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3H1L
Asym. Unit
Info
Asym.Unit (675 KB)
Biol.Unit 1 (661 KB)
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Title
:
CHICKEN CYTOCHROME BC1 COMPLEX WITH ASCOCHLORIN BOUND AT QO AND QI SITES
Authors
:
E. A. Berry, L. S. Huang, N. Minagawa
Date
:
12 Apr 09 (Deposition) - 05 Jan 10 (Release) - 23 Feb 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.21
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,N,O,P,Q,R,S,T,U,V,W
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,N,O,P,Q,R,S,T,U,V,W (1x)
Keywords
:
Cytochrome Bc1, Membrane Protein, Heme Protein, Rieske Iron Sulfur Protein, Cytochrome B, Cytochrome C1, Complex Iii, Ascochlorin, Ubiquinone, Oxidoreductase, Redox Enzyme, Respiratory Chain, Electron Transport, Heme, Inner Membrane Iron, Membrane, Metal-Binding, Mitochondrion, Transmembrane, Iron, Mitochondrion Inner Membrane, Transport, 2Fe-2S, Disulfide Bond, Iron-Sulfur, Transit Peptide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. A. Berry, L. S. Huang, D. W. Lee, F. Daldal, K. Nagai, N. Minagawa
Ascochlorin Is A Novel, Specific Inhibitor Of The Mitochondrial Cytochrome Bc(1) Complex.
Biochim. Biophys. Acta V. 1797 360 2010
[
close entry info
]
Hetero Components
(10, 66)
Info
All Hetero Components
01a: 3-CHLORO-4,6-DIHYDROXY-2-METHYL-5-... (3H1a)
01b: 3-CHLORO-4,6-DIHYDROXY-2-METHYL-5-... (3H1b)
01c: 3-CHLORO-4,6-DIHYDROXY-2-METHYL-5-... (3H1c)
01d: 3-CHLORO-4,6-DIHYDROXY-2-METHYL-5-... (3H1d)
02a: B-OCTYLGLUCOSIDE (BOGa)
02b: B-OCTYLGLUCOSIDE (BOGb)
03a: CARDIOLIPIN (CDLa)
03b: CARDIOLIPIN (CDLb)
03c: CARDIOLIPIN (CDLc)
03d: CARDIOLIPIN (CDLd)
04a: FE2/S2 (INORGANIC) CLUSTER (FESa)
04b: FE2/S2 (INORGANIC) CLUSTER (FESb)
05a: GLYCEROL (GOLa)
05b: GLYCEROL (GOLb)
06a: HEME C (HECa)
06b: HEME C (HECb)
07a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
07b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
07c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
07d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
08a: PHOSPHATIDYLETHANOLAMINE (PEEa)
08b: PHOSPHATIDYLETHANOLAMINE (PEEb)
08c: PHOSPHATIDYLETHANOLAMINE (PEEc)
08d: PHOSPHATIDYLETHANOLAMINE (PEEd)
08e: PHOSPHATIDYLETHANOLAMINE (PEEe)
08f: PHOSPHATIDYLETHANOLAMINE (PEEf)
09a: (UNKa)
09aa: (UNKaa)
09ab: (UNKab)
09b: (UNKb)
09c: (UNKc)
09d: (UNKd)
09e: (UNKe)
09f: (UNKf)
09g: (UNKg)
09h: (UNKh)
09i: (UNKi)
09j: (UNKj)
09k: (UNKk)
09l: (UNKl)
09m: (UNKm)
09n: (UNKn)
09o: (UNKo)
09p: (UNKp)
09q: (UNKq)
09r: (UNKr)
09s: (UNKs)
09t: (UNKt)
09u: (UNKu)
09v: (UNKv)
09w: (UNKw)
09x: (UNKx)
09y: (UNKy)
09z: (UNKz)
10a: UNKNOWN LIGAND (UNLa)
10b: UNKNOWN LIGAND (UNLb)
10c: UNKNOWN LIGAND (UNLc)
10d: UNKNOWN LIGAND (UNLd)
10e: UNKNOWN LIGAND (UNLe)
10f: UNKNOWN LIGAND (UNLf)
10g: UNKNOWN LIGAND (UNLg)
10h: UNKNOWN LIGAND (UNLh)
10i: UNKNOWN LIGAND (UNLi)
10j: UNKNOWN LIGAND (UNLj)
10k: UNKNOWN LIGAND (UNLk)
10l: UNKNOWN LIGAND (UNLl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3H1
4
Ligand/Ion
3-CHLORO-4,6-DIHYDROXY-2-METHYL-5-{(2E,4E)-3-METHYL-5-[(1R,2R,6R)-1,2,6-TRIMETHYL-3-OXOCYCLOHEXYL]PENTA-2,4-DIEN-1-YL}BENZALDEHYDE
2
BOG
2
Ligand/Ion
B-OCTYLGLUCOSIDE
3
CDL
4
Ligand/Ion
CARDIOLIPIN
4
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
GOL
2
Ligand/Ion
GLYCEROL
6
HEC
2
Ligand/Ion
HEME C
7
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
8
PEE
6
Ligand/Ion
PHOSPHATIDYLETHANOLAMINE
9
UNK
28
Mod. Amino Acid
10
UNL
12
Ligand/Ion
UNKNOWN LIGAND
[
close Hetero Component info
]
Sites
(36, 36)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:442 , HIS C:222 , PEE E:2005
BINDING SITE FOR RESIDUE PEE A 2008
02
AC2
SOFTWARE
GLN C:45 , GLY C:49 , LEU C:50 , LEU C:52 , ARG C:81 , HIS C:84 , LEU C:124 , THR C:127 , ALA C:128 , GLY C:131 , TYR C:132 , LEU C:134 , PRO C:135 , HIS C:183 , PRO C:187
BINDING SITE FOR RESIDUE HEM C 501
03
AC3
SOFTWARE
TRP C:32 , GLY C:35 , LEU C:38 , ALA C:39 , HIS C:98 , ILE C:99 , ARG C:101 , SER C:107 , GLY C:117 , LEU C:120 , THR C:194 , HIS C:197 , LEU C:198 , LEU C:201 , ASN C:207 , HOH C:381 , HOH C:384 , 3H1 C:2002
BINDING SITE FOR RESIDUE HEM C 502
04
AC4
SOFTWARE
ALA C:126 , GLY C:143 , VAL C:146 , ILE C:147 , PRO C:271 , PHE C:275 , TYR C:279 , LEU C:282 , UNL C:2010 , CYS R:160 , HIS R:161
BINDING SITE FOR RESIDUE 3H1 C 2001
05
AC5
SOFTWARE
LEU C:19 , LEU C:22 , SER C:36 , ALA C:39 , LEU C:198 , LEU C:201 , HIS C:202 , SER C:206 , ASP C:229 , ILE C:230 , HOH C:383 , HOH C:385 , HEM C:502
BINDING SITE FOR RESIDUE 3H1 C 2002
06
AC6
SOFTWARE
ALA C:30 , GLY C:232 , MET C:236 , TYR D:220 , LYS D:223 , ARG D:224 , HIS F:72 , ARG F:73 , ALA G:33 , ARG G:40 , CDL G:2004
BINDING SITE FOR RESIDUE CDL C 2003
07
AC7
SOFTWARE
TRP C:31 , PHE C:96 , TYR C:104 , TYR C:105 , PHE C:277 , THR C:317 , TRP C:327 , TYR F:29 , GLN G:44 , CDL G:2004
BINDING SITE FOR RESIDUE PEE C 2007
08
AC8
SOFTWARE
TYR C:132 , 3H1 C:2001
BINDING SITE FOR RESIDUE UNL C 2010
09
AC9
SOFTWARE
ASN C:149 , UNL R:2103
BINDING SITE FOR RESIDUE UNL C 2104
10
BC1
SOFTWARE
THR C:199
BINDING SITE FOR RESIDUE UNL C 3015
11
BC2
SOFTWARE
PHE C:64 , ARG C:81 , ASN C:256 , PHE C:257 , TYR D:115
BINDING SITE FOR RESIDUE GOL C 2011
12
BC3
SOFTWARE
VAL D:36 , CYS D:37 , CYS D:40 , HIS D:41 , ASN D:105 , ALA D:108 , PRO D:110 , ARG D:120 , TYR D:126 , LEU D:131 , PHE D:153 , GLY D:159 , MET D:160 , PRO D:163
BINDING SITE FOR RESIDUE HEC D 501
13
BC4
SOFTWARE
TYR C:76 , GLN D:200 , ARG D:203 , LYS D:207 , ASN E:53 , GLN E:57
BINDING SITE FOR RESIDUE BOG D 2009
14
BC5
SOFTWARE
CYS E:139 , HIS E:141 , LEU E:142 , CYS E:158 , HIS E:161 , SER E:163
BINDING SITE FOR RESIDUE FES E 501
15
BC6
SOFTWARE
PEE A:2008 , PHE C:227 , LYS D:226 , TYR E:37 , THR E:40
BINDING SITE FOR RESIDUE PEE E 2005
16
BC7
SOFTWARE
TYR E:178
BINDING SITE FOR RESIDUE UNL E 2105
17
BC8
SOFTWARE
SER C:29 , ALA C:30 , TRP C:31 , TYR C:105 , CDL C:2003 , PEE C:2007 , HIS F:72 , ARG G:40 , GLN G:44
BINDING SITE FOR RESIDUE CDL G 2004
18
BC9
SOFTWARE
GLN P:45 , GLY P:49 , LEU P:50 , LEU P:52 , ARG P:81 , HIS P:84 , LEU P:124 , THR P:127 , ALA P:128 , GLY P:131 , TYR P:132 , LEU P:134 , PRO P:135 , HIS P:183 , PRO P:187
BINDING SITE FOR RESIDUE HEM P 501
19
CC1
SOFTWARE
TRP P:32 , GLY P:35 , LEU P:38 , ALA P:39 , HIS P:98 , ARG P:101 , SER P:107 , GLY P:117 , LEU P:120 , THR P:194 , HIS P:197 , LEU P:201 , ASN P:207 , HOH P:381 , HOH P:384 , 3H1 P:3002
BINDING SITE FOR RESIDUE HEM P 502
20
CC2
SOFTWARE
THR P:199
BINDING SITE FOR RESIDUE UNL P 2015
21
CC3
SOFTWARE
LEU P:250
BINDING SITE FOR RESIDUE UNL P 2106
22
CC4
SOFTWARE
CYS E:160 , HIS E:161 , MET P:125 , ALA P:126 , PHE P:129 , GLY P:143 , VAL P:146 , PRO P:271 , GLU P:272 , PHE P:275 , TYR P:279 , LEU P:282
BINDING SITE FOR RESIDUE 3H1 P 3001
23
CC5
SOFTWARE
LEU P:19 , LEU P:22 , SER P:36 , ALA P:39 , LEU P:198 , LEU P:201 , HIS P:202 , SER P:206 , PHE P:221 , TYR P:225 , ASP P:229 , ILE P:230 , HOH P:382 , HEM P:502 , HOH P:959
BINDING SITE FOR RESIDUE 3H1 P 3002
24
CC6
SOFTWARE
ALA P:30 , GLY P:232 , MET P:236 , TYR Q:220 , LYS Q:223 , ARG Q:224 , HIS S:72 , ARG S:73 , ARG T:40 , CDL T:3004
BINDING SITE FOR RESIDUE CDL P 3003
25
CC7
SOFTWARE
TRP P:31 , TYR P:104 , TYR P:105 , PHE P:277 , THR P:317 , TRP P:327 , LEU P:333 , TYR S:29 , GLN T:44 , VAL T:48 , PHE T:52 , CDL T:3004
BINDING SITE FOR RESIDUE PEE P 3007
26
CC8
SOFTWARE
TYR N:442 , HIS P:222
BINDING SITE FOR RESIDUE PEE P 3008
27
CC9
SOFTWARE
ALA P:85 , TYR P:274
BINDING SITE FOR RESIDUE UNL P 3010
28
DC1
SOFTWARE
ASN P:149
BINDING SITE FOR RESIDUE UNL P 3103
29
DC2
SOFTWARE
ASN P:149 , VAL P:162
BINDING SITE FOR RESIDUE UNL P 3104
30
DC3
SOFTWARE
PHE P:64 , ARG P:81 , PRO P:135 , ASN P:256 , PHE P:257 , TYR Q:115
BINDING SITE FOR RESIDUE GOL P 3011
31
DC4
SOFTWARE
VAL Q:36 , CYS Q:37 , CYS Q:40 , HIS Q:41 , ASN Q:105 , ALA Q:108 , ARG Q:120 , TYR Q:126 , PHE Q:153 , GLY Q:159 , MET Q:160 , PRO Q:163
BINDING SITE FOR RESIDUE HEC Q 501
32
DC5
SOFTWARE
CYS R:139 , HIS R:141 , LEU R:142 , CYS R:158 , HIS R:161 , SER R:163
BINDING SITE FOR RESIDUE FES R 501
33
DC6
SOFTWARE
UNL C:2104
BINDING SITE FOR RESIDUE UNL R 2103
34
DC7
SOFTWARE
PHE P:227 , LEU P:233 , LYS Q:226 , TYR R:37 , THR R:40 , PHE W:14 , ARG W:15 , THR W:17
BINDING SITE FOR RESIDUE PEE R 3005
35
DC8
SOFTWARE
TYR P:76 , GLN Q:200 , ARG Q:203 , LYS Q:207 , ASN R:53 , GLN R:57
BINDING SITE FOR RESIDUE BOG R 3009
36
DC9
SOFTWARE
ALA P:30 , TRP P:31 , TYR P:105 , CDL P:3003 , PEE P:3007 , ARG T:40 , GLN T:44
BINDING SITE FOR RESIDUE CDL T 3004
[
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
(3, 5)
Info
All PROSITE Patterns/Profiles
1: CYTB_NTER (C:1-210)
2: RIESKE (E:96-194,R:96-194)
3: CYTB_CTER (C:211-380,P:211-380)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTB_NTER
PS51002
Cytochrome b/b6 N-terminal region profile.
CYB_CHICK
1-210
1
C:1-210
2
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
UCRI_CHICK
172-270
2
E:96-194
R:96-194
3
CYTB_CTER
PS51003
Cytochrome b/b6 C-terminal region profile.
CYB_CHICK
211-380
2
C:211-380
P:211-380
[
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]
Exons
(0, 0)
Info
All Exons
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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
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
[
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]
CATH Domains
(11, 28)
Info
all CATH domains
01a: CATH_3h1lA02 (A:239-442)
01b: CATH_3h1lN02 (N:239-442)
01c: CATH_3h1lB01 (B:19-227)
01d: CATH_3h1lO01 (O:18-227)
01e: CATH_3h1lB02 (B:239-439)
01f: CATH_3h1lO02 (O:239-439)
01g: CATH_3h1lA01 (A:14-227)
01h: CATH_3h1lN01 (N:14-227)
02a: CATH_3h1lD01 (D:1-196)
02b: CATH_3h1lQ01 (Q:1-196)
03a: CATH_3h1lF00 (F:10-110)
03b: CATH_3h1lS00 (S:10-110)
04a: CATH_3h1lH00 (H:9-78)
04b: CATH_3h1lU00 (U:12-78)
05a: CATH_3h1lP00 (P:2-380)
05b: CATH_3h1lC00 (C:1-380)
06a: CATH_3h1lD02 (D:197-241)
06b: CATH_3h1lQ02 (Q:197-241)
07a: CATH_3h1lG00 (G:1-81)
07b: CATH_3h1lT00 (T:1-79)
08a: CATH_3h1lW00 (W:4-62)
08b: CATH_3h1lJ00 (J:4-64)
09a: CATH_3h1lE01 (E:1-67)
09b: CATH_3h1lR01 (R:1-67)
10a: CATH_3h1lE02 (E:68-196)
10b: CATH_3h1lR02 (R:68-196)
11a: CATH_3h1lI00 (I:28-77)
11b: CATH_3h1lV00 (V:28-77)
View:
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Classes
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)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Cytochrome Bc1 Complex; Chain A, domain 1
(45)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain A, domain 1
(45)
Chicken (Gallus gallus)
(15)
01a
3h1lA02
A:239-442
01b
3h1lN02
N:239-442
01c
3h1lB01
B:19-227
01d
3h1lO01
O:18-227
01e
3h1lB02
B:239-439
01f
3h1lO02
O:239-439
01g
3h1lA01
A:14-227
01h
3h1lN01
N:14-227
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Chicken (Gallus gallus)
(15)
02a
3h1lD01
D:1-196
02b
3h1lQ01
Q:1-196
Topology
:
Cytochrome Bc1 Complex; Chain F
(39)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain F
(39)
Chicken (Gallus gallus)
(15)
03a
3h1lF00
F:10-110
03b
3h1lS00
S:10-110
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.20, no name defined]
(39)
Chicken (Gallus gallus)
(15)
04a
3h1lH00
H:9-78
04b
3h1lU00
U:12-78
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome Bc1 Complex; Chain C
(51)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain C
(51)
Chicken (Gallus gallus)
(15)
05a
3h1lP00
P:2-380
05b
3h1lC00
C:1-380
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
[code=1.20.5.100, no name defined]
(56)
Chicken (Gallus gallus)
(15)
06a
3h1lD02
D:197-241
06b
3h1lQ02
Q:197-241
Homologous Superfamily
:
[code=1.20.5.210, no name defined]
(39)
Chicken (Gallus gallus)
(15)
07a
3h1lG00
G:1-81
07b
3h1lT00
T:1-79
Homologous Superfamily
:
[code=1.20.5.260, no name defined]
(39)
Chicken (Gallus gallus)
(15)
08a
3h1lW00
W:4-62
08b
3h1lJ00
J:4-64
Homologous Superfamily
:
[code=1.20.5.270, no name defined]
(39)
Chicken (Gallus gallus)
(15)
09a
3h1lE01
E:1-67
09b
3h1lR01
R:1-67
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Chicken (Gallus gallus)
(15)
10a
3h1lE02
E:68-196
10b
3h1lR02
R:68-196
Architecture
:
Ribbon
(789)
Topology
:
Cytochrome Bc1 Complex; Chain I
(29)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain I
(29)
Chicken (Gallus gallus)
(12)
11a
3h1lI00
I:28-77
11b
3h1lV00
V:28-77
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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Atom Selection
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Protein & NOT PROSITE
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Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain N
Chain O
Chain P
Chain Q
Chain R
Chain S
Chain T
Chain U
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Chain W
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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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 (675 KB)
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