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.
2VJX
Asym. Unit
Info
Asym.Unit (314 KB)
Biol.Unit 1 (158 KB)
Biol.Unit 2 (156 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
:
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
(4, 67)
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
7
Ligand/Ion
BROMIDE ION
2
CL
12
Ligand/Ion
CHLORIDE ION
3
EDO
46
Ligand/Ion
1,2-ETHANEDIOL
4
IFL
2
Ligand/Ion
(3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-2-ONE
[
close Hetero Component info
]
Sites
(66, 66)
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)
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
AC2
SOFTWARE
TRP B:198 , ASP B:199 , TRP B:200 , TRP B:395 , CYS B:424 , ASN B:461 , GLU B:462 , TRP B:533 , TYR B:537 , GLU B:555 , TRP B:645 , EDO B:1877
BINDING SITE FOR RESIDUE IFL B1867
03
AC3
SOFTWARE
GLN A:365 , ASN A:648 , ASP A:649 , ILE A:659 , ASP A:660
BINDING SITE FOR RESIDUE EDO A1866
04
AC4
SOFTWARE
TRP B:525 , SER B:530 , ASN B:532 , ASP B:548 , LEU B:549 , PRO B:550 , MET B:553 , HOH B:2621
BINDING SITE FOR RESIDUE EDO B1868
05
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
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:2619
BINDING SITE FOR RESIDUE EDO A1868
07
AC7
SOFTWARE
ARG A:331 , ARG A:507 , HOH A:2267 , HOH A:2619 , HOH A:2620
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:613 , HOH A:2621 , HOH A:2622
BINDING SITE FOR RESIDUE EDO A1871
10
BC1
SOFTWARE
ASN A:337 , TYR A:515 , HOH A:2623 , HOH A:2624
BINDING SITE FOR RESIDUE EDO A1872
11
BC2
SOFTWARE
ASN B:337 , VAL B:510 , HIS B:511 , TYR B:515 , HOH B:2622 , HOH B:2623 , HOH B:2624
BINDING SITE FOR RESIDUE EDO B1869
12
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
13
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
14
BC5
SOFTWARE
THR A:432 , HOH A:2093 , LEU B:126 , LEU B:127 , LYS B:129
BINDING SITE FOR RESIDUE EDO B1871
15
BC6
SOFTWARE
ARG A:634 , ASN A:635 , TYR A:693 , HOH A:2627
BINDING SITE FOR RESIDUE EDO A1874
16
BC7
SOFTWARE
VAL A:442 , ARG A:446 , HOH A:2342
BINDING SITE FOR RESIDUE EDO A1875
17
BC8
SOFTWARE
SER B:43 , GLN B:44 , SER B:45 , GLY B:46 , THR B:47 , GLU B:48 , GLU B:90 , HOH B:2625
BINDING SITE FOR RESIDUE EDO B1872
18
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
19
CC1
SOFTWARE
PHE B:542 , GLU B:543 , ASP B:603 , GLY B:624 , HOH B:2499
BINDING SITE FOR RESIDUE EDO B1873
20
CC2
SOFTWARE
ARG A:382 , ILE A:840 , HOH A:2305 , HOH A:2599
BINDING SITE FOR RESIDUE EDO A1877
21
CC3
SOFTWARE
ARG B:331 , ASP B:506 , ARG B:507 , HOH B:2287 , HOH B:2626
BINDING SITE FOR RESIDUE EDO B1874
22
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
23
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
24
CC6
SOFTWARE
GLN B:365 , ASN B:648 , ASP B:649 , ILE B:659 , ASP B:660
BINDING SITE FOR RESIDUE EDO B1875
25
CC7
SOFTWARE
GLU B:465 , LYS B:468 , TYR B:469 , PRO B:514 , LEU B:516 , ALA B:517
BINDING SITE FOR RESIDUE EDO B1876
26
CC8
SOFTWARE
ASN B:178 , ASP B:199 , CYS B:424 , GLU B:462 , TRP B:470 , IFL B:1867
BINDING SITE FOR RESIDUE EDO B1877
27
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
28
DC1
SOFTWARE
PHE A:775 , ARG A:777 , CL A:1896
BINDING SITE FOR RESIDUE EDO A1881
29
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
30
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
31
DC4
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 B1878
32
DC5
SOFTWARE
ARG A:626 , GLN A:671 , ARG A:674 , SER A:772 , VAL A:773
BINDING SITE FOR RESIDUE EDO A1884
33
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
34
DC7
SOFTWARE
ASP A:603 , TYR A:604 , LYS A:778 , THR A:779 , EDO A:1890
BINDING SITE FOR RESIDUE EDO A1886
35
DC8
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 B1879
36
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
37
EC1
SOFTWARE
LEU B:819 , GLN B:820 , ARG B:845
BINDING SITE FOR RESIDUE EDO B1880
38
EC2
SOFTWARE
PHE B:775 , ARG B:777 , CL B:1889 , HOH B:2627
BINDING SITE FOR RESIDUE EDO B1881
39
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
40
EC4
SOFTWARE
PHE B:42 , SER B:43 , GLN B:44 , THR B:47 , LYS B:49 , MET B:51 , LEU B:68
BINDING SITE FOR RESIDUE EDO B1882
41
EC5
SOFTWARE
PRO B:212 , HOH B:2074 , HOH B:2344 , HOH B:2628
BINDING SITE FOR RESIDUE EDO B1883
42
EC6
SOFTWARE
ARG A:376 , TYR A:661 , TYR A:662 , HOH A:2633
BINDING SITE FOR RESIDUE EDO A1889
43
EC7
SOFTWARE
ARG B:382 , ARG B:823 , SER B:825 , ILE B:840 , THR B:842 , HOH B:2629 , HOH B:2630
BINDING SITE FOR RESIDUE EDO B1884
44
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
45
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
46
FC1
SOFTWARE
ILE A:107 , LYS A:142 , HOH A:2068
BINDING SITE FOR RESIDUE BR A1891
47
FC2
SOFTWARE
ILE B:107 , LYS B:142
BINDING SITE FOR RESIDUE BR B1886
48
FC3
SOFTWARE
HIS A:284
BINDING SITE FOR RESIDUE BR A1892
49
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
50
FC5
SOFTWARE
HOH A:2624
BINDING SITE FOR RESIDUE BR A1894
51
FC6
SOFTWARE
GLN B:685 , ASP B:688
BINDING SITE FOR RESIDUE BR B1887
52
FC7
SOFTWARE
GLN B:108
BINDING SITE FOR RESIDUE CL B1888
53
FC8
SOFTWARE
GLN B:685 , HIS B:774 , EDO B:1881 , HOH B:2531
BINDING SITE FOR RESIDUE CL B1889
54
FC9
SOFTWARE
GLN A:108 , HOH A:2210
BINDING SITE FOR RESIDUE CL A1895
55
GC1
SOFTWARE
HIS A:627 , ILE A:684 , GLN A:685 , EDO A:1881 , HOH A:2516
BINDING SITE FOR RESIDUE CL A1896
56
GC2
SOFTWARE
GLN A:685 , ASP A:688
BINDING SITE FOR RESIDUE CL A1897
57
GC3
SOFTWARE
HOH B:2624
BINDING SITE FOR RESIDUE CL B1895
58
GC4
SOFTWARE
ASN B:300 , ASN B:390 , HOH B:2308
BINDING SITE FOR RESIDUE CL B1890
59
GC5
SOFTWARE
ASP B:131 , ASN B:132 , ARG B:436 , HOH B:2109
BINDING SITE FOR RESIDUE CL B1891
60
GC6
SOFTWARE
ASN A:337
BINDING SITE FOR RESIDUE CL A1901
61
GC7
SOFTWARE
PRO A:786 , THR A:787 , GLU A:861 , HOH A:2613
BINDING SITE FOR RESIDUE CL A1898
62
GC8
SOFTWARE
ASN A:300 , ASN A:390
BINDING SITE FOR RESIDUE BR A1899
63
GC9
SOFTWARE
ARG B:376 , TYR B:661
BINDING SITE FOR RESIDUE EDO B1892
64
HC1
SOFTWARE
ARG B:597 , PRO B:607 , GLU B:608 , SER B:609 , PHE B:613 , HOH B:2631
BINDING SITE FOR RESIDUE EDO B1893
65
HC2
SOFTWARE
GLN B:623 , ARG B:626 , HIS B:774 , PHE B:775 , HOH B:2569 , HOH B:2627 , HOH B:2632 , HOH B:2633
BINDING SITE FOR RESIDUE EDO B1894
66
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 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_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:
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: 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:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
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
]
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 (314 KB)
Header - Asym.Unit
Biol.Unit 1 (158 KB)
Header - Biol.Unit 1
Biol.Unit 2 (156 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
2VJX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
