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2Z66
Asym. Unit
Info
Asym.Unit (226 KB)
Biol.Unit 1 (58 KB)
Biol.Unit 2 (58 KB)
Biol.Unit 3 (58 KB)
Biol.Unit 4 (58 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE VT3 HYBRID OF HUMAN TLR4 AND HAGFISH VLRB.61
Authors
:
J. -O. Lee, H. M. Kim, B. S. Park
Date
:
22 Jul 07 (Deposition) - 18 Sep 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Tlr4, Toll-Like Receptor, Md-2, Lps, Leucine-Rich Repeat, Glycoprotein, Immune Response, Inflammatory Response, Innate Immunity, Membrane, Transmembrane, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. M. Kim, B. S. Park, J. -I. Kim, S. E. Kim, J. Lee, S. C. Oh, P. Enkhbayar, N. Matsushima, H. Lee, O. J. Yoo, J. -O. Lee
Crystal Structure Of The Tlr4-Md-2 Complex With Bound Endotoxin Antagonist Eritoran
Cell(Cambridge, Mass. ) V. 130 906 2007
[
close entry info
]
Hetero Components
(4, 48)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
1e: BETA-D-MANNOSE (BMAe)
1f: BETA-D-MANNOSE (BMAf)
1g: BETA-D-MANNOSE (BMAg)
1h: BETA-D-MANNOSE (BMAh)
2a: BETA-L-FUCOSE (FULa)
2b: BETA-L-FUCOSE (FULb)
2c: BETA-L-FUCOSE (FULc)
2d: BETA-L-FUCOSE (FULd)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
3ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
3ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
3ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
3ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
3af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3o: N-ACETYL-D-GLUCOSAMINE (NAGo)
3p: N-ACETYL-D-GLUCOSAMINE (NAGp)
3q: N-ACETYL-D-GLUCOSAMINE (NAGq)
3r: N-ACETYL-D-GLUCOSAMINE (NAGr)
3s: N-ACETYL-D-GLUCOSAMINE (NAGs)
3t: N-ACETYL-D-GLUCOSAMINE (NAGt)
3u: N-ACETYL-D-GLUCOSAMINE (NAGu)
3v: N-ACETYL-D-GLUCOSAMINE (NAGv)
3w: N-ACETYL-D-GLUCOSAMINE (NAGw)
3x: N-ACETYL-D-GLUCOSAMINE (NAGx)
3y: N-ACETYL-D-GLUCOSAMINE (NAGy)
3z: N-ACETYL-D-GLUCOSAMINE (NAGz)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
8
Ligand/Ion
BETA-D-MANNOSE
2
FUL
4
Ligand/Ion
BETA-L-FUCOSE
3
NAG
32
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
SO4
4
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
ASP A:550 , SER A:552 , ASN A:575 , VAL A:602 , NAG A:1421 , NAG A:1432 , HOH A:2338 , HOH A:2474
BINDING SITE FOR RESIDUE NAG A 1431
02
AC2
SOFTWARE
VAL A:548 , PHE A:573 , NAG A:1421 , NAG A:1431 , BMA A:1433
BINDING SITE FOR RESIDUE NAG A 1432
03
AC3
SOFTWARE
NAG A:1432
BINDING SITE FOR RESIDUE BMA A 1433
04
AC4
SOFTWARE
SER A:504 , GLN A:505 , ASN A:526 , ASP A:550 , NAG A:1422 , NAG A:1431 , NAG A:1432 , HOH A:2133 , HOH A:2361
BINDING SITE FOR RESIDUE NAG A 1421
05
AC5
SOFTWARE
LEU A:553 , NAG A:1421 , HOH A:2474
BINDING SITE FOR RESIDUE NAG A 1422
06
AC6
SOFTWARE
ASN A:624 , FUL A:1402 , NAG A:1403
BINDING SITE FOR RESIDUE NAG A 1401
07
AC7
SOFTWARE
NAG A:1401 , NAG A:1403
BINDING SITE FOR RESIDUE FUL A 1402
08
AC8
SOFTWARE
NAG A:1401 , FUL A:1402 , BMA A:1404
BINDING SITE FOR RESIDUE NAG A 1403
09
AC9
SOFTWARE
NAG A:1403
BINDING SITE FOR RESIDUE BMA A 1404
10
BC1
SOFTWARE
SER A:472 , ASN A:497 , NAG A:1412
BINDING SITE FOR RESIDUE NAG A 1411
11
BC2
SOFTWARE
NAG A:1411
BINDING SITE FOR RESIDUE NAG A 1412
12
BC3
SOFTWARE
ASP B:550 , SER B:552 , ASN B:575 , VAL B:602 , NAG B:1421 , NAG B:1432 , HOH B:2298
BINDING SITE FOR RESIDUE NAG B 1431
13
BC4
SOFTWARE
VAL B:548 , PHE B:573 , NAG B:1421 , NAG B:1431 , BMA B:1433
BINDING SITE FOR RESIDUE NAG B 1432
14
BC5
SOFTWARE
NAG B:1432
BINDING SITE FOR RESIDUE BMA B 1433
15
BC6
SOFTWARE
SER B:504 , GLN B:505 , ASN B:526 , ASP B:550 , NAG B:1422 , NAG B:1431 , NAG B:1432 , HOH B:2118 , HOH B:2348
BINDING SITE FOR RESIDUE NAG B 1421
16
BC7
SOFTWARE
LEU B:553 , NAG B:1421
BINDING SITE FOR RESIDUE NAG B 1422
17
BC8
SOFTWARE
ASN B:624 , FUL B:1402 , NAG B:1403 , HOH B:2142
BINDING SITE FOR RESIDUE NAG B 1401
18
BC9
SOFTWARE
NAG B:1401 , NAG B:1403
BINDING SITE FOR RESIDUE FUL B 1402
19
CC1
SOFTWARE
NAG B:1401 , FUL B:1402 , BMA B:1404
BINDING SITE FOR RESIDUE NAG B 1403
20
CC2
SOFTWARE
NAG B:1403
BINDING SITE FOR RESIDUE BMA B 1404
21
CC3
SOFTWARE
SER B:472 , ASN B:497 , NAG B:1412
BINDING SITE FOR RESIDUE NAG B 1411
22
CC4
SOFTWARE
NAG B:1411
BINDING SITE FOR RESIDUE NAG B 1412
23
CC5
SOFTWARE
ASP C:550 , SER C:552 , ASN C:575 , VAL C:602 , NAG C:1421 , NAG C:1432 , HOH C:2294
BINDING SITE FOR RESIDUE NAG C 1431
24
CC6
SOFTWARE
VAL C:548 , PHE C:573 , NAG C:1421 , NAG C:1431 , BMA C:1433
BINDING SITE FOR RESIDUE NAG C 1432
25
CC7
SOFTWARE
NAG C:1432
BINDING SITE FOR RESIDUE BMA C 1433
26
CC8
SOFTWARE
SER C:504 , GLN C:505 , ASN C:526 , ASP C:550 , NAG C:1422 , NAG C:1431 , NAG C:1432 , HOH C:2125 , HOH C:2441
BINDING SITE FOR RESIDUE NAG C 1421
27
CC9
SOFTWARE
LEU C:553 , NAG C:1421 , HOH C:2441
BINDING SITE FOR RESIDUE NAG C 1422
28
DC1
SOFTWARE
ASN C:624 , FUL C:1402 , NAG C:1403
BINDING SITE FOR RESIDUE NAG C 1401
29
DC2
SOFTWARE
NAG C:1401 , NAG C:1403
BINDING SITE FOR RESIDUE FUL C 1402
30
DC3
SOFTWARE
NAG C:1401 , FUL C:1402 , BMA C:1404
BINDING SITE FOR RESIDUE NAG C 1403
31
DC4
SOFTWARE
NAG C:1403
BINDING SITE FOR RESIDUE BMA C 1404
32
DC5
SOFTWARE
SER C:472 , ASN C:497 , NAG C:1412
BINDING SITE FOR RESIDUE NAG C 1411
33
DC6
SOFTWARE
NAG C:1411
BINDING SITE FOR RESIDUE NAG C 1412
34
DC7
SOFTWARE
ASP D:550 , SER D:552 , ASN D:575 , VAL D:602 , NAG D:1421 , NAG D:1432 , HOH D:2318 , HOH D:2414
BINDING SITE FOR RESIDUE NAG D 1431
35
DC8
SOFTWARE
VAL D:548 , PHE D:573 , NAG D:1421 , NAG D:1431 , BMA D:1433 , HOH D:2466
BINDING SITE FOR RESIDUE NAG D 1432
36
DC9
SOFTWARE
NAG D:1432
BINDING SITE FOR RESIDUE BMA D 1433
37
EC1
SOFTWARE
SER D:504 , GLN D:505 , ASN D:526 , ASP D:550 , NAG D:1422 , NAG D:1431 , NAG D:1432 , HOH D:2128 , HOH D:2363
BINDING SITE FOR RESIDUE NAG D 1421
38
EC2
SOFTWARE
LEU D:553 , NAG D:1421 , HOH D:2414
BINDING SITE FOR RESIDUE NAG D 1422
39
EC3
SOFTWARE
ASN D:624 , FUL D:1402 , NAG D:1403
BINDING SITE FOR RESIDUE NAG D 1401
40
EC4
SOFTWARE
NAG D:1401 , NAG D:1403
BINDING SITE FOR RESIDUE FUL D 1402
41
EC5
SOFTWARE
NAG D:1401 , FUL D:1402 , BMA D:1404
BINDING SITE FOR RESIDUE NAG D 1403
42
EC6
SOFTWARE
NAG D:1403
BINDING SITE FOR RESIDUE BMA D 1404
43
EC7
SOFTWARE
SER D:472 , ASN D:497 , NAG D:1412
BINDING SITE FOR RESIDUE NAG D 1411
44
EC8
SOFTWARE
NAG D:1411
BINDING SITE FOR RESIDUE NAG D 1412
45
EC9
SOFTWARE
THR A:558 , GLU A:586 , HIS A:587 , SER A:589 , PHE A:590 , HOH A:2038 , HOH A:2126 , SER B:26 , ARG B:27 , HOH B:2144
BINDING SITE FOR RESIDUE SO4 A 2001
46
FC1
SOFTWARE
SER A:26 , ARG A:27 , HOH A:2148 , THR B:558 , GLU B:586 , HIS B:587 , SER B:589 , PHE B:590 , HOH B:2048 , HOH B:2108
BINDING SITE FOR RESIDUE SO4 B 2002
47
FC2
SOFTWARE
THR C:558 , GLU C:586 , HIS C:587 , SER C:589 , PHE C:590 , HOH C:2042 , HOH C:2110 , HOH C:2146 , SER D:26 , ARG D:27
BINDING SITE FOR RESIDUE SO4 C 2003
48
FC3
SOFTWARE
SER C:26 , ARG C:27 , HOH C:2159 , THR D:558 , GLU D:586 , HIS D:587 , SER D:589 , PHE D:590 , HOH D:2036 , HOH D:2119
BINDING SITE FOR RESIDUE SO4 D 2004
[
close Site info
]
SAPs(SNPs)/Variants
(8, 32)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_021977 (T54A, chain A/B/C/D, )
2: VAR_018729 (Q64R, chain A/B/C/D, )
3: VAR_037668 (L385F, chain A/B/C/D, )
4: VAR_012740 (T399I, chain A/B/C/D, )
5: VAR_020335 (S400N, chain A/B/C/D, )
6: VAR_018732 (F443L, chain A/B/C/D, )
7: VAR_018733 (E474K, chain A/B/C/D, )
8: VAR_018734 (Q510H, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_021977
T
175
A
TLR4_HUMAN
Polymorphism
16906079
A/B/C/D
T
54
A
2
UniProt
VAR_018729
Q
188
R
TLR4_HUMAN
Polymorphism
5030713
A/B/C/D
Q
64
R
3
UniProt
VAR_037668
L
385
F
TLR4_HUMAN
Polymorphism
11536884
A/B/C/D
L
385
F
4
UniProt
VAR_012740
T
399
I
TLR4_HUMAN
Polymorphism
4986791
A/B/C/D
T
399
I
5
UniProt
VAR_020335
S
400
N
TLR4_HUMAN
Polymorphism
4987233
A/B/C/D
S
400
N
6
UniProt
VAR_018732
F
443
L
TLR4_HUMAN
Polymorphism
5030716
A/B/C/D
F
443
L
7
UniProt
VAR_018733
E
474
K
TLR4_HUMAN
Polymorphism
5030718
A/B/C/D
E
474
K
8
UniProt
VAR_018734
Q
510
H
TLR4_HUMAN
Polymorphism
5030719
A/B/C/D
Q
510
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 40)
Info
All PROSITE Patterns/Profiles
1: LRR (-|A:26-28,B:26-28,C:26-28,D:26-28|...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LRR
PS51450
Leucine-rich repeat profile.
TLR4_HUMAN
55-76
79-100
103-124
176-199
151-172
374-394
400-422
423-444
497-518
521-542
545-565
40
-
A:26-28
B:26-28
C:26-28
D:26-28
A:32-41
B:32-41
C:32-41
D:32-41
A:56-65
B:56-65
C:56-65
D:56-65
A:51-51
B:51-51
C:51-51
D:51-51
A:383-394
B:383-394
C:383-394
D:383-394
A:400-422
B:400-422
C:400-422
D:400-422
A:423-444
B:423-444
C:423-444
D:423-444
A:497-518
B:497-518
C:497-518
D:497-518
A:521-542
B:521-542
C:521-542
D:521-542
A:545-565
B:545-565
C:545-565
D:545-565
[
close PROSITE info
]
Exons
(3, 12)
Info
All Exons
Exon 1.1b (A:24-25 | B:24-25 | C:24-25 | D:24...)
Exon 1.3a (A:26-27 | B:26-27 | C:26-27 | D:26...)
Exon 1.4c (A:27-627 (gaps) | B:27-627 (gaps) ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1b
2: Boundary 1.1b/1.3a
3: Boundary 1.3a/1.4c
4: Boundary 1.4c/-
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
1.1b
ENST00000355622
1b
ENSE00001946124
chr9:
120466650-120466843
194
TLR4_HUMAN
1-31
31
4
A:24-25
B:24-25
C:24-25
D:24-25
2
2
2
2
1.3a
ENST00000355622
3a
ENSE00001654637
chr9:
120470841-120471007
167
TLR4_HUMAN
32-87
56
4
A:26-27
B:26-27
C:26-27
D:26-27
2
2
2
2
1.4c
ENST00000355622
4c
ENSE00001462052
chr9:
120474667-120479149
4483
TLR4_HUMAN
87-839
753
4
A:27-627 (gaps)
B:27-627 (gaps)
C:27-627 (gaps)
D:27-627 (gaps)
541
541
541
541
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 24)
Info
all PFAM domains
1a: PFAM_LRR_6_2z66D01 (D:383-395)
1b: PFAM_LRR_6_2z66D02 (D:383-395)
1c: PFAM_LRR_6_2z66D03 (D:383-395)
1d: PFAM_LRR_6_2z66D04 (D:383-395)
2a: PFAM_LRR_8_2z66D05 (D:496-556)
2b: PFAM_LRR_8_2z66D06 (D:496-556)
2c: PFAM_LRR_8_2z66D07 (D:496-556)
2d: PFAM_LRR_8_2z66D08 (D:496-556)
2e: PFAM_LRR_8_2z66D09 (D:496-556)
2f: PFAM_LRR_8_2z66D10 (D:496-556)
2g: PFAM_LRR_8_2z66D11 (D:496-556)
2h: PFAM_LRR_8_2z66D12 (D:496-556)
2i: PFAM_LRR_8_2z66D13 (D:496-556)
2j: PFAM_LRR_8_2z66D14 (D:496-556)
2k: PFAM_LRR_8_2z66D15 (D:496-556)
2l: PFAM_LRR_8_2z66D16 (D:496-556)
2m: PFAM_LRR_8_2z66D17 (D:496-556)
2n: PFAM_LRR_8_2z66D18 (D:496-556)
2o: PFAM_LRR_8_2z66D19 (D:496-556)
2p: PFAM_LRR_8_2z66D20 (D:496-556)
2q: PFAM_LRR_8_2z66D21 (D:496-556)
2r: PFAM_LRR_8_2z66D22 (D:496-556)
2s: PFAM_LRR_8_2z66D23 (D:496-556)
2t: PFAM_LRR_8_2z66D24 (D:496-556)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
LRR
(77)
Family
:
LRR_6
(24)
Homo sapiens (Human)
(4)
1a
LRR_6-2z66D01
D:383-395
1b
LRR_6-2z66D02
D:383-395
1c
LRR_6-2z66D03
D:383-395
1d
LRR_6-2z66D04
D:383-395
Family
:
LRR_8
(41)
Homo sapiens (Human)
(24)
2a
LRR_8-2z66D05
D:496-556
2b
LRR_8-2z66D06
D:496-556
2c
LRR_8-2z66D07
D:496-556
2d
LRR_8-2z66D08
D:496-556
2e
LRR_8-2z66D09
D:496-556
2f
LRR_8-2z66D10
D:496-556
2g
LRR_8-2z66D11
D:496-556
2h
LRR_8-2z66D12
D:496-556
2i
LRR_8-2z66D13
D:496-556
2j
LRR_8-2z66D14
D:496-556
2k
LRR_8-2z66D15
D:496-556
2l
LRR_8-2z66D16
D:496-556
2m
LRR_8-2z66D17
D:496-556
2n
LRR_8-2z66D18
D:496-556
2o
LRR_8-2z66D19
D:496-556
2p
LRR_8-2z66D20
D:496-556
2q
LRR_8-2z66D21
D:496-556
2r
LRR_8-2z66D22
D:496-556
2s
LRR_8-2z66D23
D:496-556
2t
LRR_8-2z66D24
D:496-556
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Atom Selection
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Asymmetric Unit 1
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Example Commands
Example Command
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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 (226 KB)
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