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2F1D
Asym. Unit
Info
Asym.Unit (395 KB)
Biol.Unit 1 (571 KB)
Biol.Unit 2 (196 KB)
Biol.Unit 3 (573 KB)
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(1)
Title
:
X-RAY STRUCTURE OF IMIDAZOLEGLYCEROL-PHOSPHATE DEHYDRATASE
Authors
:
D. W. Rice, S. E. Glynn, P. J. Baker, S. E. Sedelnikova, C. L. Davies, T. C.
Date
:
14 Nov 05 (Deposition) - 24 Jan 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D,E,F,G,H (3x)
Biol. Unit 2: I,J,K,L,M,N,O,P (1x)
Biol. Unit 3: I,J,K,L,M,N,O,P (3x)
Keywords
:
Igpd, Herbicide, Manganese, Histidine Biosynthesis, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. E. Glynn, P. J. Baker, S. E. Sedelnikova, C. L. Davies, T. C. Eadsforth, C. W. Levy, H. F. Rodgers, G. M. Blackburn, T. R. Hawkes R. Viner, D. W. Rice
Structure And Mechanism Of Imidazoleglycerol-Phosphate Dehydratase.
Structure V. 13 1809 2005
[
close entry info
]
Hetero Components
(2, 48)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1aa: MANGANESE (II) ION (MNaa)
1ab: MANGANESE (II) ION (MNab)
1ac: MANGANESE (II) ION (MNac)
1ad: MANGANESE (II) ION (MNad)
1ae: MANGANESE (II) ION (MNae)
1af: MANGANESE (II) ION (MNaf)
1b: MANGANESE (II) ION (MNb)
1c: MANGANESE (II) ION (MNc)
1d: MANGANESE (II) ION (MNd)
1e: MANGANESE (II) ION (MNe)
1f: MANGANESE (II) ION (MNf)
1g: MANGANESE (II) ION (MNg)
1h: MANGANESE (II) ION (MNh)
1i: MANGANESE (II) ION (MNi)
1j: MANGANESE (II) ION (MNj)
1k: MANGANESE (II) ION (MNk)
1l: MANGANESE (II) ION (MNl)
1m: MANGANESE (II) ION (MNm)
1n: MANGANESE (II) ION (MNn)
1o: MANGANESE (II) ION (MNo)
1p: MANGANESE (II) ION (MNp)
1q: MANGANESE (II) ION (MNq)
1r: MANGANESE (II) ION (MNr)
1s: MANGANESE (II) ION (MNs)
1t: MANGANESE (II) ION (MNt)
1u: MANGANESE (II) ION (MNu)
1v: MANGANESE (II) ION (MNv)
1w: MANGANESE (II) ION (MNw)
1x: MANGANESE (II) ION (MNx)
1y: MANGANESE (II) ION (MNy)
1z: MANGANESE (II) ION (MNz)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MN
32
Ligand/Ion
MANGANESE (II) ION
2
SO4
16
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(48, 48)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:170 , HIS B:73 , GLU B:77 , HIS B:145
BINDING SITE FOR RESIDUE MN A 300
02
AC2
SOFTWARE
HIS A:47 , HIS A:169 , GLU A:173 , HIS B:74
BINDING SITE FOR RESIDUE MN A 301
03
AC3
SOFTWARE
HIS A:55 , ARG A:99 , LYS A:177
BINDING SITE FOR RESIDUE SO4 A 398
04
AC4
SOFTWARE
HIS B:170 , HIS G:73 , GLU G:77 , HIS G:145
BINDING SITE FOR RESIDUE MN B 300
05
AC5
SOFTWARE
HIS B:47 , HIS B:169 , GLU B:173 , HIS G:74
BINDING SITE FOR RESIDUE MN B 301
06
AC6
SOFTWARE
GLN B:51 , HIS B:55 , LYS B:177 , ARG C:99
BINDING SITE FOR RESIDUE SO4 B 398
07
AC7
SOFTWARE
HIS C:170 , HIS H:73 , GLU H:77 , HIS H:145
BINDING SITE FOR RESIDUE MN C 300
08
AC8
SOFTWARE
HIS C:47 , HIS C:169 , GLU C:173 , HIS H:74
BINDING SITE FOR RESIDUE MN C 301
09
AC9
SOFTWARE
GLN C:51 , HIS C:55 , LYS C:177 , ARG D:99
BINDING SITE FOR RESIDUE SO4 C 398
10
BC1
SOFTWARE
HIS A:73 , GLU A:77 , HIS A:145 , ASP D:108 , HIS D:170
BINDING SITE FOR RESIDUE MN D 300
11
BC2
SOFTWARE
HIS A:74 , HIS D:47 , HIS D:169 , GLU D:173
BINDING SITE FOR RESIDUE MN D 301
12
BC3
SOFTWARE
ARG B:99 , GLN D:51 , HIS D:55 , LYS D:177
BINDING SITE FOR RESIDUE SO4 D 398
13
BC4
SOFTWARE
HIS E:170 , HIS F:73 , GLU F:77 , HIS F:145
BINDING SITE FOR RESIDUE MN E 300
14
BC5
SOFTWARE
HIS E:47 , HIS E:169 , GLU E:173 , HIS F:74
BINDING SITE FOR RESIDUE MN E 301
15
BC6
SOFTWARE
GLN E:51 , HIS E:55 , ARG E:99 , LYS E:177
BINDING SITE FOR RESIDUE SO4 E 398
16
BC7
SOFTWARE
HIS C:73 , GLU C:77 , HIS C:145 , HIS F:170
BINDING SITE FOR RESIDUE MN F 300
17
BC8
SOFTWARE
HIS C:74 , HIS F:47 , HIS F:169 , GLU F:173
BINDING SITE FOR RESIDUE MN F 301
18
BC9
SOFTWARE
GLN F:51 , HIS F:55 , LYS F:177 , ARG G:99
BINDING SITE FOR RESIDUE SO4 F 398
19
CC1
SOFTWARE
HIS D:73 , GLU D:77 , HIS D:145 , HIS G:170
BINDING SITE FOR RESIDUE MN G 300
20
CC2
SOFTWARE
HIS D:74 , HIS G:47 , HIS G:169 , GLU G:173
BINDING SITE FOR RESIDUE MN G 301
21
CC3
SOFTWARE
HIS G:55 , LYS G:177 , ARG H:99
BINDING SITE FOR RESIDUE SO4 G 398
22
CC4
SOFTWARE
HIS E:73 , GLU E:77 , HIS E:145 , HIS H:170
BINDING SITE FOR RESIDUE MN H 300
23
CC5
SOFTWARE
HIS E:74 , HIS H:47 , HIS H:169 , GLU H:173
BINDING SITE FOR RESIDUE MN H 301
24
CC6
SOFTWARE
ARG F:99 , GLN H:51 , HIS H:55 , LYS H:177
BINDING SITE FOR RESIDUE SO4 H 398
25
CC7
SOFTWARE
HIS I:170 , HIS J:73 , GLU J:77 , HIS J:145
BINDING SITE FOR RESIDUE MN I 300
26
CC8
SOFTWARE
HIS I:47 , HIS I:169 , GLU I:173 , HIS J:74
BINDING SITE FOR RESIDUE MN I 301
27
CC9
SOFTWARE
HIS I:55 , ARG I:99 , LYS I:177
BINDING SITE FOR RESIDUE SO4 I 398
28
DC1
SOFTWARE
HIS J:170 , HIS O:73 , GLU O:77 , HIS O:145
BINDING SITE FOR RESIDUE MN J 300
29
DC2
SOFTWARE
HIS J:47 , HIS J:169 , GLU J:173 , HIS O:74
BINDING SITE FOR RESIDUE MN J 301
30
DC3
SOFTWARE
HIS J:55 , LYS J:177 , ARG K:99
BINDING SITE FOR RESIDUE SO4 J 398
31
DC4
SOFTWARE
HIS K:170 , HIS P:73 , GLU P:77 , HIS P:145
BINDING SITE FOR RESIDUE MN K 300
32
DC5
SOFTWARE
HIS K:47 , HIS K:169 , GLU K:173 , HIS P:74
BINDING SITE FOR RESIDUE MN K 301
33
DC6
SOFTWARE
GLN K:51 , HIS K:55 , LYS K:177 , ARG L:99
BINDING SITE FOR RESIDUE SO4 K 398
34
DC7
SOFTWARE
HIS I:73 , GLU I:77 , HIS I:145 , HIS L:170
BINDING SITE FOR RESIDUE MN L 300
35
DC8
SOFTWARE
HIS I:74 , HIS L:47 , HIS L:169 , GLU L:173
BINDING SITE FOR RESIDUE MN L 301
36
DC9
SOFTWARE
ARG J:99 , GLN L:51 , HIS L:55 , LYS L:177
BINDING SITE FOR RESIDUE SO4 L 398
37
EC1
SOFTWARE
HIS M:170 , HIS N:73 , GLU N:77 , HIS N:145
BINDING SITE FOR RESIDUE MN M 300
38
EC2
SOFTWARE
HIS M:47 , HIS M:169 , GLU M:173 , HIS N:74
BINDING SITE FOR RESIDUE MN M 301
39
EC3
SOFTWARE
HIS M:55 , ARG M:99 , LYS M:177
BINDING SITE FOR RESIDUE SO4 M 398
40
EC4
SOFTWARE
HIS K:73 , GLU K:77 , HIS K:145 , HIS N:170
BINDING SITE FOR RESIDUE MN N 300
41
EC5
SOFTWARE
HIS K:74 , HIS N:47 , HIS N:169 , GLU N:173
BINDING SITE FOR RESIDUE MN N 301
42
EC6
SOFTWARE
HIS N:55 , LYS N:177 , ARG O:99
BINDING SITE FOR RESIDUE SO4 N 398
43
EC7
SOFTWARE
HIS L:73 , GLU L:77 , HIS L:145 , HIS O:170
BINDING SITE FOR RESIDUE MN O 300
44
EC8
SOFTWARE
HIS L:74 , HIS O:47 , HIS O:169 , GLU O:173
BINDING SITE FOR RESIDUE MN O 301
45
EC9
SOFTWARE
GLN O:51 , HIS O:55 , LYS O:177 , ARG P:99
BINDING SITE FOR RESIDUE SO4 O 398
46
FC1
SOFTWARE
HIS M:73 , GLU M:77 , HIS M:145 , HIS P:170
BINDING SITE FOR RESIDUE MN P 300
47
FC2
SOFTWARE
HIS M:74 , HIS P:47 , HIS P:169 , GLU P:173
BINDING SITE FOR RESIDUE MN P 301
48
FC3
SOFTWARE
ARG N:99 , GLN P:51 , HIS P:55 , LYS P:177
BINDING SITE FOR RESIDUE SO4 P 398
[
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
(2, 32)
Info
All PROSITE Patterns/Profiles
1: IGP_DEHYDRATASE_1 (A:70-83,B:70-83,C:70-83,D:70-83,E:...)
2: IGP_DEHYDRATASE_2 (A:165-177,B:165-177,C:165-177,D:16...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IGP_DEHYDRATASE_1
PS00954
Imidazoleglycerol-phosphate dehydratase signature 1.
HIS5A_ARATH
133-146
16
A:70-83
B:70-83
C:70-83
D:70-83
E:70-83
F:70-83
G:70-83
H:70-83
I:70-83
J:70-83
K:70-83
L:70-83
M:70-83
N:70-83
O:70-83
P:70-83
2
IGP_DEHYDRATASE_2
PS00955
Imidazoleglycerol-phosphate dehydratase signature 2.
HIS5A_ARATH
228-240
16
A:165-177
B:165-177
C:165-177
D:165-177
E:165-177
F:165-177
G:165-177
H:165-177
I:165-177
J:165-177
K:165-177
L:165-177
M:165-177
N:165-177
O:165-177
P:165-177
[
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
(2, 32)
Info
All SCOP Domains
1a: SCOP_d2f1db1 (B:10-95)
1b: SCOP_d2f1db2 (B:96-192)
1c: SCOP_d2f1dg1 (G:10-95)
1d: SCOP_d2f1dg2 (G:96-192)
1e: SCOP_d2f1dh1 (H:10-95)
1f: SCOP_d2f1dh2 (H:96-192)
1g: SCOP_d2f1di1 (I:10-95)
1h: SCOP_d2f1di2 (I:96-192)
1i: SCOP_d2f1dj1 (J:10-95)
1j: SCOP_d2f1dj2 (J:96-192)
1k: SCOP_d2f1dk1 (K:10-95)
1l: SCOP_d2f1dk2 (K:96-192)
1m: SCOP_d2f1dc1 (C:10-95)
1n: SCOP_d2f1dl1 (L:10-95)
1o: SCOP_d2f1dl2 (L:96-192)
1p: SCOP_d2f1dm1 (M:10-95)
1q: SCOP_d2f1dm2 (M:96-192)
1r: SCOP_d2f1dn1 (N:10-95)
1s: SCOP_d2f1dn2 (N:96-192)
1t: SCOP_d2f1do1 (O:10-95)
1u: SCOP_d2f1do2 (O:96-192)
1v: SCOP_d2f1dp1 (P:10-95)
1w: SCOP_d2f1dp2 (P:96-192)
1x: SCOP_d2f1dc2 (C:96-192)
1y: SCOP_d2f1dd1 (D:10-95)
1z: SCOP_d2f1dd2 (D:96-192)
1aa: SCOP_d2f1de1 (E:10-95)
1ab: SCOP_d2f1de2 (E:96-192)
1ac: SCOP_d2f1df1 (F:10-95)
1ad: SCOP_d2f1df2 (F:96-192)
2a: SCOP_d2f1da1 (A:10-95)
2b: SCOP_d2f1da2 (A:96-192)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ribosomal protein S5 domain 2-like
(306)
Superfamily
:
Ribosomal protein S5 domain 2-like
(306)
Family
:
Imidazole glycerol phosphate dehydratase
(4)
Protein domain
:
automated matches
(1)
Thale cress (Arabidopsis thaliana) [TaxId: 3702]
(1)
1a
d2f1db1
B:10-95
1b
d2f1db2
B:96-192
1c
d2f1dg1
G:10-95
1d
d2f1dg2
G:96-192
1e
d2f1dh1
H:10-95
1f
d2f1dh2
H:96-192
1g
d2f1di1
I:10-95
1h
d2f1di2
I:96-192
1i
d2f1dj1
J:10-95
1j
d2f1dj2
J:96-192
1k
d2f1dk1
K:10-95
1l
d2f1dk2
K:96-192
1m
d2f1dc1
C:10-95
1n
d2f1dl1
L:10-95
1o
d2f1dl2
L:96-192
1p
d2f1dm1
M:10-95
1q
d2f1dm2
M:96-192
1r
d2f1dn1
N:10-95
1s
d2f1dn2
N:96-192
1t
d2f1do1
O:10-95
1u
d2f1do2
O:96-192
1v
d2f1dp1
P:10-95
1w
d2f1dp2
P:96-192
1x
d2f1dc2
C:96-192
1y
d2f1dd1
D:10-95
1z
d2f1dd2
D:96-192
1aa
d2f1de1
E:10-95
1ab
d2f1de2
E:96-192
1ac
d2f1df1
F:10-95
1ad
d2f1df2
F:96-192
Protein domain
:
Imidazole glycerol phosphate dehydratase
(3)
Thale cress (Arabidopsis thaliana) [TaxId: 3702]
(1)
2a
d2f1da1
A:10-95
2b
d2f1da2
A:96-192
[
close SCOP info
]
CATH Domains
(1, 32)
Info
all CATH domains
1a: CATH_2f1dA02 (A:99-192)
1b: CATH_2f1dB02 (B:99-192)
1c: CATH_2f1dK02 (K:99-192)
1d: CATH_2f1dL02 (L:99-192)
1e: CATH_2f1dM02 (M:99-192)
1f: CATH_2f1dN02 (N:99-192)
1g: CATH_2f1dO02 (O:99-192)
1h: CATH_2f1dP02 (P:99-192)
1i: CATH_2f1dA01 (A:10-98)
1j: CATH_2f1dB01 (B:10-98)
1k: CATH_2f1dC01 (C:10-98)
1l: CATH_2f1dD01 (D:10-98)
1m: CATH_2f1dC02 (C:99-192)
1n: CATH_2f1dE01 (E:10-98)
1o: CATH_2f1dF01 (F:10-98)
1p: CATH_2f1dG01 (G:10-98)
1q: CATH_2f1dH01 (H:10-98)
1r: CATH_2f1dI01 (I:10-98)
1s: CATH_2f1dJ01 (J:10-98)
1t: CATH_2f1dK01 (K:10-98)
1u: CATH_2f1dL01 (L:10-98)
1v: CATH_2f1dM01 (M:10-98)
1w: CATH_2f1dN01 (N:10-98)
1x: CATH_2f1dD02 (D:99-192)
1y: CATH_2f1dO01 (O:10-98)
1z: CATH_2f1dP01 (P:10-98)
1aa: CATH_2f1dE02 (E:99-192)
1ab: CATH_2f1dF02 (F:99-192)
1ac: CATH_2f1dG02 (G:99-192)
1ad: CATH_2f1dH02 (H:99-192)
1ae: CATH_2f1dI02 (I:99-192)
1af: CATH_2f1dJ02 (J:99-192)
View:
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Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Ribosomal Protein S5; domain 2
(189)
Homologous Superfamily
:
Imidazole glycerol phosphate dehydratase; domain 1
(3)
Thale cress (Arabidopsis thaliana)
(1)
1a
2f1dA02
A:99-192
1b
2f1dB02
B:99-192
1c
2f1dK02
K:99-192
1d
2f1dL02
L:99-192
1e
2f1dM02
M:99-192
1f
2f1dN02
N:99-192
1g
2f1dO02
O:99-192
1h
2f1dP02
P:99-192
1i
2f1dA01
A:10-98
1j
2f1dB01
B:10-98
1k
2f1dC01
C:10-98
1l
2f1dD01
D:10-98
1m
2f1dC02
C:99-192
1n
2f1dE01
E:10-98
1o
2f1dF01
F:10-98
1p
2f1dG01
G:10-98
1q
2f1dH01
H:10-98
1r
2f1dI01
I:10-98
1s
2f1dJ01
J:10-98
1t
2f1dK01
K:10-98
1u
2f1dL01
L:10-98
1v
2f1dM01
M:10-98
1w
2f1dN01
N:10-98
1x
2f1dD02
D:99-192
1y
2f1dO01
O:10-98
1z
2f1dP01
P:10-98
1aa
2f1dE02
E:99-192
1ab
2f1dF02
F:99-192
1ac
2f1dG02
G:99-192
1ad
2f1dH02
H:99-192
1ae
2f1dI02
I:99-192
1af
2f1dJ02
J:99-192
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Asymmetric Unit 1
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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") .
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") .
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Asym.Unit (395 KB)
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