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3H1I
Asym. Unit
Info
Asym.Unit (678 KB)
Biol.Unit 1 (663 KB)
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(1)
Title
:
STIGMATELLIN AND ANTIMYCIN BOUND CYTOCHROME BC1 COMPLEX FROM CHICKEN
Authors
:
Z. Zhang, L. Huang, V. M. Shulmeister, Y. I. Chi, K. K. Kim, L. W. Hung, A. R E. A. Berry, S. H. Kim
Date
:
12 Apr 09 (Deposition) - 28 Apr 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.53
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, Mitochondrial Processing Protease, Ubiquinone, Oxidoreductase, Redox Enzyme, Respiratory Chain, Stigmatellin, Antimycin, Electron Transport, Heme, Iron, Membrane, Metal-Binding, Mitochondrion, Mitochondrion Inner Membrane, Transmembrane, Transport, Disulfide Bond, Iron- Sulfur, Transit Peptide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Zhang, L. Huang, V. M. Shulmeister, Y. I. Chi, K. K. Kim, L. W. Hung, A. R. Crofts, E. A. Berry, S. H. Kim
Electron Transfer By Domain Movement In Cytochrome Bc1
Nature V. 392 677 1998
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(11, 64)
Info
All Hetero Components
01a: 2-METHYL-BUTYRIC ACID 3-(3-FORMYLA... (ANYa)
01b: 2-METHYL-BUTYRIC ACID 3-(3-FORMYLA... (ANYb)
02a: CARDIOLIPIN (CDLa)
02b: CARDIOLIPIN (CDLb)
02c: CARDIOLIPIN (CDLc)
02d: CARDIOLIPIN (CDLd)
03a: FE2/S2 (INORGANIC) CLUSTER (FESa)
03b: FE2/S2 (INORGANIC) CLUSTER (FESb)
04a: GLYCEROL (GOLa)
04b: GLYCEROL (GOLb)
05a: HEME C (HECa)
05b: HEME C (HECb)
06a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
06b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
06c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
06d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
07a: PHOSPHATIDYLETHANOLAMINE (PEEa)
07b: PHOSPHATIDYLETHANOLAMINE (PEEb)
07c: PHOSPHATIDYLETHANOLAMINE (PEEc)
07d: PHOSPHATIDYLETHANOLAMINE (PEEd)
07e: PHOSPHATIDYLETHANOLAMINE (PEEe)
07f: PHOSPHATIDYLETHANOLAMINE (PEEf)
08a: DIUNDECYL PHOSPHATIDYL CHOLINE (PLCa)
08b: DIUNDECYL PHOSPHATIDYL CHOLINE (PLCb)
09a: STIGMATELLIN A (SMAa)
09b: STIGMATELLIN A (SMAb)
10a: (UNKa)
10aa: (UNKaa)
10ab: (UNKab)
10b: (UNKb)
10c: (UNKc)
10d: (UNKd)
10e: (UNKe)
10f: (UNKf)
10g: (UNKg)
10h: (UNKh)
10i: (UNKi)
10j: (UNKj)
10k: (UNKk)
10l: (UNKl)
10m: (UNKm)
10n: (UNKn)
10o: (UNKo)
10p: (UNKp)
10q: (UNKq)
10r: (UNKr)
10s: (UNKs)
10t: (UNKt)
10u: (UNKu)
10v: (UNKv)
10w: (UNKw)
10x: (UNKx)
10y: (UNKy)
10z: (UNKz)
11a: UNKNOWN LIGAND (UNLa)
11b: UNKNOWN LIGAND (UNLb)
11c: UNKNOWN LIGAND (UNLc)
11d: UNKNOWN LIGAND (UNLd)
11e: UNKNOWN LIGAND (UNLe)
11f: UNKNOWN LIGAND (UNLf)
11g: UNKNOWN LIGAND (UNLg)
11h: UNKNOWN LIGAND (UNLh)
11i: UNKNOWN LIGAND (UNLi)
11j: UNKNOWN LIGAND (UNLj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ANY
2
Ligand/Ion
2-METHYL-BUTYRIC ACID 3-(3-FORMYLAMINO-2-HYDROXY-BENZOYLAMINO)-8-HEPTYL-2,6-DIMETHYL-4,9-DIOXO-[1,5]DIOXONAN-7-YL ESTER
2
CDL
4
Ligand/Ion
CARDIOLIPIN
3
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
GOL
2
Ligand/Ion
GLYCEROL
5
HEC
2
Ligand/Ion
HEME C
6
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
7
PEE
6
Ligand/Ion
PHOSPHATIDYLETHANOLAMINE
8
PLC
2
Ligand/Ion
DIUNDECYL PHOSPHATIDYL CHOLINE
9
SMA
2
Ligand/Ion
STIGMATELLIN A
10
UNK
28
Mod. Amino Acid
11
UNL
10
Ligand/Ion
UNKNOWN LIGAND
[
close Hetero Component info
]
Sites
(34, 34)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN C:45 , ILE C:46 , GLY C:49 , LEU C:52 , ALA C:53 , TYR C:56 , ARG C:81 , HIS C:84 , ALA C:85 , LEU C:124 , THR C:127 , GLY C:131 , TYR C:132 , LEU C:134 , PRO C:135 , HIS C:183 , PHE C:184 , PRO C:187
BINDING SITE FOR RESIDUE HEM C 501
02
AC2
SOFTWARE
TRP C:32 , GLY C:35 , LEU C:38 , ALA C:39 , HIS C:98 , ARG C:101 , SER C:107 , THR C:113 , TRP C:114 , GLY C:117 , VAL C:118 , LEU C:120 , LEU C:121 , ILE C:190 , THR C:194 , HIS C:197 , LEU C:201 , SER C:206 , ASN C:207 , ANY C:2002
BINDING SITE FOR RESIDUE HEM C 502
03
AC3
SOFTWARE
VAL D:32 , 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 , PHE D:153 , GLY D:159 , MET D:160 , PRO D:163
BINDING SITE FOR RESIDUE HEC D 501
04
AC4
SOFTWARE
CYS E:139 , HIS E:141 , LEU E:142 , CYS E:144 , CYS E:158 , HIS E:161 , SER E:163
BINDING SITE FOR RESIDUE FES E 501
05
AC5
SOFTWARE
GLN P:45 , ILE P:46 , GLY P:49 , LEU P:52 , ALA P:53 , ARG P:81 , HIS P:84 , ALA P:85 , LEU P:124 , THR P:127 , GLY P:131 , TYR P:132 , LEU P:134 , PRO P:135 , HIS P:183 , PHE P:184 , PRO P:187
BINDING SITE FOR RESIDUE HEM P 501
06
AC6
SOFTWARE
TRP P:32 , GLY P:35 , LEU P:38 , ALA P:39 , HIS P:98 , ARG P:101 , SER P:107 , THR P:113 , TRP P:114 , GLY P:117 , VAL P:118 , LEU P:120 , LEU P:121 , THR P:194 , HIS P:197 , LEU P:201 , ASN P:207 , ANY P:3002
BINDING SITE FOR RESIDUE HEM P 502
07
AC7
SOFTWARE
VAL Q:32 , VAL Q:36 , CYS Q:37 , CYS Q:40 , HIS Q:41 , ASN Q:105 , ALA Q:108 , PRO Q:110 , 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
08
AC8
SOFTWARE
CYS R:139 , HIS R:141 , LEU R:142 , GLY R:143 , CYS R:144 , CYS R:158 , HIS R:161 , SER R:163
BINDING SITE FOR RESIDUE FES R 501
09
AC9
SOFTWARE
LEU C:122 , MET C:125 , ALA C:126 , PHE C:129 , GLY C:143 , VAL C:146 , ILE C:147 , PRO C:271 , GLU C:272 , PHE C:275 , TYR C:279 , HIS R:161
BINDING SITE FOR RESIDUE SMA C 2001
10
BC1
SOFTWARE
SER C:18 , LEU C:19 , ILE C:28 , TRP C:32 , SER C:36 , ALA C:39 , LEU C:42 , THR C:194 , ILE C:195 , LEU C:198 , PHE C:221 , TYR C:225 , ASP C:229 , HEM C:502
BINDING SITE FOR RESIDUE ANY C 2002
11
BC2
SOFTWARE
ALA C:30 , ASN C:33 , LEU C:231 , GLY C:232 , MET C:236 , CDL C:2004 , TYR D:220 , LYS D:223 , ARG D:224 , HIS F:72 , ARG F:73 , ARG G:40
BINDING SITE FOR RESIDUE CDL D 2003
12
BC3
SOFTWARE
SER C:29 , ALA C:30 , TRP C:31 , PEE C:2007 , CDL D:2003 , ARG G:40 , PHE G:41 , GLN G:44
BINDING SITE FOR RESIDUE CDL C 2004
13
BC4
SOFTWARE
PEE A:2008 , PHE C:227 , ILE C:230 , LYS D:226 , TYR E:37 , THR E:40 , THR E:47 , PHE J:14
BINDING SITE FOR RESIDUE PEE E 2005
14
BC5
SOFTWARE
TRP C:31 , PHE C:96 , ARG C:101 , TYR C:104 , TYR C:105 , PHE C:277 , THR C:317 , TRP C:327 , CDL C:2004 , TYR F:29 , GLN G:44
BINDING SITE FOR RESIDUE PEE C 2007
15
BC6
SOFTWARE
TYR A:442 , HIS C:222 , PEE E:2005
BINDING SITE FOR RESIDUE PEE A 2008
16
BC7
SOFTWARE
LEU C:79 , LEU C:241 , GLN D:200 , MET D:204 , LYS D:207 , MET D:208 , TYR E:49 , ALA E:50 , VAL E:54 , GLN E:57 , ASP J:36
BINDING SITE FOR RESIDUE PLC E 2009
17
BC8
SOFTWARE
PHE C:64 , ARG C:81 , ASN C:256 , PHE C:257 , TYR D:115
BINDING SITE FOR RESIDUE GOL C 2011
18
BC9
SOFTWARE
THR P:199
BINDING SITE FOR RESIDUE UNL P 2015
19
CC1
SOFTWARE
THR R:140
BINDING SITE FOR RESIDUE UNL R 2103
20
CC2
SOFTWARE
ASN C:149
BINDING SITE FOR RESIDUE UNL C 2104
21
CC3
SOFTWARE
TYR E:178
BINDING SITE FOR RESIDUE UNL E 2105
22
CC4
SOFTWARE
HIS E:161 , LEU P:122 , MET P:125 , ALA P:126 , PHE P:129 , GLY P:143 , VAL P:146 , ILE P:147 , LEU P:182 , LYS P:270 , PRO P:271 , GLU P:272 , PHE P:275 , TYR P:279
BINDING SITE FOR RESIDUE SMA P 3001
23
CC5
SOFTWARE
LEU P:19 , ILE P:28 , TRP P:32 , SER P:36 , ALA P:39 , LEU P:42 , THR P:194 , ILE P:195 , LEU P:198 , PHE P:221 , TYR P:225 , ASP P:229 , HEM P:502
BINDING SITE FOR RESIDUE ANY P 3002
24
CC6
SOFTWARE
ALA P:30 , ASN P:33 , LEU P:231 , GLY P:232 , MET P:236 , CDL P:3004 , TYR Q:220 , LYS Q:223 , ARG Q:224 , HIS S:72 , ARG S:73 , ARG T:40
BINDING SITE FOR RESIDUE CDL Q 3003
25
CC7
SOFTWARE
SER P:29 , ALA P:30 , TRP P:31 , PEE P:3007 , CDL Q:3003 , HIS S:72 , ARG T:40 , PHE T:41 , GLN T:44
BINDING SITE FOR RESIDUE CDL P 3004
26
CC8
SOFTWARE
PHE P:227 , ILE P:230 , LYS Q:226 , TYR R:37 , THR R:40 , THR R:47 , PHE W:14 , GLU W:32
BINDING SITE FOR RESIDUE PEE P 3005
27
CC9
SOFTWARE
TRP P:31 , PHE P:96 , ARG P:101 , TYR P:104 , TYR P:105 , PHE P:277 , THR P:317 , TRP P:327 , LEU P:333 , CDL P:3004 , TYR S:29 , GLN T:44
BINDING SITE FOR RESIDUE PEE P 3007
28
DC1
SOFTWARE
TYR N:442 , HIS P:222
BINDING SITE FOR RESIDUE PEE N 3008
29
DC2
SOFTWARE
THR P:44 , TYR P:76 , LEU P:79 , GLN Q:200 , MET Q:204 , LYS Q:207 , TYR R:49 , ALA R:50 , VAL R:54 , GLN R:57
BINDING SITE FOR RESIDUE PLC R 3009
30
DC3
SOFTWARE
ALA P:85
BINDING SITE FOR RESIDUE UNL P 3010
31
DC4
SOFTWARE
PHE P:64 , ARG P:81 , ASN P:256 , TYR Q:115
BINDING SITE FOR RESIDUE GOL P 3011
32
DC5
SOFTWARE
THR C:199 , HIS C:202
BINDING SITE FOR RESIDUE UNL C 3015
33
DC6
SOFTWARE
THR E:140
BINDING SITE FOR RESIDUE UNL E 3103
34
DC7
SOFTWARE
ASN P:149 , HIS P:159
BINDING SITE FOR RESIDUE UNL P 3104
[
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
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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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:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(11, 28)
Info
all CATH domains
01a: CATH_3h1iA02 (A:239-442)
01b: CATH_3h1iA01 (A:14-227)
01c: CATH_3h1iN01 (N:14-227)
01d: CATH_3h1iN02 (N:239-442)
01e: CATH_3h1iB01 (B:19-227)
01f: CATH_3h1iO01 (O:18-227)
01g: CATH_3h1iB02 (B:239-439)
01h: CATH_3h1iO02 (O:239-439)
02a: CATH_3h1iD01 (D:1-196)
02b: CATH_3h1iQ01 (Q:1-196)
03a: CATH_3h1iF00 (F:10-110)
03b: CATH_3h1iS00 (S:10-110)
04a: CATH_3h1iH00 (H:9-78)
04b: CATH_3h1iU00 (U:12-78)
05a: CATH_3h1iP00 (P:2-380)
05b: CATH_3h1iC00 (C:1-380)
06a: CATH_3h1iD02 (D:197-241)
06b: CATH_3h1iQ02 (Q:197-241)
07a: CATH_3h1iG00 (G:1-81)
07b: CATH_3h1iT00 (T:1-79)
08a: CATH_3h1iW00 (W:4-62)
08b: CATH_3h1iJ00 (J:4-64)
09a: CATH_3h1iE01 (E:1-67)
09b: CATH_3h1iR01 (R:1-67)
10a: CATH_3h1iE02 (E:68-196)
10b: CATH_3h1iR02 (R:68-196)
11a: CATH_3h1iI00 (I:28-77)
11b: CATH_3h1iV00 (V:28-77)
View:
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Classes
(
)
(
)
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
3h1iA02
A:239-442
01b
3h1iA01
A:14-227
01c
3h1iN01
N:14-227
01d
3h1iN02
N:239-442
01e
3h1iB01
B:19-227
01f
3h1iO01
O:18-227
01g
3h1iB02
B:239-439
01h
3h1iO02
O:239-439
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
3h1iD01
D:1-196
02b
3h1iQ01
Q:1-196
Topology
:
Cytochrome Bc1 Complex; Chain F
(39)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain F
(39)
Chicken (Gallus gallus)
(15)
03a
3h1iF00
F:10-110
03b
3h1iS00
S:10-110
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.20, no name defined]
(39)
Chicken (Gallus gallus)
(15)
04a
3h1iH00
H:9-78
04b
3h1iU00
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
3h1iP00
P:2-380
05b
3h1iC00
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
3h1iD02
D:197-241
06b
3h1iQ02
Q:197-241
Homologous Superfamily
:
[code=1.20.5.210, no name defined]
(39)
Chicken (Gallus gallus)
(15)
07a
3h1iG00
G:1-81
07b
3h1iT00
T:1-79
Homologous Superfamily
:
[code=1.20.5.260, no name defined]
(39)
Chicken (Gallus gallus)
(15)
08a
3h1iW00
W:4-62
08b
3h1iJ00
J:4-64
Homologous Superfamily
:
[code=1.20.5.270, no name defined]
(39)
Chicken (Gallus gallus)
(15)
09a
3h1iE01
E:1-67
09b
3h1iR01
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
3h1iE02
E:68-196
10b
3h1iR02
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
3h1iI00
I:28-77
11b
3h1iV00
V:28-77
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
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Protein & NOT Site
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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
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Chain U
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Chain W
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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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