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2VMF
Asym. Unit
Info
Asym.Unit (307 KB)
Biol.Unit 1 (152 KB)
Biol.Unit 2 (153 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
:
25 Jan 08 (Deposition) - 01 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, Mannosidase, Glycoside Hydrolase, 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, 69)
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)
1l: BROMIDE ION (BRl)
1m: BROMIDE ION (BRm)
1n: BROMIDE ION (BRn)
1o: BROMIDE ION (BRo)
1p: BROMIDE ION (BRp)
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)
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)
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: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLa)
4b: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BR
16
Ligand/Ion
BROMIDE ION
2
CL
11
Ligand/Ion
CHLORIDE ION
3
EDO
40
Ligand/Ion
1,2-ETHANEDIOL
4
MVL
2
Ligand/Ion
(5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDRO-1H-IMIDAZO[1,2-A]PYRIDIN-4-IUM
[
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 A:198 , ASP A:199 , TRP A:200 , TRP A:395 , ASN A:461 , GLU A:462 , TRP A:533 , TYR A:537 , GLU A:555 , TRP A:645 , TRP A:656 , EDO A:1876
BINDING SITE FOR RESIDUE MVL A1865
02
AC2
SOFTWARE
GLN A:365 , ASN A:648 , ASP A:649 , ILE A:659 , ASP A:660
BINDING SITE FOR RESIDUE EDO A1866
03
AC3
SOFTWARE
TRP A:519 , TRP A:525 , SER A:530 , ASN A:532 , ASP A:548 , PRO A:550 , MET A:553 , HOH A:2461
BINDING SITE FOR RESIDUE EDO A1867
04
AC4
SOFTWARE
ILE A:328 , GLY A:329 , ASN A:450 , HIS A:451 , ALA A:452 , ARG A:507
BINDING SITE FOR RESIDUE EDO A1868
05
AC5
SOFTWARE
GLN A:230 , ARG A:331 , ASP A:506 , ARG A:507 , HOH A:2462 , HOH A:2463
BINDING SITE FOR RESIDUE EDO A1869
06
AC6
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
AC7
SOFTWARE
ARG A:597 , PRO A:607 , GLU A:608 , SER A:609 , PHE A:610 , PHE A:613 , HOH A:2336
BINDING SITE FOR RESIDUE EDO A1871
08
AC8
SOFTWARE
ASN A:337 , HIS A:511 , TYR A:515 , HOH A:2464 , HOH A:2465
BINDING SITE FOR RESIDUE EDO A1872
09
AC9
SOFTWARE
ARG A:634 , GLN A:686 , TYR A:693 , HOH A:2321
BINDING SITE FOR RESIDUE EDO A1873
10
BC1
SOFTWARE
SER A:825 , THR A:842 , HOH A:2466
BINDING SITE FOR RESIDUE EDO A1874
11
BC2
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 A1875
12
BC3
SOFTWARE
ASN A:178 , ASP A:199 , CYS A:424 , GLU A:462 , TRP A:470 , MVL A:1865
BINDING SITE FOR RESIDUE EDO A1876
13
BC4
SOFTWARE
PHE A:775 , PHE A:776
BINDING SITE FOR RESIDUE EDO A1877
14
BC5
SOFTWARE
HIS A:326 , ARG A:327 , ASP A:407 , ASN A:450 , HIS A:451 , HOH A:2249 , HOH A:2275 , HOH A:2467
BINDING SITE FOR RESIDUE EDO A1878
15
BC6
SOFTWARE
PHE A:42 , SER A:43 , GLN A:44 , THR A:47 , LYS A:49
BINDING SITE FOR RESIDUE EDO A1879
16
BC7
SOFTWARE
ASP A:88 , HIS A:157 , ARG A:161 , ARG B:161
BINDING SITE FOR RESIDUE EDO A1880
17
BC8
SOFTWARE
HIS A:284
BINDING SITE FOR RESIDUE BR A1882
18
BC9
SOFTWARE
ILE A:107 , LYS A:142
BINDING SITE FOR RESIDUE BR A1881
19
CC1
SOFTWARE
HIS A:284
BINDING SITE FOR RESIDUE BR A1882
20
CC2
SOFTWARE
GLN A:108
BINDING SITE FOR RESIDUE BR A1884
21
CC3
SOFTWARE
GLN A:685 , ASP A:688
BINDING SITE FOR RESIDUE BR A1885
22
CC4
SOFTWARE
THR A:477
BINDING SITE FOR RESIDUE BR A1886
23
CC5
SOFTWARE
ILE A:684 , GLN A:685 , HOH A:2392
BINDING SITE FOR RESIDUE CL A1887
24
CC6
SOFTWARE
TYR A:347 , PRO A:637 , MET A:640 , HOH A:2370 , HOH A:2468
BINDING SITE FOR RESIDUE EDO A1888
25
CC7
SOFTWARE
GLN A:577 , ILE A:578 , GLU A:579
BINDING SITE FOR RESIDUE BR A1889
26
CC8
SOFTWARE
ASN A:402
BINDING SITE FOR RESIDUE BR A1890
27
CC9
SOFTWARE
ARG A:447 , HOH A:2269
BINDING SITE FOR RESIDUE CL A1891
28
DC1
SOFTWARE
GLU A:708 , MET A:709 , LYS A:710 , LYS A:758 , ILE A:760
BINDING SITE FOR RESIDUE EDO A1892
29
DC2
SOFTWARE
ASP A:105 , VAL A:250 , GLN A:252
BINDING SITE FOR RESIDUE EDO A1893
30
DC3
SOFTWARE
ARG A:626
BINDING SITE FOR RESIDUE BR A1894
31
DC4
SOFTWARE
ASP A:119 , LYS A:129 , HIS A:157 , GLN A:162 , ASP B:119 , LYS B:129 , HIS B:157 , GLN B:162
BINDING SITE FOR RESIDUE EDO A1895
32
DC5
SOFTWARE
ARG A:296 , MET A:298 , THR A:304 , THR A:306
BINDING SITE FOR RESIDUE EDO A1896
33
DC6
SOFTWARE
ASN A:77 , HOH A:2018 , HOH A:2032
BINDING SITE FOR RESIDUE CL A1897
34
DC7
SOFTWARE
TRP B:198 , ASP B:199 , TRP B:200 , TRP B:395 , ASN B:461 , GLU B:462 , TRP B:533 , TYR B:537 , GLU B:555 , TRP B:645 , TRP B:656 , EDO B:1874
BINDING SITE FOR RESIDUE MVL B1868
35
DC8
SOFTWARE
TRP B:519 , TRP B:525 , SER B:530 , ASN B:532 , ASP B:548 , PRO B:550
BINDING SITE FOR RESIDUE EDO B1869
36
DC9
SOFTWARE
ARG B:331 , ASP B:506 , ARG B:507 , EDO B:1899 , HOH B:2218 , HOH B:2472
BINDING SITE FOR RESIDUE EDO B1870
37
EC1
SOFTWARE
SER B:43 , GLN B:44 , GLY B:46 , THR B:47 , GLU B:48 , GLU B:90
BINDING SITE FOR RESIDUE EDO B1871
38
EC2
SOFTWARE
GLN B:365 , ASN B:648 , ASP B:649 , ILE B:659 , ASP B:660
BINDING SITE FOR RESIDUE EDO B1872
39
EC3
SOFTWARE
GLU B:465 , LYS B:468 , TYR B:469 , PRO B:514 , LEU B:516 , ALA B:517 , ASN B:518
BINDING SITE FOR RESIDUE EDO B1873
40
EC4
SOFTWARE
ASN B:178 , ASP B:199 , CYS B:424 , GLU B:462 , TRP B:470 , MVL B:1868
BINDING SITE FOR RESIDUE EDO B1874
41
EC5
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 B1875
42
EC6
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 B1876
43
EC7
SOFTWARE
PHE B:775 , ARG B:777 , LYS B:778 , HOH B:2473
BINDING SITE FOR RESIDUE EDO B1877
44
EC8
SOFTWARE
PHE B:42 , SER B:43 , GLN B:44 , THR B:47 , LYS B:49
BINDING SITE FOR RESIDUE EDO B1878
45
EC9
SOFTWARE
ILE B:107 , LYS B:142 , HOH B:2084
BINDING SITE FOR RESIDUE BR B1879
46
FC1
SOFTWARE
GLN B:685 , ASP B:688
BINDING SITE FOR RESIDUE BR B1880
47
FC2
SOFTWARE
HOH B:2320
BINDING SITE FOR RESIDUE BR B1881
48
FC3
SOFTWARE
THR B:477
BINDING SITE FOR RESIDUE BR B1882
49
FC4
SOFTWARE
TYR B:443 , ARG B:446
BINDING SITE FOR RESIDUE CL B1883
50
FC5
SOFTWARE
HIS B:181 , HOH B:2116
BINDING SITE FOR RESIDUE CL B1884
51
FC6
SOFTWARE
GLN B:108
BINDING SITE FOR RESIDUE CL B1885
52
FC7
SOFTWARE
GLN B:685 , HOH B:2404
BINDING SITE FOR RESIDUE CL B1886
53
FC8
SOFTWARE
ARG B:376 , TYR B:661
BINDING SITE FOR RESIDUE EDO B1888
54
FC9
SOFTWARE
HIS B:326 , ARG B:327 , ASP B:407 , ASN B:450 , HIS B:451 , HOH B:2212 , HOH B:2288 , HOH B:2474
BINDING SITE FOR RESIDUE EDO B1889
55
GC1
SOFTWARE
PRO B:637 , HOH B:2385 , HOH B:2475
BINDING SITE FOR RESIDUE EDO B1890
56
GC2
SOFTWARE
ASN B:300 , ASN B:390 , HOH B:2234
BINDING SITE FOR RESIDUE BR B1891
57
GC3
SOFTWARE
MET B:298 , TRP B:302 , ASN B:351
BINDING SITE FOR RESIDUE CL B1892
58
GC4
SOFTWARE
GLN B:324 , SER B:325 , HOH B:2209
BINDING SITE FOR RESIDUE CL B1893
59
GC5
SOFTWARE
ASN B:261 , HOH B:2477
BINDING SITE FOR RESIDUE EDO B1894
60
GC6
SOFTWARE
ARG B:626 , HOH B:2473
BINDING SITE FOR RESIDUE BR B1901
61
GC7
SOFTWARE
LEU B:307 , ASP B:309 , ARG B:327 , HOH B:2167
BINDING SITE FOR RESIDUE EDO B1895
62
GC8
SOFTWARE
LYS B:565 , THR B:817 , PRO B:818 , HOH B:2354 , HOH B:2478
BINDING SITE FOR RESIDUE EDO B1896
63
GC9
SOFTWARE
GLN B:577 , ILE B:578
BINDING SITE FOR RESIDUE CL B1897
64
HC1
SOFTWARE
ILE B:282 , HIS B:284 , HOH B:2479
BINDING SITE FOR RESIDUE EDO B1898
65
HC2
SOFTWARE
GLN B:230 , LEU B:231 , THR B:332 , ASP B:506 , EDO B:1870 , HOH B:2480
BINDING SITE FOR RESIDUE EDO B1899
66
HC3
SOFTWARE
TRP B:665 , TYR B:670 , ARG B:823 , TYR B:824 , HOH B:2481
BINDING SITE FOR RESIDUE EDO B1900
67
HC4
SOFTWARE
ASN A:300 , TRP A:302 , PHE A:356 , LYS A:358 , ASN A:390 , ASP A:697 , HOH A:2217
BINDING SITE FOR RESIDUE EDO A1899
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
close PROSITE info
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Exons
(0, 0)
Info
All Exons
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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_d2vmfa4 (A:28-219)
1b: SCOP_d2vmfb4 (B:27-219)
2a: SCOP_d2vmfa1 (A:220-330)
2b: SCOP_d2vmfa2 (A:784-864)
2c: SCOP_d2vmfa3 (A:679-783)
2d: SCOP_d2vmfb1 (B:220-330)
2e: SCOP_d2vmfb2 (B:784-867)
2f: SCOP_d2vmfb3 (B:679-783)
3a: SCOP_d2vmfa5 (A:331-678)
3b: SCOP_d2vmfb5 (B:331-678)
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Classes
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)
(
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Folds
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)
Superfamilies
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)
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)
Families
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)
(
)
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
d2vmfa4
A:28-219
1b
d2vmfb4
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
d2vmfa1
A:220-330
2b
d2vmfa2
A:784-864
2c
d2vmfa3
A:679-783
2d
d2vmfb1
B:220-330
2e
d2vmfb2
B:784-867
2f
d2vmfb3
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
d2vmfa5
A:331-678
3b
d2vmfb5
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
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
(currently selected atoms:
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)
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Nucleic
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Protein & NOT Site
Protein & NOT PROSITE
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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)
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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") .
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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).
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Asym.Unit (307 KB)
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