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2D2C
Asym. Unit
Info
Asym.Unit (297 KB)
Biol.Unit 1 (283 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CYTOCHROME B6F COMPLEX WITH DBMIB FROM M. LAMINOSUS
Authors
:
J. Yan, G. Kurisu, W. A. Cramer
Date
:
07 Sep 05 (Deposition) - 13 Dec 05 (Release) - 26 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,N,O,P,Q,R,S,T,U
Biol. Unit 1: A,B,C,D,E,F,G,H,N,O,P,Q,R,S,T,U (1x)
Keywords
:
Photosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Yan, G. Kurisu, W. A. Cramer
Intraprotein Transfer Of The Quinone Analogue Inhibitor 2, 5-Dibromo-3-Methyl-6-Isopropyl-P-Benzoquinone In The Cytochrome B6F Complex
Proc. Natl. Acad. Sci. Usa V. 103 69 2006
[
close entry info
]
Hetero Components
(7, 20)
Info
All Hetero Components
1a: BETA-CAROTENE (BCRa)
1b: BETA-CAROTENE (BCRb)
2a: 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBE... (BNTa)
2b: 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBE... (BNTb)
3a: CHLOROPHYLL A (CLAa)
3b: CHLOROPHYLL A (CLAb)
4a: FE2/S2 (INORGANIC) CLUSTER (FESa)
4b: FE2/S2 (INORGANIC) CLUSTER (FESb)
5a: HEME C (HECa)
5b: HEME C (HECb)
6a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
6b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
6c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
6d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
6e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
6f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
7a: (7R,17E)-4-HYDROXY-N,N,N,7-TETRAME... (OPCa)
7b: (7R,17E)-4-HYDROXY-N,N,N,7-TETRAME... (OPCb)
7c: (7R,17E)-4-HYDROXY-N,N,N,7-TETRAME... (OPCc)
7d: (7R,17E)-4-HYDROXY-N,N,N,7-TETRAME... (OPCd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCR
2
Ligand/Ion
BETA-CAROTENE
2
BNT
2
Ligand/Ion
2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE
3
CLA
2
Ligand/Ion
CHLOROPHYLL A
4
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
HEC
2
Ligand/Ion
HEME C
6
HEM
6
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
7
OPC
4
Ligand/Ion
(7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:44 , GLN A:47 , PHE A:48 , GLY A:51 , PHE A:52 , THR A:55 , ARG A:83 , HIS A:86 , ALA A:90 , MET A:93 , PHE A:131 , GLY A:135 , TYR A:136 , LEU A:138 , PRO A:139 , HIS A:187 , THR A:188 , PHE N:189
BINDING SITE FOR RESIDUE HEM A 301
02
AC2
SOFTWARE
GLY A:37 , GLY A:38 , MET A:97 , HIS A:100 , GLY A:109 , THR A:117 , TRP A:118 , GLY A:121 , VAL A:122 , LEU A:124 , ALA A:125 , THR A:128 , HIS A:202 , PHE A:203 , ILE A:206 , HEC A:303 , HOH A:304
BINDING SITE FOR RESIDUE HEM A 302
03
AC3
SOFTWARE
TYR A:34 , CYS A:35 , GLY A:38 , LYS A:208 , HEM A:302 , HOH A:304 , GLU B:29 , PHE B:40 , VAL B:43 , ILE B:44
BINDING SITE FOR RESIDUE HEC A 303
04
AC4
SOFTWARE
LEU B:37 , PRO B:41 , OPC C:306
BINDING SITE FOR RESIDUE OPC B 305
05
AC5
SOFTWARE
TYR B:38 , OPC B:305 , LYS C:275 , GLN D:17 , ASN D:20
BINDING SITE FOR RESIDUE OPC C 306
06
AC6
SOFTWARE
MET B:61 , GLY B:63 , GLU B:64 , PRO B:65 , TYR C:147 , ALA C:148
BINDING SITE FOR RESIDUE BNT B 309
07
AC7
SOFTWARE
VAL A:101 , VAL A:129 , TYR B:80 , PRO B:83 , VAL B:84 , ILE B:87 , VAL B:104 , PRO B:105 , ILE B:132 , PHE B:133 , GLY B:136
BINDING SITE FOR RESIDUE CLA B 201
08
AC8
SOFTWARE
TYR C:1 , PRO C:2 , TRP C:4 , CYS C:22 , CYS C:25 , HIS C:26 , GLN C:60 , ASN C:71 , GLY C:73 , ALA C:74 , ASN C:154 , GLY C:156 , ARG C:157 , GLY C:158 , ILE C:160 , TYR C:161
BINDING SITE FOR RESIDUE HEM C 301
09
AC9
SOFTWARE
CYS D:108 , HIS D:110 , LEU D:111 , CYS D:113 , CYS D:126 , HIS D:129 , SER D:131 , PRO D:143
BINDING SITE FOR RESIDUE FES D 201
10
BC1
SOFTWARE
PHE A:33 , ILE A:39 , LEU A:99 , GLY B:46 , ALA E:13 , PHE E:16 , GLY E:17 , ILE F:17 , PHE F:18 , TRP F:21 , GLN G:23
BINDING SITE FOR RESIDUE BCR E 101
11
BC2
SOFTWARE
PHE A:189 , PHE N:44 , GLN N:47 , PHE N:48 , GLY N:51 , PHE N:52 , MET N:54 , THR N:55 , VAL N:69 , ARG N:83 , HIS N:86 , ARG N:87 , ALA N:90 , PHE N:131 , GLY N:135 , TYR N:136 , PRO N:139 , HIS N:187 , THR N:188 , MET O:61
BINDING SITE FOR RESIDUE HEM N 301
12
BC3
SOFTWARE
TYR N:34 , GLY N:37 , GLY N:38 , LEU N:41 , HIS N:100 , VAL N:101 , ARG N:103 , VAL N:104 , GLY N:109 , ARG N:114 , TRP N:118 , GLY N:121 , VAL N:122 , LEU N:124 , ALA N:125 , THR N:128 , MET N:199 , HIS N:202 , GLN N:209 , GLY N:210 , HEC N:303 , HOH N:1306
BINDING SITE FOR RESIDUE HEM N 302
13
BC4
SOFTWARE
CYS N:35 , GLY N:38 , LEU N:41 , THR N:42 , PHE N:203 , ILE N:206 , HEM N:302 , OPC N:1305 , HOH N:1306 , PHE O:40 , VAL O:43 , ILE O:44
BINDING SITE FOR RESIDUE HEC N 303
14
BC5
SOFTWARE
LEU N:45 , HEC N:303 , OPC O:1306
BINDING SITE FOR RESIDUE OPC N 1305
15
BC6
SOFTWARE
OPC N:1305 , TYR O:38 , LYS P:275
BINDING SITE FOR RESIDUE OPC O 1306
16
BC7
SOFTWARE
MET O:61 , VAL O:62 , GLY O:63 , GLU O:74 , TYR P:147 , ALA P:148
BINDING SITE FOR RESIDUE BNT O 1309
17
BC8
SOFTWARE
VAL N:101 , PHE N:102 , TYR N:105 , TYR O:80 , PRO O:83 , VAL O:84 , MET O:101 , VAL O:104 , PRO O:105 , ALA O:129 , ILE O:132 , PHE O:133 , GLY O:136 , THR O:140
BINDING SITE FOR RESIDUE CLA O 1201
18
BC9
SOFTWARE
TYR P:1 , PRO P:2 , TRP P:4 , CYS P:22 , CYS P:25 , HIS P:26 , GLN P:60 , ASN P:71 , GLY P:73 , ALA P:74 , ASN P:154 , GLY P:156 , ARG P:157 , GLY P:158 , ILE P:160 , TYR P:161
BINDING SITE FOR RESIDUE HEM P 301
19
CC1
SOFTWARE
CYS Q:108 , HIS Q:110 , LEU Q:111 , GLY Q:112 , CYS Q:113 , CYS Q:126 , HIS Q:129 , SER Q:131 , PRO Q:143
BINDING SITE FOR RESIDUE FES Q 201
20
CC2
SOFTWARE
PHE N:33 , ILE N:39 , VAL O:43 , ALA R:13 , PHE R:16 , GLY R:17 , ILE S:17 , PHE S:18 , TRP S:21 , GLN T:23
BINDING SITE FOR RESIDUE BCR R 1101
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: CYTB_CTER (B:35-154,O:35-154)
2: RIESKE (D:61-162,Q:61-162)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTB_CTER
PS51003
Cytochrome b/b6 C-terminal region profile.
PETD_MASLA
35-160
2
B:35-154
O:35-154
2
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
UCRI_MASLA
61-162
2
D:61-162
Q:61-162
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(8, 16)
Info
All SCOP Domains
1a: SCOP_d2d2cd1 (D:46-179)
1b: SCOP_d2d2cq1 (Q:46-179)
2a: SCOP_d2d2cb1 (B:18-154)
2b: SCOP_d2d2co1 (O:18-154)
3a: SCOP_d2d2ca1 (A:13-214)
3b: SCOP_d2d2cn1 (N:13-214)
4a: SCOP_d2d2cd2 (D:12-45)
4b: SCOP_d2d2cq2 (Q:12-45)
5a: SCOP_d2d2cg1 (G:4-30)
5b: SCOP_d2d2ct1 (T:4-30)
6a: SCOP_d2d2ce1 (E:1-32)
6b: SCOP_d2d2cr1 (R:1-32)
7a: SCOP_d2d2cf1 (F:2-36)
7b: SCOP_d2d2cs1 (S:2-36)
8a: SCOP_d2d2ch1 (H:1-27)
8b: SCOP_d2d2cu1 (U:1-27)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
ISP domain
(115)
Superfamily
:
ISP domain
(115)
Family
:
Rieske iron-sulfur protein (ISP)
(50)
Protein domain
:
ISP subunit from the cytochrome b6f complex, soluble domain
(5)
Mastigocladus laminosus [TaxId: 83541]
(4)
1a
d2d2cd1
D:46-179
1b
d2d2cq1
Q:46-179
Class
:
Membrane and cell surface proteins and peptides
(2046)
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
:
Subunit IV of the cytochrome b6f complex
(8)
Mastigocladus laminosus [TaxId: 83541]
(7)
2a
d2d2cb1
B:18-154
2b
d2d2co1
O:18-154
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
:
Cytochrome b6 subunit of the cytochrome b6f complex
(5)
Mastigocladus laminosus [TaxId: 83541]
(4)
3a
d2d2ca1
A:13-214
3b
d2d2cn1
N:13-214
Fold
:
Single transmembrane helix
(568)
Superfamily
:
ISP transmembrane anchor
(35)
Family
:
ISP transmembrane anchor
(32)
Protein domain
:
ISP subunit from the cytochrome b6f complex, transmembrane anchor
(5)
Mastigocladus laminosus [TaxId: 83541]
(4)
4a
d2d2cd2
D:12-45
4b
d2d2cq2
Q:12-45
Superfamily
:
PetG subunit of the cytochrome b6f complex
(8)
Family
:
PetG subunit of the cytochrome b6f complex
(8)
Protein domain
:
PetG subunit of the cytochrome b6f complex
(5)
Mastigocladus laminosus [TaxId: 83541]
(4)
5a
d2d2cg1
G:4-30
5b
d2d2ct1
T:4-30
Superfamily
:
PetL subunit of the cytochrome b6f complex
(7)
Family
:
PetL subunit of the cytochrome b6f complex
(7)
Protein domain
:
PetL subunit of the cytochrome b6f complex
(7)
Mastigocladus laminosus [TaxId: 83541]
(6)
6a
d2d2ce1
E:1-32
6b
d2d2cr1
R:1-32
Superfamily
:
PetM subunit of the cytochrome b6f complex
(9)
Family
:
PetM subunit of the cytochrome b6f complex
(9)
Protein domain
:
PetM subunit of the cytochrome b6f complex
(8)
Mastigocladus laminosus [TaxId: 83541]
(7)
7a
d2d2cf1
F:2-36
7b
d2d2cs1
S:2-36
Superfamily
:
PetN subunit of the cytochrome b6f complex
(9)
Family
:
PetN subunit of the cytochrome b6f complex
(9)
Protein domain
:
PetN subunit of the cytochrome b6f complex
(5)
Mastigocladus laminosus [TaxId: 83541]
(4)
8a
d2d2ch1
H:1-27
8b
d2d2cu1
U:1-27
[
close SCOP info
]
CATH Domains
(7, 14)
Info
all CATH domains
1a: CATH_2d2cB01 (B:21-66)
1b: CATH_2d2cO01 (O:21-66)
2a: CATH_2d2cB02 (B:67-154)
2b: CATH_2d2cO02 (O:67-154)
3a: CATH_2d2cA00 (A:13-214)
3b: CATH_2d2cN00 (N:13-214)
4a: CATH_2d2cC03 (C:255-286)
4b: CATH_2d2cP03 (P:255-286)
5a: CATH_2d2cD02 (D:48-179)
5b: CATH_2d2cQ02 (Q:48-179)
6a: CATH_2d2cC02 (C:172-233)
6b: CATH_2d2cP02 (P:172-233)
7a: CATH_2d2cC01 (C:1-171,C:234-254)
7b: CATH_2d2cP01 (P:1-171,P:234-254)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Cytochrome C Oxidase; Chain M
(30)
Homologous Superfamily
:
Cytochrome C Oxidase, chain M
(29)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
1a
2d2cB01
B:21-66
1b
2d2cO01
O:21-66
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
plastocyanin oxidoreductase
(7)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
2a
2d2cB02
B:67-154
2b
2d2cO02
O:67-154
Architecture
:
Up-down Bundle
(3216)
Topology
:
Cytochrome Bc1 Complex; Chain C
(51)
Homologous Superfamily
:
Cytochrome Bc1 Complex; Chain C
(51)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
3a
2d2cA00
A:13-214
3b
2d2cN00
N:13-214
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
Single helix bin
(6)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
4a
2d2cC03
C:255-286
4b
2d2cP03
P:255-286
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
5a
2d2cD02
D:48-179
5b
2d2cQ02
Q:48-179
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
[code=2.40.50.100, no name defined]
(113)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
6a
2d2cC02
C:172-233
6b
2d2cP02
P:172-233
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.830, no name defined]
(19)
Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid: 83541. Mastigocladus laminosus. Organism_taxid:83541. Mastigocladus laminosus. Organism_taxid: 83541.
(4)
7a
2d2cC01
C:1-171,C:234-254
7b
2d2cP01
P:1-171,P:234-254
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Protein & NOT PROSITE
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Chain B
Chain C
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Chain E
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Chain O
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Chain S
Chain T
Chain U
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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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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") .
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Asym.Unit (297 KB)
Header - Asym.Unit
Biol.Unit 1 (283 KB)
Header - Biol.Unit 1
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