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2QJY
Biol. Unit 1
Info
Asym.Unit (885 KB)
Biol.Unit 1 (297 KB)
Biol.Unit 2 (298 KB)
Biol.Unit 3 (296 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RHODOBACTER SPHAEROIDES DOUBLE MUTANT WITH STIGMATELLIN AND UQ2
Authors
:
L. Esser, D. Xia
Date
:
09 Jul 07 (Deposition) - 25 Dec 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Biol. Unit 3: M,N,O,P,Q,R (1x)
Keywords
:
Cytochrome B, 8 Tm Helixces Cytochrome C1, 1 C-Term Tm Helix Rieske, 1 N-Term Tm Helix, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Esser, M. Elberry, F. Zhou, C. A. Yu, L. Yu, D. Xia
Inhibitor-Complexed Structures Of The Cytochrome Bc1 From The Photosynthetic Bacterium Rhodobacter Sphaeroides.
J. Biol. Chem. V. 283 2846 2008
[
close entry info
]
Hetero Components
(6, 16)
Info
All Hetero Components
1a: B-2-OCTYLGLUCOSIDE (BGLa)
1b: B-2-OCTYLGLUCOSIDE (BGLb)
1c: B-2-OCTYLGLUCOSIDE (BGLc)
1d: B-2-OCTYLGLUCOSIDE (BGLd)
1e: B-2-OCTYLGLUCOSIDE (BGLe)
1f: B-2-OCTYLGLUCOSIDE (BGLf)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3b: FE2/S2 (INORGANIC) CLUSTER (FESb)
3c: FE2/S2 (INORGANIC) CLUSTER (FESc)
3d: FE2/S2 (INORGANIC) CLUSTER (FESd)
3e: FE2/S2 (INORGANIC) CLUSTER (FESe)
3f: FE2/S2 (INORGANIC) CLUSTER (FESf)
4a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
4b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
4c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
4d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
4e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
4f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
4g: PROTOPORPHYRIN IX CONTAINING FE (HEMg)
4h: PROTOPORPHYRIN IX CONTAINING FE (HEMh)
4i: PROTOPORPHYRIN IX CONTAINING FE (HEMi)
4j: PROTOPORPHYRIN IX CONTAINING FE (HEMj)
4k: PROTOPORPHYRIN IX CONTAINING FE (HEMk)
4l: PROTOPORPHYRIN IX CONTAINING FE (HEMl)
4m: PROTOPORPHYRIN IX CONTAINING FE (HEMm)
4n: PROTOPORPHYRIN IX CONTAINING FE (HEMn)
4o: PROTOPORPHYRIN IX CONTAINING FE (HEMo)
4p: PROTOPORPHYRIN IX CONTAINING FE (HEMp)
4q: PROTOPORPHYRIN IX CONTAINING FE (HEMq)
4r: PROTOPORPHYRIN IX CONTAINING FE (HEMr)
5a: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPa)
5b: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPb)
5c: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPc)
5d: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPd)
5e: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPe)
5f: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDRO... (LOPf)
6a: SODIUM ION (NAa)
7a: STIGMATELLIN A (SMAa)
7b: STIGMATELLIN A (SMAb)
7c: STIGMATELLIN A (SMAc)
7d: STIGMATELLIN A (SMAd)
7e: STIGMATELLIN A (SMAe)
7f: STIGMATELLIN A (SMAf)
8a: STRONTIUM ION (SRa)
8b: STRONTIUM ION (SRb)
8c: STRONTIUM ION (SRc)
8d: STRONTIUM ION (SRd)
8e: STRONTIUM ION (SRe)
8f: STRONTIUM ION (SRf)
8g: STRONTIUM ION (SRg)
8h: STRONTIUM ION (SRh)
8i: STRONTIUM ION (SRi)
9a: UBIQUINONE-2 (UQ2a)
9b: UBIQUINONE-2 (UQ2b)
9c: UBIQUINONE-2 (UQ2c)
9d: UBIQUINONE-2 (UQ2d)
9e: UBIQUINONE-2 (UQ2e)
9f: UBIQUINONE-2 (UQ2f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGL
2
Ligand/Ion
B-2-OCTYLGLUCOSIDE
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
4
HEM
6
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
5
LOP
2
Ligand/Ion
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
6
NA
-1
Ligand/Ion
SODIUM ION
7
SMA
2
Ligand/Ion
STIGMATELLIN A
8
SR
-1
Ligand/Ion
STRONTIUM ION
9
UQ2
2
Ligand/Ion
UBIQUINONE-2
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC7 (SOFTWARE)
06: BC8 (SOFTWARE)
07: BC9 (SOFTWARE)
08: CC1 (SOFTWARE)
09: CC2 (SOFTWARE)
10: CC3 (SOFTWARE)
11: CC4 (SOFTWARE)
12: CC5 (SOFTWARE)
13: CC6 (SOFTWARE)
14: CC7 (SOFTWARE)
15: CC8 (SOFTWARE)
16: CC9 (SOFTWARE)
17: DC1 (SOFTWARE)
18: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:265 , PHE A:269 , PHE B:13 , GLU B:14 , GLY B:15 , ASN B:123 , GLY B:124 , LYS B:227 , HOH B:1060
BINDING SITE FOR RESIDUE BGL B 1041
02
AC2
SOFTWARE
PHE D:269 , PHE E:13 , GLU E:14 , GLY E:15 , PRO E:16 , LYS E:227
BINDING SITE FOR RESIDUE BGL E 1042
03
AC7
SOFTWARE
ASP B:8 , VAL B:9 , GLU B:14 , GLU B:129
BINDING SITE FOR RESIDUE SR B 1011
04
AC8
SOFTWARE
ASP E:8 , VAL E:9 , GLU E:14 , GLU E:129
BINDING SITE FOR RESIDUE SR E 1012
05
BC7
SOFTWARE
TRP A:45 , GLY A:48 , LEU A:51 , ALA A:52 , HIS A:111 , ARG A:114 , SER A:120 , ARG A:125 , GLY A:132 , MET A:133 , ILE A:135 , VAL A:209 , HIS A:212 , PHE A:216 , GLY A:220 , ASN A:221 , ASN A:222 , UQ2 A:1101 , HOH A:1171 , HOH A:1172
BINDING SITE FOR RESIDUE HEM A 501
06
BC8
SOFTWARE
GLN A:58 , GLY A:62 , ILE A:63 , ALA A:66 , ARG A:94 , HIS A:97 , THR A:142 , GLY A:146 , LEU A:149 , PRO A:150 , HIS A:198 , TYR A:199 , PRO A:202 , HOH A:1173
BINDING SITE FOR RESIDUE HEM A 502
07
BC9
SOFTWARE
LEU A:137 , MET A:154 , GLY A:158 , VAL A:161 , ILE A:162 , ILE A:292 , PRO A:294 , GLU A:295 , PHE A:298 , TYR A:302 , MET A:336 , PHE A:337 , ILE A:340 , CYS F:151 , HIS F:152
BINDING SITE FOR RESIDUE SMA A 1001
08
CC1
SOFTWARE
MET A:44 , LEU A:103 , ILE A:106 , TYR A:117 , TYR A:118 , ARG A:358 , TRP A:368 , PHE A:374
BINDING SITE FOR RESIDUE LOP A 1021
09
CC2
SOFTWARE
ILE A:35 , VAL A:49 , PHE A:216 , HIS A:217 , PHE A:244 , HEM A:501
BINDING SITE FOR RESIDUE UQ2 A 1101
10
CC3
SOFTWARE
VAL B:35 , CYS B:36 , CYS B:39 , HIS B:40 , LEU B:94 , ASN B:96 , PRO B:98 , MET B:103 , ARG B:107 , TYR B:130 , PHE B:160 , ILE B:183 , ALA B:184 , MET B:185 , PRO B:188 , HOH B:1055
BINDING SITE FOR RESIDUE HEM B 301
11
CC4
SOFTWARE
CYS C:129 , HIS C:131 , LEU C:132 , CYS C:149 , HIS C:152 , SER C:154
BINDING SITE FOR RESIDUE FES C 200
12
CC5
SOFTWARE
TRP D:45 , GLY D:48 , PHE D:104 , HIS D:111 , ARG D:114 , SER D:120 , ARG D:125 , TRP D:129 , GLY D:132 , MET D:133 , ILE D:135 , HIS D:212 , PHE D:216 , GLY D:220 , ASN D:221 , ASN D:222 , UQ2 D:1102 , HOH D:1115 , HOH D:1161 , HOH D:1162 , HOH D:1163
BINDING SITE FOR RESIDUE HEM D 501
13
CC6
SOFTWARE
GLN D:58 , GLY D:62 , ILE D:63 , ALA D:66 , ARG D:94 , HIS D:97 , THR D:142 , ALA D:143 , GLY D:146 , LEU D:149 , PRO D:150 , HIS D:198 , TYR D:199 , PRO D:202 , HOH D:1164 , HOH D:1165
BINDING SITE FOR RESIDUE HEM D 502
14
CC7
SOFTWARE
HIS C:152 , MET D:140 , PHE D:144 , MET D:154 , GLY D:158 , VAL D:161 , ILE D:162 , PHE D:194 , ILE D:292 , PRO D:294 , GLU D:295 , PHE D:298 , TYR D:302 , MET D:336 , PHE D:337 , ILE D:340
BINDING SITE FOR RESIDUE SMA D 1002
15
CC8
SOFTWARE
MET D:44 , LEU D:103 , PHE D:113 , TYR D:117 , TYR D:118 , LEU D:274 , ARG D:358 , TRP D:368 , PHE D:374
BINDING SITE FOR RESIDUE LOP D 1022
16
CC9
SOFTWARE
VAL D:49 , ILE D:213 , PHE D:216 , HIS D:217 , PHE D:244 , ASP D:252 , HEM D:501
BINDING SITE FOR RESIDUE UQ2 D 1102
17
DC1
SOFTWARE
VAL E:35 , CYS E:36 , CYS E:39 , HIS E:40 , LEU E:94 , ASN E:96 , PRO E:98 , MET E:103 , ARG E:107 , TYR E:130 , LEU E:135 , PHE E:160 , ILE E:183 , ALA E:184 , MET E:185 , HOH E:1056
BINDING SITE FOR RESIDUE HEM E 301
18
DC2
SOFTWARE
CYS F:129 , HIS F:131 , LEU F:132 , CYS F:149 , HIS F:152 , SER F:154
BINDING SITE FOR RESIDUE FES F 200
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 8)
Info
All PROSITE Patterns/Profiles
1: CYTB_NTER (A:15-225,D:15-225)
2: CYTC (B:23-142,E:23-142)
3: RIESKE (C:117-185,F:117-185)
4: CYTB_CTER (A:234-422,D:234-422)
;
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_RHOSH
15-225
2
A:15-225
D:15-225
-
-
-
-
2
CYTC
PS51007
Cytochrome c family profile.
CY1_RHOSH
45-164
2
B:23-142
E:23-142
-
-
-
-
3
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
UCRI_RHOSH
117-185
2
C:117-185
F:117-185
-
-
-
-
4
CYTB_CTER
PS51003
Cytochrome b/b6 C-terminal region profile.
CYB_RHOSH
234-422
2
A:234-422
D:234-422
-
-
-
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(5, 30)
Info
all CATH domains
1a: CATH_2qjyB01 (B:1-221)
1b: CATH_2qjyE01 (E:1-221)
1c: CATH_2qjyH01 (H:1-221)
1d: CATH_2qjyK01 (K:1-221)
1e: CATH_2qjyN01 (N:1-221)
1f: CATH_2qjyQ01 (Q:1-221)
2a: CATH_2qjyA00 (A:3-430)
2b: CATH_2qjyD00 (D:3-430)
2c: CATH_2qjyG00 (G:3-430)
2d: CATH_2qjyJ00 (J:3-430)
2e: CATH_2qjyM00 (M:3-430)
2f: CATH_2qjyP00 (P:3-430)
3a: CATH_2qjyB02 (B:222-256)
3b: CATH_2qjyE02 (E:222-256)
3c: CATH_2qjyH02 (H:222-256)
3d: CATH_2qjyK02 (K:222-256)
3e: CATH_2qjyN02 (N:222-256)
3f: CATH_2qjyQ02 (Q:222-256)
4a: CATH_2qjyC01 (C:9-41)
4b: CATH_2qjyF01 (F:9-41)
4c: CATH_2qjyI01 (I:9-41)
4d: CATH_2qjyL01 (L:9-41)
4e: CATH_2qjyO01 (O:9-41)
4f: CATH_2qjyR01 (R:9-41)
5a: CATH_2qjyC02 (C:42-187)
5b: CATH_2qjyF02 (F:42-187)
5c: CATH_2qjyI02 (I:42-187)
5d: CATH_2qjyL02 (L:42-187)
5e: CATH_2qjyO02 (O:42-187)
5f: CATH_2qjyR02 (R:42-187)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(4)
1a
2qjyB01
B:1-221
1b
2qjyE01
E:1-221
1c
2qjyH01
H:1-221
1d
2qjyK01
K:1-221
1e
2qjyN01
N:1-221
1f
2qjyQ01
Q:1-221
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome Bc1 Complex; Chain C
(51)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain C
(51)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(4)
2a
2qjyA00
A:3-430
2b
2qjyD00
D:3-430
2c
2qjyG00
G:3-430
2d
2qjyJ00
J:3-430
2e
2qjyM00
M:3-430
2f
2qjyP00
P:3-430
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)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(4)
3a
2qjyB02
B:222-256
3b
2qjyE02
E:222-256
3c
2qjyH02
H:222-256
3d
2qjyK02
K:222-256
3e
2qjyN02
N:222-256
3f
2qjyQ02
Q:222-256
Homologous Superfamily
:
Single helix bin
(16)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(4)
4a
2qjyC01
C:9-41
4b
2qjyF01
F:9-41
4c
2qjyI01
I:9-41
4d
2qjyL01
L:9-41
4e
2qjyO01
O:9-41
4f
2qjyR01
R:9-41
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Rhodobacter sphaeroides. Organism_taxid: 1063.
(10)
5a
2qjyC02
C:42-187
5b
2qjyF02
F:42-187
5c
2qjyI02
I:42-187
5d
2qjyL02
L:42-187
5e
2qjyO02
O:42-187
5f
2qjyR02
R:42-187
[
close CATH info
]
Pfam Domains
(5, 30)
Info
all PFAM domains
1a: PFAM_Cytochrom_B_N_2_2qjyP01 (P:102-277)
1b: PFAM_Cytochrom_B_N_2_2qjyP02 (P:102-277)
1c: PFAM_Cytochrom_B_N_2_2qjyP03 (P:102-277)
1d: PFAM_Cytochrom_B_N_2_2qjyP04 (P:102-277)
1e: PFAM_Cytochrom_B_N_2_2qjyP05 (P:102-277)
1f: PFAM_Cytochrom_B_N_2_2qjyP06 (P:102-277)
2a: PFAM_Cytochrom_C1_2qjyQ01 (Q:11-255)
2b: PFAM_Cytochrom_C1_2qjyQ02 (Q:11-255)
2c: PFAM_Cytochrom_C1_2qjyQ03 (Q:11-255)
2d: PFAM_Cytochrom_C1_2qjyQ04 (Q:11-255)
2e: PFAM_Cytochrom_C1_2qjyQ05 (Q:11-255)
2f: PFAM_Cytochrom_C1_2qjyQ06 (Q:11-255)
3a: PFAM_Rieske_2qjyR01 (R:95-180)
3b: PFAM_Rieske_2qjyR02 (R:95-180)
3c: PFAM_Rieske_2qjyR03 (R:95-180)
3d: PFAM_Rieske_2qjyR04 (R:95-180)
3e: PFAM_Rieske_2qjyR05 (R:95-180)
3f: PFAM_Rieske_2qjyR06 (R:95-180)
4a: PFAM_UCR_Fe_S_N_2qjyR07 (R:9-41)
4b: PFAM_UCR_Fe_S_N_2qjyR08 (R:9-41)
4c: PFAM_UCR_Fe_S_N_2qjyR09 (R:9-41)
4d: PFAM_UCR_Fe_S_N_2qjyR10 (R:9-41)
4e: PFAM_UCR_Fe_S_N_2qjyR11 (R:9-41)
4f: PFAM_UCR_Fe_S_N_2qjyR12 (R:9-41)
5a: PFAM_Cytochrom_B_C_2qjyP07 (P:282-416)
5b: PFAM_Cytochrom_B_C_2qjyP08 (P:282-416)
5c: PFAM_Cytochrom_B_C_2qjyP09 (P:282-416)
5d: PFAM_Cytochrom_B_C_2qjyP10 (P:282-416)
5e: PFAM_Cytochrom_B_C_2qjyP11 (P:282-416)
5f: PFAM_Cytochrom_B_C_2qjyP12 (P:282-416)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
2heme_cytochrom
(31)
Family
:
Cytochrom_B_N_2
(27)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(3)
1a
Cytochrom_B_N_2-2qjyP01
P:102-277
1b
Cytochrom_B_N_2-2qjyP02
P:102-277
1c
Cytochrom_B_N_2-2qjyP03
P:102-277
1d
Cytochrom_B_N_2-2qjyP04
P:102-277
1e
Cytochrom_B_N_2-2qjyP05
P:102-277
1f
Cytochrom_B_N_2-2qjyP06
P:102-277
Clan
:
Cytochrome-c
(108)
Family
:
Cytochrom_C1
(24)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(3)
2a
Cytochrom_C1-2qjyQ01
Q:11-255
2b
Cytochrom_C1-2qjyQ02
Q:11-255
2c
Cytochrom_C1-2qjyQ03
Q:11-255
2d
Cytochrom_C1-2qjyQ04
Q:11-255
2e
Cytochrom_C1-2qjyQ05
Q:11-255
2f
Cytochrom_C1-2qjyQ06
Q:11-255
Clan
:
ISP-domain
(54)
Family
:
Rieske
(53)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(8)
3a
Rieske-2qjyR01
R:95-180
3b
Rieske-2qjyR02
R:95-180
3c
Rieske-2qjyR03
R:95-180
3d
Rieske-2qjyR04
R:95-180
3e
Rieske-2qjyR05
R:95-180
3f
Rieske-2qjyR06
R:95-180
Clan
:
TAT
(4)
Family
:
UCR_Fe-S_N
(4)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(3)
4a
UCR_Fe-S_N-2qjyR07
R:9-41
4b
UCR_Fe-S_N-2qjyR08
R:9-41
4c
UCR_Fe-S_N-2qjyR09
R:9-41
4d
UCR_Fe-S_N-2qjyR10
R:9-41
4e
UCR_Fe-S_N-2qjyR11
R:9-41
4f
UCR_Fe-S_N-2qjyR12
R:9-41
Clan
:
no clan defined [family: Cytochrom_B_C]
(27)
Family
:
Cytochrom_B_C
(27)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(3)
5a
Cytochrom_B_C-2qjyP07
P:282-416
5b
Cytochrom_B_C-2qjyP08
P:282-416
5c
Cytochrom_B_C-2qjyP09
P:282-416
5d
Cytochrom_B_C-2qjyP10
P:282-416
5e
Cytochrom_B_C-2qjyP11
P:282-416
5f
Cytochrom_B_C-2qjyP12
P:282-416
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