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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3FXI
Asym. Unit
Info
Asym.Unit (264 KB)
Biol.Unit 1 (253 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE HUMAN TLR4-HUMAN MD-2-E.COLI LPS RA COMPLEX
Authors
:
B. S. Park, D. H. Song, H. M. Kim, J. -O. Lee
Date
:
21 Jan 09 (Deposition) - 03 Mar 09 (Release) - 20 Jun 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Leucine Rich Repeat, Glycoprotein, Immune Response, Inflammatory Response, Innate Immunity, Membrane, Receptor, Transmembrane, Secreted, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. S. Park, D. H. Song, H. M. Kim, B. -S. Choi, H. Lee, J. -O. Lee
The Structural Basis Of Lipopolysaccharide Recognition By The Tlr4-Md-2 Complex
Nature V. 458 1191 2009
[
close entry info
]
Hetero Components
(10, 52)
Info
All Hetero Components
01a: LAURIC ACID (DAOa)
01b: LAURIC ACID (DAOb)
02a: 3-HYDROXY-TETRADECANOIC ACID (FTTa)
02b: 3-HYDROXY-TETRADECANOIC ACID (FTTb)
02c: 3-HYDROXY-TETRADECANOIC ACID (FTTc)
02d: 3-HYDROXY-TETRADECANOIC ACID (FTTd)
02e: 3-HYDROXY-TETRADECANOIC ACID (FTTe)
02f: 3-HYDROXY-TETRADECANOIC ACID (FTTf)
02g: 3-HYDROXY-TETRADECANOIC ACID (FTTg)
02h: 3-HYDROXY-TETRADECANOIC ACID (FTTh)
03a: D-GLUCOSAMINE (GCSa)
04a: L-GLYCERO-D-MANNO-HEPTOPYRANOSE (GMHa)
04b: L-GLYCERO-D-MANNO-HEPTOPYRANOSE (GMHb)
04c: L-GLYCERO-D-MANNO-HEPTOPYRANOSE (GMHc)
04d: L-GLYCERO-D-MANNO-HEPTOPYRANOSE (GMHd)
04e: L-GLYCERO-D-MANNO-HEPTOPYRANOSE (GMHe)
04f: L-GLYCERO-D-MANNO-HEPTOPYRANOSE (GMHf)
05a: 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACI... (KDOa)
05b: 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACI... (KDOb)
05c: 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACI... (KDOc)
05d: 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACI... (KDOd)
06a: MAGNESIUM ION (MGa)
06b: MAGNESIUM ION (MGb)
07a: MYRISTIC ACID (MYRa)
07b: MYRISTIC ACID (MYRb)
08a: N-ACETYL-D-GLUCOSAMINE (NAGa)
08b: N-ACETYL-D-GLUCOSAMINE (NAGb)
08c: N-ACETYL-D-GLUCOSAMINE (NAGc)
08d: N-ACETYL-D-GLUCOSAMINE (NAGd)
08e: N-ACETYL-D-GLUCOSAMINE (NAGe)
08f: N-ACETYL-D-GLUCOSAMINE (NAGf)
08g: N-ACETYL-D-GLUCOSAMINE (NAGg)
08h: N-ACETYL-D-GLUCOSAMINE (NAGh)
08i: N-ACETYL-D-GLUCOSAMINE (NAGi)
08j: N-ACETYL-D-GLUCOSAMINE (NAGj)
08k: N-ACETYL-D-GLUCOSAMINE (NAGk)
08l: N-ACETYL-D-GLUCOSAMINE (NAGl)
08m: N-ACETYL-D-GLUCOSAMINE (NAGm)
08n: N-ACETYL-D-GLUCOSAMINE (NAGn)
08o: N-ACETYL-D-GLUCOSAMINE (NAGo)
08p: N-ACETYL-D-GLUCOSAMINE (NAGp)
09a: 2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRAN... (PA1a)
09b: 2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRAN... (PA1b)
09c: 2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRAN... (PA1c)
10a: PHOSPHATE ION (PO4a)
10b: PHOSPHATE ION (PO4b)
10c: PHOSPHATE ION (PO4c)
10d: PHOSPHATE ION (PO4d)
10e: PHOSPHATE ION (PO4e)
10f: PHOSPHATE ION (PO4f)
10g: PHOSPHATE ION (PO4g)
10h: PHOSPHATE ION (PO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DAO
2
Ligand/Ion
LAURIC ACID
2
FTT
8
Ligand/Ion
3-HYDROXY-TETRADECANOIC ACID
3
GCS
1
Ligand/Ion
D-GLUCOSAMINE
4
GMH
6
Ligand/Ion
L-GLYCERO-D-MANNO-HEPTOPYRANOSE
5
KDO
4
Ligand/Ion
3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
6
MG
2
Ligand/Ion
MAGNESIUM ION
7
MYR
2
Ligand/Ion
MYRISTIC ACID
8
NAG
16
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
9
PA1
3
Ligand/Ion
2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE
10
PO4
8
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(52, 52)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PA1 A:1002 , FTT A:1005 , FTT A:1006 , PO4 A:1010 , KDO A:1012 , SER C:120
BINDING SITE FOR RESIDUE PA1 A 1001
02
AC2
SOFTWARE
PA1 A:1001 , FTT A:1003 , FTT A:1004 , FTT A:1005 , PO4 A:1011 , LYS C:122
BINDING SITE FOR RESIDUE PA1 A 1002
03
AC3
SOFTWARE
TYR A:296 , LYS A:341 , PA1 A:1001 , KDO A:1013 , GMH A:1014 , GMH A:1015 , GMH A:1016
BINDING SITE FOR RESIDUE KDO A 1012
04
AC4
SOFTWARE
KDO A:1012 , GMH A:1016 , PO4 A:1018 , LYS C:58
BINDING SITE FOR RESIDUE KDO A 1013
05
AC5
SOFTWARE
PO4 A:1011 , KDO A:1012 , GMH A:1015 , PO4 A:1018
BINDING SITE FOR RESIDUE GMH A 1014
06
AC6
SOFTWARE
TYR A:296 , KDO A:1012 , GMH A:1014 , GMH A:1016 , PO4 A:1017
BINDING SITE FOR RESIDUE GMH A 1015
07
AC7
SOFTWARE
ASP A:294 , KDO A:1012 , KDO A:1013 , GMH A:1015
BINDING SITE FOR RESIDUE GMH A 1016
08
AC8
SOFTWARE
PA1 A:1002 , GLN B:436 , VAL C:82 , LEU C:87 , SER C:127 , TYR C:131
BINDING SITE FOR RESIDUE FTT A 1003
09
AC9
SOFTWARE
PA1 A:1002 , PHE C:121 , LYS C:122 , ILE C:124 , PHE C:151
BINDING SITE FOR RESIDUE FTT A 1004
10
BC1
SOFTWARE
PA1 A:1001 , PA1 A:1002 , DAO A:1007 , PHE C:119 , PHE C:151
BINDING SITE FOR RESIDUE FTT A 1005
11
BC2
SOFTWARE
ARG A:264 , PA1 A:1001 , MYR A:1008 , PO4 A:1010 , TYR C:65 , LEU C:71 , PHE C:104 , ILE C:117 , SER C:118 , PHE C:119
BINDING SITE FOR RESIDUE FTT A 1006
12
BC3
SOFTWARE
FTT A:1005 , ARG C:90 , TYR C:131
BINDING SITE FOR RESIDUE DAO A 1007
13
BC4
SOFTWARE
FTT A:1006 , ILE C:46 , ILE C:63 , PHE C:76 , GLU C:92
BINDING SITE FOR RESIDUE MYR A 1008
14
BC5
SOFTWARE
ARG A:264 , PA1 A:1001 , FTT A:1006 , MG A:2001 , SER C:118
BINDING SITE FOR RESIDUE PO4 A 1010
15
BC6
SOFTWARE
PA1 A:1002 , GMH A:1014
BINDING SITE FOR RESIDUE PO4 A 1011
16
BC7
SOFTWARE
GMH A:1015
BINDING SITE FOR RESIDUE PO4 A 1017
17
BC8
SOFTWARE
KDO A:1013 , GMH A:1014
BINDING SITE FOR RESIDUE PO4 A 1018
18
BC9
SOFTWARE
HIS A:148 , ASN A:173
BINDING SITE FOR RESIDUE NAG A 711
19
CC1
SOFTWARE
GLU A:178 , HIS A:179 , ASN A:205 , SER A:207
BINDING SITE FOR RESIDUE NAG A 721
20
CC2
SOFTWARE
SER A:504 , GLN A:505 , ASN A:526 , ASP A:550 , NAG A:732 , NAG A:761
BINDING SITE FOR RESIDUE NAG A 731
21
CC3
SOFTWARE
NAG A:731 , NAG A:761 , NAG A:762
BINDING SITE FOR RESIDUE NAG A 732
22
CC4
SOFTWARE
ASN A:497 , ASP A:614
BINDING SITE FOR RESIDUE NAG A 741
23
CC5
SOFTWARE
ASP A:550 , ASN A:575 , THR A:577 , NAG A:731 , NAG A:732 , NAG A:762
BINDING SITE FOR RESIDUE NAG A 761
24
CC6
SOFTWARE
NAG A:732 , NAG A:761
BINDING SITE FOR RESIDUE NAG A 762
25
CC7
SOFTWARE
HOH A:1 , ASP A:294 , PO4 A:1010
BINDING SITE FOR RESIDUE MG A 2001
26
CC8
SOFTWARE
PA1 B:1002 , FTT B:1005 , FTT B:1006 , PO4 B:1010 , KDO B:1012 , SER D:120
BINDING SITE FOR RESIDUE GCS B 1001
27
CC9
SOFTWARE
GCS B:1001 , FTT B:1003 , FTT B:1004 , FTT B:1005 , PO4 B:1011 , LYS D:122
BINDING SITE FOR RESIDUE PA1 B 1002
28
DC1
SOFTWARE
TYR B:296 , LYS B:341 , GCS B:1001 , KDO B:1013 , GMH B:1014 , GMH B:1015 , GMH B:1016
BINDING SITE FOR RESIDUE KDO B 1012
29
DC2
SOFTWARE
KDO B:1012 , GMH B:1016 , PO4 B:1018 , LYS D:58
BINDING SITE FOR RESIDUE KDO B 1013
30
DC3
SOFTWARE
PO4 B:1011 , KDO B:1012 , GMH B:1015 , PO4 B:1018
BINDING SITE FOR RESIDUE GMH B 1014
31
DC4
SOFTWARE
TYR B:296 , KDO B:1012 , GMH B:1014 , GMH B:1016 , PO4 B:1017
BINDING SITE FOR RESIDUE GMH B 1015
32
DC5
SOFTWARE
ASP B:294 , KDO B:1012 , KDO B:1013 , GMH B:1015
BINDING SITE FOR RESIDUE GMH B 1016
33
DC6
SOFTWARE
GLN A:436 , PA1 B:1002 , VAL D:82 , LEU D:87 , SER D:127 , TYR D:131
BINDING SITE FOR RESIDUE FTT B 1003
34
DC7
SOFTWARE
PA1 B:1002 , PHE D:121 , LYS D:122 , ILE D:124 , PHE D:151
BINDING SITE FOR RESIDUE FTT B 1004
35
DC8
SOFTWARE
GCS B:1001 , PA1 B:1002 , DAO B:1007 , PHE D:119 , PHE D:151
BINDING SITE FOR RESIDUE FTT B 1005
36
DC9
SOFTWARE
ARG B:264 , GCS B:1001 , MYR B:1008 , PO4 B:1010 , TYR D:65 , LEU D:71 , PHE D:104 , ILE D:117 , SER D:118 , PHE D:119
BINDING SITE FOR RESIDUE FTT B 1006
37
EC1
SOFTWARE
FTT B:1005 , MYR B:1008 , ARG D:90
BINDING SITE FOR RESIDUE DAO B 1007
38
EC2
SOFTWARE
FTT B:1006 , DAO B:1007 , ILE D:46 , ILE D:63 , PHE D:76 , GLU D:92
BINDING SITE FOR RESIDUE MYR B 1008
39
EC3
SOFTWARE
ARG B:264 , GCS B:1001 , FTT B:1006 , MG B:2001 , SER D:118
BINDING SITE FOR RESIDUE PO4 B 1010
40
EC4
SOFTWARE
PA1 B:1002 , GMH B:1014
BINDING SITE FOR RESIDUE PO4 B 1011
41
EC5
SOFTWARE
ARG B:322 , GMH B:1015
BINDING SITE FOR RESIDUE PO4 B 1017
42
EC6
SOFTWARE
KDO B:1013 , GMH B:1014
BINDING SITE FOR RESIDUE PO4 B 1018
43
EC7
SOFTWARE
ASN B:173
BINDING SITE FOR RESIDUE NAG B 811
44
EC8
SOFTWARE
GLU B:178 , HIS B:179 , ASN B:205
BINDING SITE FOR RESIDUE NAG B 821
45
EC9
SOFTWARE
SER B:504 , GLN B:505 , ASN B:526 , ASP B:550 , NAG B:832 , NAG B:861 , NAG B:862
BINDING SITE FOR RESIDUE NAG B 831
46
FC1
SOFTWARE
NAG B:831 , NAG B:861 , NAG B:862
BINDING SITE FOR RESIDUE NAG B 832
47
FC2
SOFTWARE
SER B:472 , ASN B:497
BINDING SITE FOR RESIDUE NAG B 841
48
FC3
SOFTWARE
ASP B:550 , SER B:552 , PHE B:573 , ASN B:575 , THR B:577 , VAL B:602 , NAG B:831 , NAG B:832 , NAG B:862
BINDING SITE FOR RESIDUE NAG B 861
49
FC4
SOFTWARE
NAG B:831 , NAG B:832 , NAG B:861
BINDING SITE FOR RESIDUE NAG B 862
50
FC5
SOFTWARE
ASP B:294 , PO4 B:1010
BINDING SITE FOR RESIDUE MG B 2001
51
FC6
SOFTWARE
PHE C:64 , ASN C:114
BINDING SITE FOR RESIDUE NAG C 751
52
FC7
SOFTWARE
PHE D:64 , ASN D:114
BINDING SITE FOR RESIDUE NAG D 851
[
close Site info
]
SAPs(SNPs)/Variants
(16, 32)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_050030 (G56G, chain C/D, )
02: VAR_024532 (P157S, chain C/D, )
03: VAR_021977 (T175A, chain A/B, )
04: VAR_018729 (Q188R, chain A/B, )
05: VAR_018730 (C246S, chain A/B, )
06: VAR_012739 (D299G, chain A/B, )
07: VAR_047563 (C306W, chain A/B, )
08: VAR_047564 (V310G, chain A/B, )
09: VAR_018731 (N329S, chain A/B, )
10: VAR_020334 (F342Y, chain A/B, )
11: VAR_037668 (L385F, chain A/B, )
12: VAR_012740 (T399I, chain A/B, )
13: VAR_020335 (S400N, chain A/B, )
14: VAR_018732 (F443L, chain A/B, )
15: VAR_018733 (E474K, chain A/B, )
16: VAR_018734 (Q510H, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_050030
R
56
G
LY96_HUMAN
Polymorphism
6472812
C/D
G
56
G
02
UniProt
VAR_024532
P
157
S
LY96_HUMAN
Polymorphism
11466004
C/D
P
157
S
03
UniProt
VAR_021977
T
175
A
TLR4_HUMAN
Polymorphism
16906079
A/B
T
175
A
04
UniProt
VAR_018729
Q
188
R
TLR4_HUMAN
Polymorphism
5030713
A/B
Q
188
R
05
UniProt
VAR_018730
C
246
S
TLR4_HUMAN
Polymorphism
5030714
A/B
C
246
S
06
UniProt
VAR_012739
D
299
G
TLR4_HUMAN
Polymorphism
4986790
A/B
D
299
G
07
UniProt
VAR_047563
C
306
W
TLR4_HUMAN
Polymorphism
2770145
A/B
C
306
W
08
UniProt
VAR_047564
V
310
G
TLR4_HUMAN
Polymorphism
2770144
A/B
V
310
G
09
UniProt
VAR_018731
N
329
S
TLR4_HUMAN
Polymorphism
5030715
A/B
N
329
S
10
UniProt
VAR_020334
F
342
Y
TLR4_HUMAN
Polymorphism
5031050
A/B
F
342
Y
11
UniProt
VAR_037668
L
385
F
TLR4_HUMAN
Polymorphism
11536884
A/B
L
385
F
12
UniProt
VAR_012740
T
399
I
TLR4_HUMAN
Polymorphism
4986791
A/B
T
399
I
13
UniProt
VAR_020335
S
400
N
TLR4_HUMAN
Polymorphism
4987233
A/B
S
400
N
14
UniProt
VAR_018732
F
443
L
TLR4_HUMAN
Polymorphism
5030716
A/B
F
443
L
15
UniProt
VAR_018733
E
474
K
TLR4_HUMAN
Polymorphism
5030718
A/B
E
474
K
16
UniProt
VAR_018734
Q
510
H
TLR4_HUMAN
Polymorphism
5030719
A/B
Q
510
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 22)
Info
All PROSITE Patterns/Profiles
1: LRR (A:55-76,B:55-76|A:79-100,B:79-100|...)
;
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
22
A:55-76
B:55-76
A:79-100
B:79-100
A:103-124
B:103-124
A:176-199
B:176-199
A:151-172
B:151-172
A:374-394
B:374-394
A:400-422
B:400-422
A:423-444
B:423-444
A:497-518
B:497-518
A:521-542
B:521-542
A:545-565
B:545-565
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.1a (C:19-38 | D:19-38)
Exon 1.2 (C:38-68 | D:38-68)
Exon 1.3 (C:68-111 | D:68-111)
Exon 1.4 (C:111-128 | D:111-128)
Exon 1.5b (C:129-158 | D:129-158)
Exon 2.1b (A:27-31 | B:27-31)
Exon 2.3a (A:32-87 | B:32-87)
Exon 2.4c (A:87-627 | B:87-627)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5b
06: Boundary 1.5b/-
07: Boundary -/2.1b
08: Boundary 2.1b/2.3a
09: Boundary 2.3a/2.4c
10: Boundary 2.4c/-
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
1.1a
ENST00000284818
1a
ENSE00001244306
chr8:
74903587-74903789
203
LY96_HUMAN
1-38
38
2
C:19-38
D:19-38
20
20
1.2
ENST00000284818
2
ENSE00001016737
chr8:
74917031-74917120
90
LY96_HUMAN
38-68
31
2
C:38-68
D:38-68
31
31
1.3
ENST00000284818
3
ENSE00001016736
chr8:
74922236-74922364
129
LY96_HUMAN
68-111
44
2
C:68-111
D:68-111
44
44
1.4
ENST00000284818
4
ENSE00001016734
chr8:
74939024-74939076
53
LY96_HUMAN
111-128
18
2
C:111-128
D:111-128
18
18
1.5b
ENST00000284818
5b
ENSE00002121776
chr8:
74941191-74941322
132
LY96_HUMAN
129-160
32
2
C:129-158
D:129-158
30
30
2.1b
ENST00000355622
1b
ENSE00001946124
chr9:
120466650-120466843
194
TLR4_HUMAN
1-31
31
2
A:27-31
B:27-31
5
5
2.3a
ENST00000355622
3a
ENSE00001654637
chr9:
120470841-120471007
167
TLR4_HUMAN
32-87
56
2
A:32-87
B:32-87
56
56
2.4c
ENST00000355622
4c
ENSE00001462052
chr9:
120474667-120479149
4483
TLR4_HUMAN
87-839
753
2
A:87-627
B:87-627
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
(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
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 (264 KB)
Header - Asym.Unit
Biol.Unit 1 (253 KB)
Header - Biol.Unit 1
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
3FXI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help