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Getting 'Exon' information from database.
3RNM
Asym. Unit
Info
Asym.Unit (635 KB)
Biol.Unit 1 (318 KB)
Biol.Unit 2 (315 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF THE SUBUNIT BINDING OF HUMAN DIHYDROLIPOAMIDE TRANSACYLASE (E2B) BOUND TO HUMAN DIHYDROLIPOAMIDE DEHYDROGENASE (E3)
Authors
:
C. A. Brautigam, R. M. Wynn, J. C. Chuang, B. B. Young, D. T. Chuang
Date
:
22 Apr 11 (Deposition) - 04 May 11 (Release) - 20 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,E (1x)
Biol. Unit 2: C,D,F (1x)
Keywords
:
Protein-Protein Interaction, Redox Protein, Mitochondrion, Oxidoreductase-Protein Binding Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. A. Brautigam, R. M. Wynn, J. L. Chuang, M. T. Naik, B. B. Young, T. H. Huang, D. T. Chuang
Structural And Thermodynamic Basis For Weak Interactions Between Dihydrolipoamide Dehydrogenase And Subunit-Binding Domain Of The Branched-Chain {Alpha}-Ketoacid Dehydrogenase Complex.
J. Biol. Chem. V. 286 23476 2011
[
close entry info
]
Hetero Components
(3, 12)
Info
All Hetero Components
1a: BETA-MERCAPTOETHANOL (BMEa)
1b: BETA-MERCAPTOETHANOL (BMEb)
1c: BETA-MERCAPTOETHANOL (BMEc)
1d: BETA-MERCAPTOETHANOL (BMEd)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
2d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
3a: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFON... (NHEa)
3b: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFON... (NHEb)
3c: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFON... (NHEc)
3d: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFON... (NHEd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BME
4
Ligand/Ion
BETA-MERCAPTOETHANOL
2
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
3
NHE
4
Ligand/Ion
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:168 , ILE A:189 , CYS A:277 , ARG A:280 , FAD A:480 , HOH A:563
BINDING SITE FOR RESIDUE BME A 500
02
AC2
SOFTWARE
ILE A:12 , GLY A:13 , GLY A:15 , PRO A:16 , GLY A:17 , GLU A:36 , LYS A:37 , ASN A:38 , GLY A:43 , THR A:44 , CYS A:45 , VAL A:48 , GLY A:49 , CYS A:50 , LYS A:54 , GLY A:117 , TYR A:118 , GLY A:119 , ALA A:147 , THR A:148 , GLY A:149 , SER A:150 , ILE A:189 , ARG A:280 , PHE A:283 , GLY A:319 , ASP A:320 , MET A:326 , LEU A:327 , ALA A:328 , HIS A:329 , TYR A:359 , HOH A:476 , HOH A:478 , HOH A:489 , BME A:500 , HOH A:535 , HOH A:547 , HIS B:452
BINDING SITE FOR RESIDUE FAD A 480
03
AC3
SOFTWARE
ASN A:225 , GLY A:402 , HOH A:536
BINDING SITE FOR RESIDUE NHE A 475
04
AC4
SOFTWARE
SER B:168 , CYS B:277 , ARG B:280 , FAD B:480
BINDING SITE FOR RESIDUE BME B 500
05
AC5
SOFTWARE
HIS A:452 , PRO A:453 , ILE B:12 , GLY B:13 , GLY B:15 , PRO B:16 , GLY B:17 , ILE B:35 , GLU B:36 , LYS B:37 , ASN B:38 , GLY B:43 , THR B:44 , CYS B:45 , VAL B:48 , GLY B:49 , CYS B:50 , LYS B:54 , TYR B:118 , GLY B:119 , ALA B:147 , THR B:148 , GLY B:149 , SER B:150 , ARG B:280 , PHE B:283 , LEU B:287 , GLY B:319 , ASP B:320 , MET B:326 , LEU B:327 , ALA B:328 , HIS B:329 , ALA B:331 , TYR B:359 , BME B:500 , HOH B:505
BINDING SITE FOR RESIDUE FAD B 480
06
AC6
SOFTWARE
ASN B:225 , GLY B:402 , MET B:403 , PHE B:474
BINDING SITE FOR RESIDUE NHE B 475
07
AC7
SOFTWARE
ILE C:189 , CYS C:277 , GLY C:279 , HOH C:503 , HOH C:527 , HIS E:160
BINDING SITE FOR RESIDUE BME C 500
08
AC8
SOFTWARE
ILE C:12 , GLY C:13 , GLY C:15 , PRO C:16 , GLY C:17 , GLU C:36 , LYS C:37 , ASN C:38 , GLY C:43 , THR C:44 , CYS C:45 , VAL C:48 , GLY C:49 , CYS C:50 , LYS C:54 , GLY C:117 , TYR C:118 , GLY C:119 , ALA C:147 , THR C:148 , GLY C:149 , SER C:150 , SER C:168 , ILE C:189 , ARG C:280 , PHE C:283 , GLY C:319 , ASP C:320 , MET C:326 , LEU C:327 , ALA C:328 , HIS C:329 , ALA C:331 , TYR C:359 , HOH C:476 , HOH C:491 , HOH C:496 , HOH C:504 , HIS D:452
BINDING SITE FOR RESIDUE FAD C 480
09
AC9
SOFTWARE
ASN C:225 , GLY C:402 , PHE C:474
BINDING SITE FOR RESIDUE NHE C 475
10
BC1
SOFTWARE
SER D:168 , ILE D:189 , CYS D:277 , ARG D:280 , FAD D:480
BINDING SITE FOR RESIDUE BME D 500
11
BC2
SOFTWARE
HIS C:452 , ILE D:12 , GLY D:13 , GLY D:15 , PRO D:16 , GLY D:17 , GLU D:36 , LYS D:37 , ASN D:38 , GLY D:43 , THR D:44 , CYS D:45 , VAL D:48 , GLY D:49 , CYS D:50 , LYS D:54 , TYR D:118 , GLY D:119 , ALA D:147 , THR D:148 , GLY D:149 , SER D:150 , SER D:168 , ILE D:189 , ARG D:280 , PHE D:283 , GLY D:319 , ASP D:320 , MET D:326 , LEU D:327 , ALA D:328 , HIS D:329 , TYR D:359 , HOH D:476 , HOH D:486 , HOH D:489 , HOH D:490 , BME D:500
BINDING SITE FOR RESIDUE FAD D 480
12
BC3
SOFTWARE
ASN D:225 , PRO D:387 , GLY D:402 , HOH D:548
BINDING SITE FOR RESIDUE NHE D 475
[
close Site info
]
SAPs(SNPs)/Variants
(7, 25)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_006907 (K37E, chain A/B/C/D, )
2: VAR_031922 (K69T, chain A/B/C/D, )
3: VAR_004978 (H158C, chain E, )
4: VAR_015820 (G194C, chain A/B/C/D, )
5: VAR_014555 (L296V, chain A/B/C/D, )
6: VAR_006908 (P453L, chain A/B/C/D, )
7: VAR_015821 (R460G, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_006907
K
72
E
DLDH_HUMAN
Disease (DLDD)
---
A/B/C/D
K
37
E
2
UniProt
VAR_031922
K
104
T
DLDH_HUMAN
Polymorphism
1130477
A/B/C/D
K
69
T
3
UniProt
VAR_004978
F
276
C
ODB2_HUMAN
Disease (MSUD2)
---
E
H
158
C
4
UniProt
VAR_015820
G
229
C
DLDH_HUMAN
Disease (DLDD)
---
A/B/C/D
G
194
C
5
UniProt
VAR_014555
L
331
V
DLDH_HUMAN
Polymorphism
17624
A/B/C/D
L
296
V
6
UniProt
VAR_006908
P
488
L
DLDH_HUMAN
Disease (DLDD)
---
A/B/C/D
P
453
L
7
UniProt
VAR_015821
R
495
G
DLDH_HUMAN
Disease (DLDD)
---
A/B/C/D
R
460
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: PYRIDINE_REDOX_1 (A:42-52,B:42-52,C:42-52,D:42-52)
2: PSBD (E:111-148,F:111-148)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PYRIDINE_REDOX_1
PS00076
Pyridine nucleotide-disulphide oxidoreductases class-I active site.
DLDH_HUMAN
77-87
4
A:42-52
B:42-52
C:42-52
D:42-52
2
PSBD
PS51826
Peripheral subunit-binding (PSBD) domain profile.
ODB2_HUMAN
172-209
2
E:111-148
F:111-148
[
close PROSITE info
]
Exons
(16, 57)
Info
All Exons
Exon 1.3a (A:3-5 | B:4-5 | C:3-5 | D:4-5)
Exon 1.4 (A:5-31 | B:5-31 | C:5-31 | D:5-31)
Exon 1.5 (A:32-54 | B:32-54 | C:32-54 | D:32...)
Exon 1.6a (A:55-78 | B:55-78 | C:55-78 | D:55...)
Exon 1.7e (A:78-111 | B:78-111 | C:78-111 | D...)
Exon 1.8b (A:112-159 | B:112-159 | C:112-159 ...)
Exon 1.9a (A:160-193 | B:160-193 | C:160-193 ...)
Exon 1.10b (A:194-257 | B:194-257 | C:194-257 ...)
Exon 1.11 (A:257-314 | B:257-314 (gaps) | C:2...)
Exon 1.12 (A:314-377 | B:314-377 | C:314-377 ...)
Exon 1.13 (A:378-423 | B:378-423 | C:378-423 ...)
Exon 1.14 (A:424-453 | B:424-453 | C:424-453 ...)
Exon 1.15e (A:454-474 | B:454-474 | C:454-474 ...)
Exon 2.5 (E:110-124 | F:111-124)
Exon 2.6 (E:125-152 | F:125-153 (gaps))
Exon 2.7 (E:153-160 | -)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.3a
02: Boundary 1.3a/1.4
03: Boundary 1.4/1.5
04: Boundary 1.5/1.6a
05: Boundary 1.6a/1.7e
06: Boundary 1.7e/1.8b
07: Boundary 1.8b/1.9a
08: Boundary 1.9a/1.10b
09: Boundary 1.10b/1.11
10: Boundary 1.11/1.12
11: Boundary 1.12/1.13
12: Boundary 1.13/1.14
13: Boundary 1.14/1.15e
14: Boundary 1.15e/-
15: Boundary 2.4/2.5
16: Boundary 2.5/2.6
17: Boundary 2.6/2.7
18: Boundary 2.7/2.8b
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
1.1a
ENST00000205402
1a
ENSE00001876887
chr7:
107531415-107531734
320
DLDH_HUMAN
1-13
13
0
-
-
1.3a
ENST00000205402
3a
ENSE00000715773
chr7:
107533645-107533723
79
DLDH_HUMAN
14-40
27
4
A:3-5
B:4-5
C:3-5
D:4-5
3
2
3
2
1.4
ENST00000205402
4
ENSE00000715774
chr7:
107542183-107542262
80
DLDH_HUMAN
40-66
27
4
A:5-31
B:5-31
C:5-31
D:5-31
27
27
27
27
1.5
ENST00000205402
5
ENSE00000715776
chr7:
107542770-107542838
69
DLDH_HUMAN
67-89
23
4
A:32-54
B:32-54
C:32-54
D:32-54
23
23
23
23
1.6a
ENST00000205402
6a
ENSE00001665843
chr7:
107543923-107543992
70
DLDH_HUMAN
90-113
24
4
A:55-78
B:55-78
C:55-78
D:55-78
24
24
24
24
1.7e
ENST00000205402
7e
ENSE00001717474
chr7:
107545403-107545503
101
DLDH_HUMAN
113-146
34
4
A:78-111
B:78-111
C:78-111
D:78-111
34
34
34
34
1.8b
ENST00000205402
8b
ENSE00001761545
chr7:
107545806-107545949
144
DLDH_HUMAN
147-194
48
4
A:112-159
B:112-159
C:112-159
D:112-159
48
48
48
48
1.9a
ENST00000205402
9a
ENSE00001638968
chr7:
107546712-107546813
102
DLDH_HUMAN
195-228
34
4
A:160-193
B:160-193
C:160-193
D:160-193
34
34
34
34
1.10b
ENST00000205402
10b
ENSE00001672433
chr7:
107555951-107556141
191
DLDH_HUMAN
229-292
64
4
A:194-257
B:194-257
C:194-257
D:194-257
64
64
64
64
1.11
ENST00000205402
11
ENSE00001609201
chr7:
107557239-107557409
171
DLDH_HUMAN
292-349
58
4
A:257-314
B:257-314 (gaps)
C:257-314
D:257-314 (gaps)
58
58
58
58
1.12
ENST00000205402
12
ENSE00001752704
chr7:
107557718-107557907
190
DLDH_HUMAN
349-412
64
4
A:314-377
B:314-377
C:314-377
D:314-377
64
64
64
64
1.13
ENST00000205402
13
ENSE00001658920
chr7:
107558369-107558506
138
DLDH_HUMAN
413-458
46
4
A:378-423
B:378-423
C:378-423
D:378-423
46
46
46
46
1.14
ENST00000205402
14
ENSE00001606668
chr7:
107559455-107559544
90
DLDH_HUMAN
459-488
30
4
A:424-453
B:424-453
C:424-453
D:424-453
30
30
30
30
1.15e
ENST00000205402
15e
ENSE00000881778
chr7:
107559639-107560360
722
DLDH_HUMAN
489-509
21
4
A:454-474
B:454-474
C:454-474
D:454-474
21
21
21
21
2.1a
ENST00000370132
1a
ENSE00001451903
chr1:
100715390-100715326
65
ODB2_HUMAN
1-17
17
0
-
-
2.2
ENST00000370132
2
ENSE00000831299
chr1:
100706440-100706317
124
ODB2_HUMAN
18-59
42
0
-
-
2.3
ENST00000370132
3
ENSE00000831298
chr1:
100701067-100700992
76
ODB2_HUMAN
59-84
26
0
-
-
2.4
ENST00000370132
4
ENSE00000831297
chr1:
100696470-100696289
182
ODB2_HUMAN
84-145
62
0
-
-
2.5
ENST00000370132
5
ENSE00000831296
chr1:
100684303-100684182
122
ODB2_HUMAN
145-185
41
2
E:110-124
F:111-124
15
14
2.6
ENST00000370132
6
ENSE00000831295
chr1:
100681755-100681539
217
ODB2_HUMAN
186-258
73
2
E:125-152
F:125-153 (gaps)
28
32
2.7
ENST00000370132
7
ENSE00000831294
chr1:
100680539-100680373
167
ODB2_HUMAN
258-313
56
1
E:153-160
-
8
-
2.8b
ENST00000370132
8b
ENSE00000831293
chr1:
100676327-100676250
78
ODB2_HUMAN
314-339
26
0
-
-
2.9
ENST00000370132
9
ENSE00000831292
chr1:
100672192-100672001
192
ODB2_HUMAN
340-403
64
0
-
-
2.10
ENST00000370132
10
ENSE00000831291
chr1:
100671857-100671786
72
ODB2_HUMAN
404-427
24
0
-
-
2.11
ENST00000370132
11
ENSE00001451905
chr1:
100661978-100659736
2243
ODB2_HUMAN
428-482
55
0
-
-
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3rnme_ (E:)
1b: SCOP_d3rnmf_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
(21)
Superfamily
:
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
(21)
Family
:
automated matches
(5)
Protein domain
:
automated matches
(5)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d3rnme_
E:
1b
d3rnmf_
F:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(4, 14)
Info
all PFAM domains
1a: PFAM_Pyr_redox_3rnmD01 (D:180-264)
1b: PFAM_Pyr_redox_3rnmD02 (D:180-264)
1c: PFAM_Pyr_redox_3rnmD03 (D:180-264)
1d: PFAM_Pyr_redox_3rnmD04 (D:180-264)
2a: PFAM_Pyr_redox_2_3rnmD05 (D:8-326)
2b: PFAM_Pyr_redox_2_3rnmD06 (D:8-326)
2c: PFAM_Pyr_redox_2_3rnmD07 (D:8-326)
2d: PFAM_Pyr_redox_2_3rnmD08 (D:8-326)
3a: PFAM_E3_binding_3rnmF01 (F:111-146)
3b: PFAM_E3_binding_3rnmF02 (F:111-146)
4a: PFAM_Pyr_redox_dim_3rnmD09 (D:354-463)
4b: PFAM_Pyr_redox_dim_3rnmD10 (D:354-463)
4c: PFAM_Pyr_redox_dim_3rnmD11 (D:354-463)
4d: PFAM_Pyr_redox_dim_3rnmD12 (D:354-463)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
Pyr_redox
(62)
Homo sapiens (Human)
(8)
1a
Pyr_redox-3rnmD01
D:180-264
1b
Pyr_redox-3rnmD02
D:180-264
1c
Pyr_redox-3rnmD03
D:180-264
1d
Pyr_redox-3rnmD04
D:180-264
Family
:
Pyr_redox_2
(69)
Homo sapiens (Human)
(8)
2a
Pyr_redox_2-3rnmD05
D:8-326
2b
Pyr_redox_2-3rnmD06
D:8-326
2c
Pyr_redox_2-3rnmD07
D:8-326
2d
Pyr_redox_2-3rnmD08
D:8-326
Clan
:
no clan defined [family: E3_binding]
(14)
Family
:
E3_binding
(14)
Homo sapiens (Human)
(3)
3a
E3_binding-3rnmF01
F:111-146
3b
E3_binding-3rnmF02
F:111-146
Clan
:
no clan defined [family: Pyr_redox_dim]
(44)
Family
:
Pyr_redox_dim
(44)
Homo sapiens (Human)
(7)
4a
Pyr_redox_dim-3rnmD09
D:354-463
4b
Pyr_redox_dim-3rnmD10
D:354-463
4c
Pyr_redox_dim-3rnmD11
D:354-463
4d
Pyr_redox_dim-3rnmD12
D:354-463
[
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
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
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(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
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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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close Script example commands
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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 (635 KB)
Header - Asym.Unit
Biol.Unit 1 (318 KB)
Header - Biol.Unit 1
Biol.Unit 2 (315 KB)
Header - Biol.Unit 2
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