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Getting 'Exon' information from database.
3EXE
Asym. Unit
Info
Asym.Unit (484 KB)
Biol.Unit 1 (243 KB)
Biol.Unit 2 (240 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE PYRUVATE DEHYDROGENASE (E1P) COMPONENT OF HUMAN PYRUVATE DEHYDROGENASE COMPLEX
Authors
:
M. Kato, R. M. Wynn, J. L. Chuang, S. -C. Tso, M. Machius, J. Li, D. T. Chuan
Date
:
16 Oct 08 (Deposition) - 25 Nov 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.98
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Heterotetramer; Thiamine Diphosphate-Dependent Enzyme; Disease Mutation; Glycolysis; Leigh Syndrome; Mitochondrion; Oxidoreductase; Phosphoprotein; Alternative Splicing; Polymorphism; Pyruvate; Thiamine Pyrophosphate; Transit Peptide, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Kato, R. M. Wynn, J. L. Chuang, S. C. Tso, M. Machius, J. Li, D. T. Chuan
Structural Basis For Inactivation Of The Human Pyruvate Dehydrogenase Complex By Phosphorylation: Role Of Disordere Phosphorylation Loops.
Structure V. 16 1849 2008
[
close entry info
]
Hetero Components
(4, 16)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
2c: POTASSIUM ION (Kc)
2d: POTASSIUM ION (Kd)
3a: MANGANESE (II) ION (MNa)
3b: MANGANESE (II) ION (MNb)
3c: MANGANESE (II) ION (MNc)
3d: MANGANESE (II) ION (MNd)
4a: THIAMINE DIPHOSPHATE (TPPa)
4b: THIAMINE DIPHOSPHATE (TPPb)
4c: THIAMINE DIPHOSPHATE (TPPc)
4d: THIAMINE DIPHOSPHATE (TPPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
4
Ligand/Ion
GLYCEROL
2
K
4
Ligand/Ion
POTASSIUM ION
3
MN
4
Ligand/Ion
MANGANESE (II) ION
4
TPP
4
Ligand/Ion
THIAMINE DIPHOSPHATE
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP C:167 , ASN C:196 , TYR C:198 , TPP C:1002 , HOH C:2234
BINDING SITE FOR RESIDUE MN C 1001
02
AC2
SOFTWARE
GLU B:28 , ILE B:57 , GLU B:59 , PHE B:85 , GLN B:88 , TYR C:89 , ARG C:90 , GLY C:136 , VAL C:138 , GLY C:166 , ASP C:167 , GLY C:168 , ALA C:169 , ASN C:196 , TYR C:198 , GLY C:199 , MET C:200 , HIS C:263 , MN C:1001 , HOH C:2200 , HOH C:2222 , HOH C:2234 , HOH C:2277 , HOH C:2489
BINDING SITE FOR RESIDUE TPP C 1002
03
AC3
SOFTWARE
ALA B:160 , ILE B:161 , ASP B:163 , HOH B:2133 , HOH B:2301
BINDING SITE FOR RESIDUE K B 1003
04
AC4
SOFTWARE
ASP A:167 , ASN A:196 , TYR A:198 , TPP A:1005 , HOH A:2039
BINDING SITE FOR RESIDUE MN A 1004
05
AC5
SOFTWARE
TYR A:89 , ARG A:90 , GLY A:136 , VAL A:138 , GLY A:166 , ASP A:167 , GLY A:168 , ALA A:169 , ASN A:196 , TYR A:198 , GLY A:199 , HIS A:263 , MN A:1004 , HOH A:2039 , HOH A:2043 , HOH A:2122 , HOH A:2149 , HOH A:2346 , GLU D:28 , ILE D:57 , GLU D:59 , PHE D:85 , GLN D:88
BINDING SITE FOR RESIDUE TPP A 1005
06
AC6
SOFTWARE
ARG D:75 , ALA D:160 , ILE D:161 , ASP D:163 , HOH D:2065 , HOH D:2159
BINDING SITE FOR RESIDUE K D 1006
07
AC7
SOFTWARE
ASP G:167 , ASN G:196 , TYR G:198 , TPP G:1008 , HOH G:2294
BINDING SITE FOR RESIDUE MN G 1007
08
AC8
SOFTWARE
GLU F:28 , ILE F:57 , GLU F:59 , MET F:81 , PHE F:85 , GLN F:88 , TYR G:89 , ARG G:90 , GLY G:136 , VAL G:138 , GLY G:166 , ASP G:167 , GLY G:168 , ALA G:169 , ASN G:196 , TYR G:198 , GLY G:199 , MET G:200 , HIS G:263 , MN G:1007 , HOH G:2062 , HOH G:2249 , HOH G:2294 , HOH G:2355 , HOH G:2447
BINDING SITE FOR RESIDUE TPP G 1008
09
AC9
SOFTWARE
ARG F:75 , ALA F:160 , ILE F:161 , ASP F:163 , HOH F:2116 , HOH F:2636
BINDING SITE FOR RESIDUE K F 1009
10
BC1
SOFTWARE
ASP E:167 , ASN E:196 , TYR E:198 , TPP E:1011 , HOH E:2223
BINDING SITE FOR RESIDUE MN E 1010
11
BC2
SOFTWARE
TYR E:89 , ARG E:90 , GLY E:136 , VAL E:138 , GLY E:166 , ASP E:167 , GLY E:168 , ALA E:169 , ASN E:196 , TYR E:198 , GLY E:199 , MET E:200 , HIS E:263 , MN E:1010 , HOH E:2130 , HOH E:2179 , HOH E:2223 , HOH E:2391 , HOH E:2500 , GLU H:28 , ILE H:57 , GLU H:59 , PHE H:85 , GLN H:88
BINDING SITE FOR RESIDUE TPP E 1011
12
BC3
SOFTWARE
ALA H:160 , ILE H:161 , ASP H:163 , HOH H:2386 , HOH H:2397
BINDING SITE FOR RESIDUE K H 1012
13
BC4
SOFTWARE
LYS A:153 , TRP A:185 , LEU A:187 , HOH A:2650 , HOH A:2946 , HOH A:3205 , ASP B:49 , ILE B:53
BINDING SITE FOR RESIDUE GOL A 1101
14
BC5
SOFTWARE
LYS C:153 , TRP C:185 , HOH C:2477 , HOH C:2998 , HOH C:3876 , ASP D:49 , ILE D:53 , HOH D:2905
BINDING SITE FOR RESIDUE GOL C 1102
15
BC6
SOFTWARE
LYS E:153 , LEU E:187 , HOH E:2656 , HOH E:3689 , HOH E:3731 , ASP F:49 , ILE F:53
BINDING SITE FOR RESIDUE GOL E 1103
16
BC7
SOFTWARE
LYS G:153 , LEU G:187 , HOH G:3129 , HOH G:3379 , ASP H:49 , ILE H:53 , HOH H:2848
BINDING SITE FOR RESIDUE GOL G 1104
[
close Site info
]
SAPs(SNPs)/Variants
(25, 100)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_004967 (L1V, chain B/D/F/H, )
02: VAR_004949 (R43C, chain A/C/E/G, )
03: VAR_004950 (H84D, chain A/C/E/G, )
04: VAR_030954 (Y102C, chain B/D/F/H, )
05: VAR_069381 (A107T, chain A/C/E/G, )
06: VAR_004951 (G133R, chain A/C/E/G, )
07: VAR_004952 (V138M, chain A/C/E/G, )
08: VAR_004953 (A170T, chain A/C/E/G, )
09: VAR_004954 (F176L, chain A/C/E/G, )
10: VAR_004955 (M181V, chain A/C/E/G, )
11: VAR_004956 (P188L, chain A/C/E/G, )
12: VAR_004957 (T202A, chain A/C/E/G, )
13: VAR_021053 (Y214N, chain A/C/E/G, )
14: VAR_004958 (D229A, chain A/C/E/G, )
15: VAR_004959 (R234G, chain A/C/E/G, )
16: VAR_004960 (R234Q, chain A/C/E/G, )
17: VAR_021054 (M253L, chain A/C/E/G, )
18: VAR_021055 (R259H, chain A/C/E/G, )
19: VAR_004961 (H263L, chain A/C/E/G, )
20: VAR_004962 (R273C, chain A/C/E/G, )
21: VAR_004963 (R273H, chain A/C/E/G, )
22: VAR_021056 (D286N, chain A/C/E/G, )
23: VAR_050436 (E304D, chain A/C/E/G, )
24: VAR_021058 (P314S, chain B/D/F/H, )
25: VAR_004966 (R349H, chain A/C/E/G, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_004967
L
31
V
ODPB_HUMAN
Polymorphism
---
B/D/F/H
L
1
V
02
UniProt
VAR_004949
R
72
C
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
R
43
C
03
UniProt
VAR_004950
H
113
D
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
H
84
D
04
UniProt
VAR_030954
Y
132
C
ODPB_HUMAN
Disease (PDHBD)
28935769
B/D/F/H
Y
102
C
05
UniProt
VAR_069381
A
136
T
ODPA_HUMAN
Disease
---
A/C/E/G
A
107
T
06
UniProt
VAR_004951
G
162
R
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
G
133
R
07
UniProt
VAR_004952
V
167
M
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
V
138
M
08
UniProt
VAR_004953
A
199
T
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
A
170
T
09
UniProt
VAR_004954
F
205
L
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
F
176
L
10
UniProt
VAR_004955
M
210
V
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
M
181
V
11
UniProt
VAR_004956
P
217
L
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
P
188
L
12
UniProt
VAR_004957
T
231
A
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
T
202
A
13
UniProt
VAR_021053
Y
243
N
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
Y
214
N
14
UniProt
VAR_004958
D
258
A
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
D
229
A
15
UniProt
VAR_004959
R
263
G
ODPA_HUMAN
Disease (PDHAD)
28936081
A/C/E/G
R
234
G
16
UniProt
VAR_004960
R
263
Q
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
R
234
Q
17
UniProt
VAR_021054
M
282
L
ODPA_HUMAN
Polymorphism
2229137
A/C/E/G
M
253
L
18
UniProt
VAR_021055
R
288
H
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
R
259
H
19
UniProt
VAR_004961
H
292
L
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
H
263
L
20
UniProt
VAR_004962
R
302
C
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
R
273
C
21
UniProt
VAR_004963
R
302
H
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
R
273
H
22
UniProt
VAR_021056
D
315
N
ODPA_HUMAN
Disease (PDHAD)
28935187
A/C/E/G
D
286
N
23
UniProt
VAR_050436
E
333
D
ODPA_HUMAN
Polymorphism
2228067
A/C/E/G
E
304
D
24
UniProt
VAR_021058
P
344
S
ODPB_HUMAN
Disease (PDHBD)
28933391
B/D/F/H
P
314
S
25
UniProt
VAR_004966
R
378
H
ODPA_HUMAN
Disease (PDHAD)
---
A/C/E/G
R
349
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(9, 36)
Info
All Exons
Exon 1.1j (B:1-2 | D:1-2 | F:1-2 | H:1-2)
Exon 1.1l (B:3-38 | D:3-38 | F:3-38 | H:3-38)
Exon 1.1n (B:39-59 | D:39-59 | F:39-59 | H:39...)
Exon 1.1q (B:60-71 | D:60-71 | F:60-71 | H:60...)
Exon 1.1t (B:72-167 | D:72-167 | F:72-167 | H...)
Exon 1.2b (B:167-204 | D:167-204 | F:167-204 ...)
Exon 1.2e (B:204-234 | D:204-234 | F:204-234 ...)
Exon 1.3a (B:235-282 | D:235-282 | F:235-282 ...)
Exon 1.3h (B:282-329 | D:282-329 | F:282-329 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1b/1.1j
02: Boundary 1.1j/1.1l
03: Boundary 1.1l/1.1n
04: Boundary 1.1n/1.1q
05: Boundary 1.1q/1.1t
06: Boundary 1.1t/1.2b
07: Boundary 1.2b/1.2e
08: Boundary 1.2e/1.3a
09: Boundary 1.3a/1.3h
10: Boundary 1.3h/-
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
1.1b
ENST00000302746
1b
ENSE00001931564
chr3:
58419579-58419495
85
ODPB_HUMAN
1-14
14
0
-
-
1.1j
ENST00000302746
1j
ENSE00001168306
chr3:
58419411-58419358
54
ODPB_HUMAN
15-32
18
4
B:1-2
D:1-2
F:1-2
H:1-2
2
2
2
2
1.1l
ENST00000302746
1l
ENSE00001168363
chr3:
58417711-58417604
108
ODPB_HUMAN
33-68
36
4
B:3-38
D:3-38
F:3-38
H:3-38
36
36
36
36
1.1n
ENST00000302746
1n
ENSE00001168356
chr3:
58417520-58417458
63
ODPB_HUMAN
69-89
21
4
B:39-59
D:39-59
F:39-59
H:39-59
21
21
21
21
1.1q
ENST00000302746
1q
ENSE00001168351
chr3:
58417355-58417320
36
ODPB_HUMAN
90-101
12
4
B:60-71
D:60-71
F:60-71
H:60-71
12
12
12
12
1.1t
ENST00000302746
1t
ENSE00001168343
chr3:
58416669-58416384
286
ODPB_HUMAN
102-197
96
4
B:72-167
D:72-167
F:72-167
H:72-167
96
96
96
96
1.2b
ENST00000302746
2b
ENSE00001168337
chr3:
58415965-58415855
111
ODPB_HUMAN
197-234
38
4
B:167-204
D:167-204
F:167-204
H:167-204
38
38
38
38
1.2e
ENST00000302746
2e
ENSE00001168326
chr3:
58415526-58415435
92
ODPB_HUMAN
234-264
31
4
B:204-234
D:204-234
F:204-234
H:204-234
31
31
31
31
1.3a
ENST00000302746
3a
ENSE00001168314
chr3:
58414341-58414200
142
ODPB_HUMAN
265-312
48
4
B:235-282
D:235-282
F:235-282
H:235-282
48
48
48
48
1.3h
ENST00000302746
3h
ENSE00001835890
chr3:
58413906-58413357
550
ODPB_HUMAN
312-359
48
4
B:282-329
D:282-329
F:282-329
H:282-329
48
48
48
48
[
close EXON info
]
SCOP Domains
(3, 12)
Info
All SCOP Domains
1a: SCOP_d3exeb1 (B:1-185)
1b: SCOP_d3exed1 (D:1-185)
1c: SCOP_d3exef1 (F:1-185)
1d: SCOP_d3exeh1 (H:1-185)
2a: SCOP_d3exea_ (A:)
2b: SCOP_d3exec_ (C:)
2c: SCOP_d3exee_ (E:)
2d: SCOP_d3exeg_ (G:)
3a: SCOP_d3exeb2 (B:186-329)
3b: SCOP_d3exed2 (D:186-329)
3c: SCOP_d3exef2 (F:186-329)
3d: SCOP_d3exeh2 (H:186-329)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
automated matches
(65)
Protein domain
:
automated matches
(65)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d3exeb1
B:1-185
1b
d3exed1
D:1-185
1c
d3exef1
F:1-185
1d
d3exeh1
H:1-185
Family
:
Branched-chain alpha-keto acid dehydrogenase PP module
(42)
Protein domain
:
E1-beta subunit of pyruvate dehydrogenase (PP module)
(7)
Human (Homo sapiens) [TaxId: 9606]
(7)
2a
d3exea_
A:
2b
d3exec_
C:
2c
d3exee_
E:
2d
d3exeg_
G:
Fold
:
TK C-terminal domain-like
(79)
Superfamily
:
TK C-terminal domain-like
(79)
Family
:
Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain
(39)
Protein domain
:
E1-beta subunit of pyruvate dehydrogenase, C-domain
(8)
Human (Homo sapiens) [TaxId: 9606]
(7)
3a
d3exeb2
B:186-329
3b
d3exed2
D:186-329
3c
d3exef2
F:186-329
3d
d3exeh2
H:186-329
[
close SCOP info
]
CATH Domains
(2, 9)
Info
all CATH domains
1a: CATH_3exeB02 (B:195-328)
1b: CATH_3exeD02 (D:195-328)
1c: CATH_3exeF02 (F:195-328)
1d: CATH_3exeH02 (H:195-328)
2a: CATH_3exeB01 (B:2-194)
2b: CATH_3exeD01 (D:2-194)
2c: CATH_3exeF01 (F:2-194)
2d: CATH_3exeH01 (H:2-194)
2e: CATH_3exeA00 (A:-1-361)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.920, no name defined]
(73)
Human (Homo sapiens)
(31)
1a
3exeB02
B:195-328
1b
3exeD02
D:195-328
1c
3exeF02
F:195-328
1d
3exeH02
H:195-328
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Human (Homo sapiens)
(31)
2a
3exeB01
B:2-194
2b
3exeD01
D:2-194
2c
3exeF01
F:2-194
2d
3exeH01
H:2-194
2e
3exeA00
A:-1-361
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Atom Selection
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All Atoms
Protein & NOT Variant
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Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
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
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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 (484 KB)
Header - Asym.Unit
Biol.Unit 1 (243 KB)
Header - Biol.Unit 1
Biol.Unit 2 (240 KB)
Header - Biol.Unit 2
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