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3J81
Asym. Unit
Info
Asym.Unit (1.7 MB)
Biol.Unit 1, α-C (1.6 MB)
Biol.Unit 1 (1.6 MB)
(using Jmol or JSmol)
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(1)
Title
:
CRYOEM STRUCTURE OF A PARTIAL YEAST 48S PREINITIATION COMPLEX
Authors
:
T. Hussain, J. L. Llacer, I. S. Fernandez, C. G. Savva, V. Ramakrishnan
Date
:
29 Aug 14 (Deposition) - 05 Nov 14 (Release) - 24 Dec 14 (Revision)
Method
:
ELECTRON MICROSCOPY
Resolution
:
4.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,1,2,3
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,1,2,3 (1x)
Keywords
:
Eukaryotic Translation Initiation, 48S, Small Ribosome Subunit, Ribosome
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Hussain, J. L. Llacer, I. S. Fernandez, A. Munoz, P. Martin-Marcos, C. G. Savva, J. R. Lorsch, A. G. Hinnebusch, V. Ramakrishnan
Structural Changes Enable Start Codon Recognition By The Eukaryotic Translation Initiation Complex.
Cell(Cambridge, Mass. ) V. 159 597 2014
[
close entry info
]
Hetero Components
(3, 85)
Info
All Hetero Components
1a: METHIONINE (METa)
2a: MAGNESIUM ION (MGa)
2aa: MAGNESIUM ION (MGaa)
2ab: MAGNESIUM ION (MGab)
2ac: MAGNESIUM ION (MGac)
2ad: MAGNESIUM ION (MGad)
2ae: MAGNESIUM ION (MGae)
2af: MAGNESIUM ION (MGaf)
2ag: MAGNESIUM ION (MGag)
2ah: MAGNESIUM ION (MGah)
2ai: MAGNESIUM ION (MGai)
2aj: MAGNESIUM ION (MGaj)
2ak: MAGNESIUM ION (MGak)
2al: MAGNESIUM ION (MGal)
2am: MAGNESIUM ION (MGam)
2an: MAGNESIUM ION (MGan)
2ao: MAGNESIUM ION (MGao)
2ap: MAGNESIUM ION (MGap)
2aq: MAGNESIUM ION (MGaq)
2ar: MAGNESIUM ION (MGar)
2as: MAGNESIUM ION (MGas)
2at: MAGNESIUM ION (MGat)
2au: MAGNESIUM ION (MGau)
2av: MAGNESIUM ION (MGav)
2aw: MAGNESIUM ION (MGaw)
2ax: MAGNESIUM ION (MGax)
2ay: MAGNESIUM ION (MGay)
2az: MAGNESIUM ION (MGaz)
2b: MAGNESIUM ION (MGb)
2ba: MAGNESIUM ION (MGba)
2bb: MAGNESIUM ION (MGbb)
2bc: MAGNESIUM ION (MGbc)
2bd: MAGNESIUM ION (MGbd)
2be: MAGNESIUM ION (MGbe)
2bf: MAGNESIUM ION (MGbf)
2bg: MAGNESIUM ION (MGbg)
2bh: MAGNESIUM ION (MGbh)
2bi: MAGNESIUM ION (MGbi)
2bj: MAGNESIUM ION (MGbj)
2bk: MAGNESIUM ION (MGbk)
2bl: MAGNESIUM ION (MGbl)
2bm: MAGNESIUM ION (MGbm)
2bn: MAGNESIUM ION (MGbn)
2bo: MAGNESIUM ION (MGbo)
2bp: MAGNESIUM ION (MGbp)
2bq: MAGNESIUM ION (MGbq)
2br: MAGNESIUM ION (MGbr)
2bs: MAGNESIUM ION (MGbs)
2bt: MAGNESIUM ION (MGbt)
2bu: MAGNESIUM ION (MGbu)
2bv: MAGNESIUM ION (MGbv)
2bw: MAGNESIUM ION (MGbw)
2bx: MAGNESIUM ION (MGbx)
2by: MAGNESIUM ION (MGby)
2bz: MAGNESIUM ION (MGbz)
2c: MAGNESIUM ION (MGc)
2ca: MAGNESIUM ION (MGca)
2cb: MAGNESIUM ION (MGcb)
2cc: MAGNESIUM ION (MGcc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
2i: MAGNESIUM ION (MGi)
2j: MAGNESIUM ION (MGj)
2k: MAGNESIUM ION (MGk)
2l: MAGNESIUM ION (MGl)
2m: MAGNESIUM ION (MGm)
2n: MAGNESIUM ION (MGn)
2o: MAGNESIUM ION (MGo)
2p: MAGNESIUM ION (MGp)
2q: MAGNESIUM ION (MGq)
2r: MAGNESIUM ION (MGr)
2s: MAGNESIUM ION (MGs)
2t: MAGNESIUM ION (MGt)
2u: MAGNESIUM ION (MGu)
2v: MAGNESIUM ION (MGv)
2w: MAGNESIUM ION (MGw)
2x: MAGNESIUM ION (MGx)
2y: MAGNESIUM ION (MGy)
2z: MAGNESIUM ION (MGz)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MET
1
Mod. Amino Acid
METHIONINE
2
MG
81
Ligand/Ion
MAGNESIUM ION
3
ZN
3
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(72, 72)
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)
68: HC5 (SOFTWARE)
69: HC6 (SOFTWARE)
70: HC7 (SOFTWARE)
71: HC8 (SOFTWARE)
72: HC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
G 2:361 , G 2:362
BINDING SITE FOR RESIDUE MG 2 1801
02
AC2
SOFTWARE
A 2:93 , G 2:95 , C 2:401 , G 2:402 , ARG E:3
BINDING SITE FOR RESIDUE MG 2 1802
03
AC3
SOFTWARE
G 2:551 , G 2:552 , A 2:554 , A 2:555
BINDING SITE FOR RESIDUE MG 2 1803
04
AC4
SOFTWARE
A 2:100 , C 2:360
BINDING SITE FOR RESIDUE MG 2 1804
05
AC5
SOFTWARE
G 2:623 , A 2:1024
BINDING SITE FOR RESIDUE MG 2 1805
06
AC6
SOFTWARE
C 2:582
BINDING SITE FOR RESIDUE MG 2 1806
07
AC7
SOFTWARE
C 2:49
BINDING SITE FOR RESIDUE MG 2 1807
08
AC8
SOFTWARE
G 2:1329 , C 2:1418
BINDING SITE FOR RESIDUE MG 2 1809
09
AC9
SOFTWARE
A 2:11
BINDING SITE FOR RESIDUE MG 2 1810
10
BC1
SOFTWARE
U 2:927 , A 2:928
BINDING SITE FOR RESIDUE MG 2 1811
11
BC2
SOFTWARE
A 2:1760 , A 2:1761 , G 2:1766 , U 2:1769 , C 2:1782
BINDING SITE FOR RESIDUE MG 2 1812
12
BC3
SOFTWARE
G 2:548
BINDING SITE FOR RESIDUE MG 2 1813
13
BC4
SOFTWARE
A 2:400
BINDING SITE FOR RESIDUE MG 2 1814
14
BC5
SOFTWARE
G 2:16
BINDING SITE FOR RESIDUE MG 2 1815
15
BC6
SOFTWARE
G 2:361 , G 2:362 , G 2:376 , A 2:377 , U 2:378
BINDING SITE FOR RESIDUE MG 2 1816
16
BC7
SOFTWARE
A 2:28 , U 2:29
BINDING SITE FOR RESIDUE MG 2 1817
17
BC8
SOFTWARE
G 2:370 , A 2:604 , G 2:606
BINDING SITE FOR RESIDUE MG 2 1818
18
BC9
SOFTWARE
A 2:997 , U 2:1003
BINDING SITE FOR RESIDUE MG 2 1819
19
CC1
SOFTWARE
C 2:426 , G 2:428
BINDING SITE FOR RESIDUE MG 2 1820
20
CC2
SOFTWARE
U 2:44 , A 2:47
BINDING SITE FOR RESIDUE MG 2 1821
21
CC3
SOFTWARE
U 2:1759 , A 2:1760 , A 2:1761 , G 2:1765 , G 2:1766
BINDING SITE FOR RESIDUE MG 2 1822
22
CC4
SOFTWARE
A 2:618 , A 2:619 , A 2:620
BINDING SITE FOR RESIDUE MG 2 1823
23
CC5
SOFTWARE
A 2:618
BINDING SITE FOR RESIDUE MG 2 1825
24
CC6
SOFTWARE
C 2:1326 , G 2:1327 , G 2:1329
BINDING SITE FOR RESIDUE MG 2 1826
25
CC7
SOFTWARE
A 2:622
BINDING SITE FOR RESIDUE MG 2 1827
26
CC8
SOFTWARE
C 2:99 , A 2:100 , U 2:101 , C 2:360
BINDING SITE FOR RESIDUE MG 2 1828
27
CC9
SOFTWARE
G 2:1108 , G 2:1109
BINDING SITE FOR RESIDUE MG 2 1830
28
DC1
SOFTWARE
U 2:1768
BINDING SITE FOR RESIDUE MG 2 1831
29
DC2
SOFTWARE
G 2:95
BINDING SITE FOR RESIDUE MG 2 1832
30
DC3
SOFTWARE
G 2:1670 , G 2:1671 , C 2:1672 , U 2:1726
BINDING SITE FOR RESIDUE MG 2 1833
31
DC4
SOFTWARE
U 2:1628 , G 2:1791
BINDING SITE FOR RESIDUE MG 2 1834
32
DC5
SOFTWARE
G 2:458 , A 2:459 , G 2:460
BINDING SITE FOR RESIDUE MG 2 1836
33
DC6
SOFTWARE
G 2:466 , A 2:467
BINDING SITE FOR RESIDUE MG 2 1837
34
DC7
SOFTWARE
A 2:622 , C 2:624 , U 2:1030
BINDING SITE FOR RESIDUE MG 2 1838
35
DC8
SOFTWARE
G 2:984 , G 2:1013
BINDING SITE FOR RESIDUE MG 2 1839
36
DC9
SOFTWARE
G 2:1416
BINDING SITE FOR RESIDUE MG 2 1840
37
EC1
SOFTWARE
A 2:104 , C 2:353
BINDING SITE FOR RESIDUE MG 2 1842
38
EC2
SOFTWARE
A 2:1064
BINDING SITE FOR RESIDUE MG 2 1843
39
EC3
SOFTWARE
G 2:403 , C 2:404 , G 2:422
BINDING SITE FOR RESIDUE MG 2 1845
40
EC4
SOFTWARE
U 2:1302
BINDING SITE FOR RESIDUE MG 2 1846
41
EC5
SOFTWARE
A 2:978
BINDING SITE FOR RESIDUE MG 2 1847
42
EC6
SOFTWARE
U 2:58
BINDING SITE FOR RESIDUE MG 2 1848
43
EC7
SOFTWARE
A 2:760
BINDING SITE FOR RESIDUE MG 2 1849
44
EC8
SOFTWARE
G 2:1139
BINDING SITE FOR RESIDUE MG 2 1850
45
EC9
SOFTWARE
C 2:826 , U 2:842
BINDING SITE FOR RESIDUE MG 2 1851
46
FC1
SOFTWARE
A 2:514 , C 2:529 , C 2:530
BINDING SITE FOR RESIDUE MG 2 1852
47
FC2
SOFTWARE
U 2:1301
BINDING SITE FOR RESIDUE MG 2 1853
48
FC3
SOFTWARE
G 2:937
BINDING SITE FOR RESIDUE MG 2 1855
49
FC4
SOFTWARE
G 2:1010
BINDING SITE FOR RESIDUE MG 2 1856
50
FC5
SOFTWARE
A 2:212 , G 2:213
BINDING SITE FOR RESIDUE MG 2 1857
51
FC6
SOFTWARE
G 2:1538 , G 2:1539
BINDING SITE FOR RESIDUE MG 2 1858
52
FC7
SOFTWARE
G 2:1636
BINDING SITE FOR RESIDUE MG 2 1860
53
FC8
SOFTWARE
U 2:1008 , LYS O:129
BINDING SITE FOR RESIDUE MG 2 1863
54
FC9
SOFTWARE
G 2:884 , G 2:924
BINDING SITE FOR RESIDUE MG 2 1866
55
GC1
SOFTWARE
C 2:1158 , U 2:1282
BINDING SITE FOR RESIDUE MG 2 1868
56
GC2
SOFTWARE
A 2:1467 , A 2:1473 , G 2:1539
BINDING SITE FOR RESIDUE MG 2 1869
57
GC3
SOFTWARE
G 2:1443 , A 2:1444
BINDING SITE FOR RESIDUE MG 2 1870
58
GC4
SOFTWARE
G 2:1175 , C 2:1455
BINDING SITE FOR RESIDUE MG 2 1871
59
GC5
SOFTWARE
G 2:1198 , G 2:1200
BINDING SITE FOR RESIDUE MG 2 1872
60
GC6
SOFTWARE
C 2:1429
BINDING SITE FOR RESIDUE MG 2 1873
61
GC7
SOFTWARE
C 2:1196 , C 2:1463
BINDING SITE FOR RESIDUE MG 2 1874
62
GC8
SOFTWARE
U 2:1268
BINDING SITE FOR RESIDUE MG 2 1875
63
GC9
SOFTWARE
G 2:1272 , C 2:1273 , G 2:1426
BINDING SITE FOR RESIDUE MG 2 1876
64
HC1
SOFTWARE
G 2:1537 , G 2:1539
BINDING SITE FOR RESIDUE MG 2 1877
65
HC2
SOFTWARE
G 2:1482 , U 2:1520
BINDING SITE FOR RESIDUE MG 2 1878
66
HC3
SOFTWARE
C 2:1273 , G 2:1426 , G 2:1427 , ARG i:14
BINDING SITE FOR RESIDUE MG 2 1879
67
HC4
SOFTWARE
A 2:1201 , A 2:1202
BINDING SITE FOR RESIDUE MG 2 1880
68
HC5
SOFTWARE
U 2:64 , A 2:168 , GLN G:176
BINDING SITE FOR RESIDUE MG G 301
69
HC6
SOFTWARE
CYS a:23 , ASN a:25 , CYS a:26 , CYS a:74 , CYS a:77
BINDING SITE FOR RESIDUE ZN a 500
70
HC7
SOFTWARE
GLY b:39
BINDING SITE FOR RESIDUE ZN b 101
71
HC8
SOFTWARE
CYS f:121 , CYS f:124 , CYS f:139 , CYS f:142 , PHE f:146
BINDING SITE FOR RESIDUE ZN f 501
72
HC9
SOFTWARE
A 1:76 , GLY k:141 , TYR k:142 , ALA k:143 , GLU k:383
BINDING SITE FOR RESIDUE MET k 601
[
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
(13, 13)
Info
All PROSITE Patterns/Profiles
01: RIBOSOMAL_S21E (V:11-19)
02: RIBOSOMAL_S2_1 (A:14-25)
03: S1 (j:17-88)
04: S1_IF1_TYPE (i:22-96)
05: SUI1 (m:26-96)
06: IF1A (i:41-63)
07: RIBOSOMAL_S6E (G:52-63)
08: RIBOSOMAL_S28E (c:58-66)
09: RIBOSOMAL_S3AE (B:61-73)
10: RIBOSOMAL_S9 (Q:71-89)
11: RIBOSOMAL_S8 (W:100-117)
12: RIBOSOMAL_S11 (O:102-124)
13: RIBOSOMAL_S2_2 (A:118-142)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBOSOMAL_S21E
PS00996
Ribosomal protein S21e signature.
RS21_KLULA
11-19
1
V:11-19
2
RIBOSOMAL_S2_1
PS00962
Ribosomal protein S2 signature 1.
RSSA_KLULA
14-25
1
A:14-25
3
S1
PS50126
S1 domain profile.
IF2A_YEAST
17-88
1
j:17-88
4
S1_IF1_TYPE
PS50832
S1 domain IF1 type profile.
IF1A_YEAST
22-96
1
i:22-96
5
SUI1
PS50296
Translation initiation factor SUI1 family profile.
SUI1_YEAST
26-96
1
m:26-96
6
IF1A
PS01262
Eukaryotic initiation factor 1A signature.
IF1A_YEAST
41-63
1
i:41-63
7
RIBOSOMAL_S6E
PS00578
Ribosomal protein S6e signature.
RS6_KLULA
52-63
1
G:52-63
8
RIBOSOMAL_S28E
PS00961
Ribosomal protein S28e signature.
RS28_KLULA
58-66
1
c:58-66
9
RIBOSOMAL_S3AE
PS01191
Ribosomal protein S3Ae signature.
RS3A_KLULA
61-73
1
B:61-73
10
RIBOSOMAL_S9
PS00360
Ribosomal protein S9 signature.
RS16_KLULA
71-89
1
Q:71-89
11
RIBOSOMAL_S8
PS00053
Ribosomal protein S8 signature.
RS22_KLULA
100-117
1
W:100-117
12
RIBOSOMAL_S11
PS00054
Ribosomal protein S11 signature.
RS14_KLULA
102-124
1
O:102-124
13
RIBOSOMAL_S2_2
PS00963
Ribosomal protein S2 signature 2.
RSSA_KLULA
118-142
1
A:118-142
[
close PROSITE info
]
Exons
(2, 2)
Info
All Exons
Exon 1.1 (j:3-265 (gaps))
Exon 2.1 (m:19-108)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
3: Boundary -/2.1
4: Boundary 2.1/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
YJR007W
1
YJR007W.1
X:451012-451926
915
IF2A_YEAST
1-304
304
1
j:3-265 (gaps)
263
2.1
YNL244C
1
YNL244C.1
XIV:187497-187171
327
SUI1_YEAST
1-108
108
1
m:19-108
90
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
Chain Q
Chain R
Chain S
Chain T
Chain U
Chain V
Chain W
Chain X
Chain Y
Chain Z
Chain a
Chain b
Chain c
Chain d
Chain e
Chain f
Chain g
Chain h
Chain i
Chain j
Chain k
Chain l
Chain m
Chain 1
Chain 2
Chain 3
Asymmetric Unit 1
Rendering
(selected part)
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by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
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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
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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).
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