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Getting 'Exon' information from database.
1EZV
Asym. Unit
Info
Asym.Unit (371 KB)
Biol.Unit 1 (678 KB)
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(1)
Title
:
STRUCTURE OF THE YEAST CYTOCHROME BC1 COMPLEX CO-CRYSTALLIZED WITH AN ANTIBODY FV-FRAGMENT
Authors
:
C. Hunte, J. Koepke, C. Lange, T. Rossmanith, H. Michel
Date
:
12 May 00 (Deposition) - 16 May 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,X,Y
Biol. Unit 1: A,B,C,D,E,F,G,H,I,X,Y (2x)
Keywords
:
Cytochrome Bc1 Complex, Complex Iii, Qcr, Mitochondria, Yeast, Antibody Fv-Fragment, Stigmatellin, Coenzyme Q6, Matrix Processing Peptidases, Ubiquinone, Electron Transfer, Proton Transfer, Q-Cycle, Oxidoreductase/Electron Transport Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Hunte, J. Koepke, C. Lange, T. Rossmanith, H. Michel
Structure At 2. 3 A Resolution Of The Cytochrome Bc(1) Complex From The Yeast Saccharomyces Cerevisiae Co-Crystallized With An Antibody Fv Fragment.
Structure Fold. Des. V. 8 669 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 6)
Info
All Hetero Components
1a: FE2/S2 (INORGANIC) CLUSTER (FESa)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
2c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
3a: STIGMATELLIN A (SMAa)
4a: 5-(3,7,11,15,19,23-HEXAMETHYL-TETR... (UQ6a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FES
1
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
2
HEM
3
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
SMA
1
Ligand/Ion
STIGMATELLIN A
4
UQ6
1
Ligand/Ion
5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU C:40 , GLN C:43 , GLY C:47 , ILE C:48 , MET C:50 , ALA C:51 , ARG C:79 , HIS C:82 , ALA C:83 , PHE C:89 , THR C:127 , ALA C:128 , GLY C:131 , VAL C:135 , HIS C:183 , TYR C:184 , PRO C:187 , HOH C:527 , HOH C:539
BINDING SITE FOR RESIDUE HEM C 401
2
AC2
SOFTWARE
TRP C:30 , GLY C:33 , LEU C:36 , HIS C:96 , LYS C:99 , SER C:105 , LEU C:113 , GLY C:117 , VAL C:118 , ILE C:120 , HIS C:197 , LEU C:201 , SER C:206 , SER C:207 , UQ6 C:506 , HOH C:508 , HOH C:528
BINDING SITE FOR RESIDUE HEM C 402
3
AC3
SOFTWARE
VAL D:100 , CYS D:101 , CYS D:104 , HIS D:105 , ASN D:169 , PRO D:175 , ARG D:184 , TYR D:190 , ILE D:191 , PHE D:218 , ILE D:223 , ALA D:224 , MET D:225 , VAL D:228 , HOH D:317 , HOH D:372
BINDING SITE FOR RESIDUE HEM D 3
4
AC4
SOFTWARE
CYS E:159 , HIS E:161 , LEU E:162 , CYS E:178 , HIS E:181 , SER E:183
BINDING SITE FOR RESIDUE FES E 4
5
AC5
SOFTWARE
ILE C:125 , PHE C:129 , VAL C:146 , ILE C:269 , PRO C:271 , GLU C:272 , LEU C:275 , TYR C:279 , MET C:295 , PHE C:296 , HOH C:548 , HIS E:181
BINDING SITE FOR RESIDUE SMA C 505
6
AC6
SOFTWARE
TYR C:16 , GLN C:22 , LEU C:40 , ILE C:44 , PHE C:49 , MET C:52 , LEU C:198 , LEU C:201 , SER C:206 , MET C:221 , HEM C:402
BINDING SITE FOR RESIDUE UQ6 C 506
[
close Site info
]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_CYB_YEAST_001 (G131S, chain C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_CYB_YEAST_001
*
G
131
S
CYB_YEAST
---
---
C
G
131
S
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(5, 5)
Info
All PROSITE Patterns/Profiles
1: CYTB_NTER (C:1-210)
2: INSULINASE (B:37-59)
3: CYTC (D:88-241)
4: RIESKE (E:123-214)
5: CYTB_CTER (C:211-381)
;
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_YEAST
1-210
1
C:1-210
2
INSULINASE
PS00143
Insulinase family, zinc-binding region signature.
QCR2_YEAST
37-59
1
B:37-59
3
CYTC
PS51007
Cytochrome c family profile.
CY1_YEAST
88-241
1
D:88-241
4
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
UCRI_YEAST
123-214
1
E:123-214
5
CYTB_CTER
PS51003
Cytochrome b/b6 C-terminal region profile.
CYB_YEAST
211-381
1
C:211-381
[
close PROSITE info
]
Exons
(14, 14)
Info
All Exons
Exon 1.1 (C:1-139)
Exon 1.2 (C:139-143)
Exon 1.3 (C:144-169)
Exon 1.4 (C:169-252)
Exon 1.5 (C:253-269)
Exon 1.6 (C:270-385)
Exon 2.1 (A:27-456 (gaps))
Exon 3.1 (F:3-127)
Exon 4.1 (E:31-215)
Exon 5.1 (H:74-147)
Exon 6.2 (I:4-58)
Exon 7.1 (G:2-94)
Exon 8.1 (D:62-306)
Exon 9.1 (B:17-368)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/-
08: Boundary -/2.1
09: Boundary 2.1/-
10: Boundary -/3.1
11: Boundary 3.1/-
12: Boundary -/4.1
13: Boundary 4.1/-
14: Boundary -/5.1
15: Boundary 5.1/-
16: Boundary 6.1/6.2
17: Boundary 6.2/-
18: Boundary -/7.1
19: Boundary 7.1/-
20: Boundary -/8.1
21: Boundary 8.1/-
22: Boundary -/9.1
23: Boundary 9.1/-
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
1.1
Q0105
1
Q0105.1
Mito:36540-36954
415
CYB_YEAST
1-139
139
1
C:1-139
139
1.2
Q0105
2
Q0105.2
Mito:37723-37736
14
CYB_YEAST
139-143
5
1
C:139-143
5
1.3
Q0105
3
Q0105.3
Mito:39141-39217
77
CYB_YEAST
144-169
26
1
C:144-169
26
1.4
Q0105
4
Q0105.4
Mito:40841-41090
250
CYB_YEAST
169-252
84
1
C:169-252
84
1.5
Q0105
5
Q0105.5
Mito:42508-42558
51
CYB_YEAST
253-269
17
1
C:253-269
17
1.6
Q0105
6
Q0105.6
Mito:43297-43647
351
CYB_YEAST
270-385
116
1
C:270-385
116
2.1
YBL045C
1
YBL045C.1
II:135519-134146
1374
QCR1_YEAST
1-457
457
1
A:27-456 (gaps)
431
3.1
YDR529C
1
YDR529C.1
IV:1496541-1496158
384
QCR7_YEAST
1-127
127
1
F:3-127
125
4.1
YEL024W
1
YEL024W.1
V:107260-107907
648
UCRI_YEAST
1-215
215
1
E:31-215
185
5.1
YFR033C
1
YFR033C.1
VI:224757-224314
444
QCR6_YEAST
1-147
147
1
H:74-147
74
6.1
YGR183C
1
YGR183C.1
VII:859481-859479
3
QCR9_YEAST
1-1
1
0
-
-
6.2
YGR183C
2
YGR183C.2
VII:859265-859068
198
QCR9_YEAST
2-66
65
1
I:4-58
55
7.1
YJL166W
1
YJL166W.1
X:106428-106712
285
QCR8_YEAST
1-94
94
1
G:2-94
93
8.1
YOR065W
1
YOR065W.1
XV:447441-448370
930
CY1_YEAST
1-309
309
1
D:62-306
245
9.1
YPR191W
1
YPR191W.1
XVI:919377-920483
1107
QCR2_YEAST
1-368
368
1
B:17-368
352
[
close EXON info
]
SCOP Domains
(14, 16)
Info
All SCOP Domains
01a: SCOP_d1ezvd1 (D:62-260)
02a: SCOP_d1ezvx_ (X:)
03a: SCOP_d1ezvy_ (Y:)
04a: SCOP_d1ezve1 (E:87-215)
05a: SCOP_d1ezva1 (A:27-239)
05b: SCOP_d1ezva2 (A:240-456)
06a: SCOP_d1ezvb1 (B:17-218)
06b: SCOP_d1ezvb2 (B:219-368)
07a: SCOP_d1ezvf_ (F:)
08a: SCOP_d1ezvc2 (C:262-385)
09a: SCOP_d1ezvc3 (C:1-261)
10a: SCOP_d1ezvh_ (H:)
11a: SCOP_d1ezvd2 (D:261-306)
12a: SCOP_d1ezve2 (E:31-86)
13a: SCOP_d1ezvi_ (I:)
14a: SCOP_d1ezvg_ (G:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
Cytochrome bc1 domain
(36)
Protein domain
:
Cytochrome bc1 domain
(27)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(7)
01a
d1ezvd1
D:62-260
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Mouse (Mus musculus), cluster 7.1 [TaxId: 10090]
(38)
02a
d1ezvx_
X:
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Mouse (Mus musculus), cluster 4 [TaxId: 10090]
(211)
03a
d1ezvy_
Y:
Fold
:
ISP domain
(115)
Superfamily
:
ISP domain
(115)
Family
:
Rieske iron-sulfur protein (ISP)
(50)
Protein domain
:
ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain
(28)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(7)
04a
d1ezve1
E:87-215
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
LuxS/MPP-like metallohydrolase
(89)
Superfamily
:
LuxS/MPP-like metallohydrolase
(89)
Family
:
MPP-like
(65)
Protein domain
:
Cytochrome bc1 core subunit 1
(27)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(7)
05a
d1ezva1
A:27-239
05b
d1ezva2
A:240-456
Protein domain
:
Cytochrome bc1 core subunit 2
(27)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(7)
06a
d1ezvb1
B:17-218
06b
d1ezvb2
B:219-368
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Superfamily
:
14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Family
:
14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Protein domain
:
14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(21)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(4)
07a
d1ezvf_
F:
Fold
:
a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(46)
Superfamily
:
a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(46)
Family
:
a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(39)
Protein domain
:
Mitochondrial cytochrome b subunit, C-terminal domain
(30)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(5)
08a
d1ezvc2
C:262-385
Fold
:
Heme-binding four-helical bundle
(113)
Superfamily
:
Transmembrane di-heme cytochromes
(48)
Family
:
Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(46)
Protein domain
:
Mitochondrial cytochrome b subunit, N-terminal domain
(30)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(5)
09a
d1ezvc3
C:1-261
Fold
:
Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Superfamily
:
Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Family
:
Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Protein domain
:
Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(20)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(5)
10a
d1ezvh_
H:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
(36)
Family
:
Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
(27)
Protein domain
:
Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor
(27)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(7)
11a
d1ezvd2
D:261-306
Superfamily
:
ISP transmembrane anchor
(35)
Family
:
ISP transmembrane anchor
(32)
Protein domain
:
Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region
(27)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(7)
12a
d1ezve2
E:31-86
Superfamily
:
Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Family
:
Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Protein domain
:
Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(25)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(4)
13a
d1ezvi_
I:
Superfamily
:
Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Family
:
Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(36)
Protein domain
:
Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
(28)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(7)
14a
d1ezvg_
G:
[
close SCOP info
]
CATH Domains
(11, 15)
Info
all CATH domains
01a: CATH_1ezvB01 (B:17-227)
01b: CATH_1ezvA02 (A:234-456)
01c: CATH_1ezvA01 (A:27-227)
01d: CATH_1ezvB02 (B:234-368)
02a: CATH_1ezvD02 (D:65-261)
03a: CATH_1ezvF00 (F:3-127)
04a: CATH_1ezvH00 (H:74-147)
05a: CATH_1ezvC00 (C:1-385)
06a: CATH_1ezvD01 (D:262-306)
07a: CATH_1ezvG00 (G:2-94)
08a: CATH_1ezvI00 (I:4-58)
09a: CATH_1ezvE01 (E:31-85)
10a: CATH_1ezvE02 (E:86-215)
11a: CATH_1ezvY00 (Y:1-107)
11b: CATH_1ezvX00 (X:1-127)
View:
Select:
Label:
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)
Baker's yeast (Saccharomyces cerevisiae)
(9)
01a
1ezvB01
B:17-227
01b
1ezvA02
A:234-456
01c
1ezvA01
A:27-227
01d
1ezvB02
B:234-368
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Baker's yeast (Saccharomyces cerevisiae)
(49)
02a
1ezvD02
D:65-261
Topology
:
Cytochrome Bc1 Complex; Chain F
(39)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain F
(39)
Baker's yeast (Saccharomyces cerevisiae)
(5)
03a
1ezvF00
F:3-127
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
[code=1.10.287.20, no name defined]
(39)
Baker's yeast (Saccharomyces cerevisiae)
(5)
04a
1ezvH00
H:74-147
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome Bc1 Complex; Chain C
(51)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain C
(51)
Baker's yeast (Saccharomyces cerevisiae)
(5)
05a
1ezvC00
C:1-385
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)
Baker's yeast (Saccharomyces cerevisiae)
(5)
06a
1ezvD01
D:262-306
Homologous Superfamily
:
[code=1.20.5.210, no name defined]
(39)
Baker's yeast (Saccharomyces cerevisiae)
(5)
07a
1ezvG00
G:2-94
Homologous Superfamily
:
[code=1.20.5.260, no name defined]
(39)
Baker's yeast (Saccharomyces cerevisiae)
(5)
08a
1ezvI00
I:4-58
Homologous Superfamily
:
[code=1.20.5.270, no name defined]
(39)
Baker's yeast (Saccharomyces cerevisiae)
(5)
09a
1ezvE01
E:31-85
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Baker's yeast (Saccharomyces cerevisiae)
(5)
10a
1ezvE02
E:86-215
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Baker's yeast (Saccharomyces cerevisiae)
(5)
11a
1ezvY00
Y:1-107
11b
1ezvX00
X:1-127
[
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
Chain E
Chain F
Chain G
Chain H
Chain I
Chain X
Chain Y
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
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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)
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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 (371 KB)
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