346 , ARG A:551 , HOH A:2377
BINDING SITE FOR RESIDUE CL A1888
52
FC7
SOFTWARE
GLU B:271
BINDING SITE FOR RESIDUE BR B1894
53
FC8
SOFTWARE
TYR B:661 , TYR B:662
BINDING SITE FOR RESIDUE EDO B1895
54
FC9
SOFTWARE
ARG B:376 , LEU B:380 , ASP B:383 , GLY B:663 , HOH B:2205
BINDING SITE FOR RESIDUE EDO B1896
55
GC1
SOFTWARE
ASN A:337
BINDING SITE FOR RESIDUE CL A1889
56
GC2
SOFTWARE
LYS B:147
BINDING SITE FOR RESIDUE CL A1898
57
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
58
GC4
SOFTWARE
GLU A:502
BINDING SITE FOR RESIDUE EDO A1891
59
GC5
SOFTWARE
THR A:477
BINDING SITE FOR RESIDUE CL A1892
60
GC6
SOFTWARE
TRP B:470 , ASN B:518 , HOH B:2288
BINDING SITE FOR RESIDUE CL B1898
61
GC7
SOFTWARE
GLN B:230 , THR B:332 , ASP B:506 , EDO B:1875 , HOH B:2458
BINDING SITE FOR RESIDUE EDO B1899
62
GC8
SOFTWARE
PRO B:541 , ARG B:602
BINDING SITE FOR RESIDUE EDO B1900
63
GC9
SOFTWARE
GLU A:708 , LYS A:710 , ILE A:760
BINDING SITE FOR RESIDUE EDO A1893
64
HC1
SOFTWARE
GLU B:708 , LYS B:710 , LYS B:758 , ILE B:760
BINDING SITE FOR RESIDUE EDO B1901
65
HC2
SOFTWARE
LYS A:129 , HIS A:157 , LYS B:129 , HIS B:157
BINDING SITE FOR RESIDUE BR A1894
66
HC3
SOFTWARE
LYS B:79 , LYS B:80 , GLN B:82 , TRP B:83
BINDING SITE FOR RESIDUE EDO B1902
67
HC4
SOFTWARE
ARG A:634 , TYR A:693 , HOH A:2125 , HOH A:2375
BINDING SITE FOR RESIDUE CL A1895
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 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.
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:
Select:
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: 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
[
close CATH info
]
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:
Select:
Label:
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
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (309 KB)
Header - Asym.Unit
Biol.Unit 1 (155 KB)
Header - Biol.Unit 1
Biol.Unit 2 (154 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2VQT
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
