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1YBA
Asym. Unit
Info
Asym.Unit (291 KB)
Biol.Unit 1 (279 KB)
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(1)
Title
:
THE ACTIVE FORM OF PHOSPHOGLYCERATE DEHYDROGENASE
Authors
:
J. R. Thompson, L. J. Banaszak
Date
:
20 Dec 04 (Deposition) - 26 Apr 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.24
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. R. Thompson, J. K. Bell, J. Bratt, G. A. Grant, L. J. Banaszak
Vmax Regulation Through Domain And Subunit Changes. The Active Form Of Phosphoglycerate Dehydrogenase
Biochemistry V. 44 5763 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 52)
Info
All Hetero Components
1a: 2-OXOGLUTARIC ACID (AKGa)
1b: 2-OXOGLUTARIC ACID (AKGb)
1c: 2-OXOGLUTARIC ACID (AKGc)
1d: 2-OXOGLUTARIC ACID (AKGd)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2ae: SELENOMETHIONINE (MSEae)
2af: SELENOMETHIONINE (MSEaf)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
3a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
3b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
3d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
4c: PHOSPHATE ION (PO4c)
4d: PHOSPHATE ION (PO4d)
4e: PHOSPHATE ION (PO4e)
5a: UNKNOWN LIGAND (UNLa)
5b: UNKNOWN LIGAND (UNLb)
5c: UNKNOWN LIGAND (UNLc)
5d: UNKNOWN LIGAND (UNLd)
5e: UNKNOWN LIGAND (UNLe)
5f: UNKNOWN LIGAND (UNLf)
5g: UNKNOWN LIGAND (UNLg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AKG
4
Ligand/Ion
2-OXOGLUTARIC ACID
2
MSE
32
Mod. Amino Acid
SELENOMETHIONINE
3
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4
PO4
5
Ligand/Ion
PHOSPHATE ION
5
UNL
7
Ligand/Ion
UNKNOWN LIGAND
[
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
LEU A:142 , ALA A:143 , ALA A:144 , HOH A:424 , HOH A:446 , HOH A:468 , HOH A:565 , ARG B:60
BINDING SITE FOR RESIDUE PO4 A 411
02
AC2
SOFTWARE
ARG C:60 , LEU D:142 , ALA D:143 , ALA D:144 , HOH D:488
BINDING SITE FOR RESIDUE PO4 D 411
03
AC3
SOFTWARE
LEU C:142 , ALA C:143 , ALA C:144 , HOH C:432 , HOH C:567 , ARG D:60
BINDING SITE FOR RESIDUE PO4 C 411
04
AC4
SOFTWARE
ARG A:60 , LEU B:142 , ALA B:143 , ALA B:144 , HOH B:541 , HOH B:557 , HOH B:663
BINDING SITE FOR RESIDUE PO4 B 411
05
AC5
SOFTWARE
GLY A:85 , THR A:86 , ASN A:87 , ARG A:240 , HOH A:587
BINDING SITE FOR RESIDUE PO4 A 412
06
AC6
SOFTWARE
ARG A:60 , SER A:61 , CYS A:83 , ILE A:84 , GLY A:85 , HOH A:447 , HOH A:488 , HOH A:674 , LYS B:141
BINDING SITE FOR RESIDUE AKG A 413
07
AC7
SOFTWARE
LYS A:141 , SER B:61 , CYS B:83 , ILE B:84 , ASN B:108 , HOH B:417 , HOH B:445 , HOH B:538 , HOH B:559 , HOH B:720
BINDING SITE FOR RESIDUE AKG B 412
08
AC8
SOFTWARE
LYS C:141 , ARG D:60 , SER D:61 , NAD D:415 , HOH D:416 , HOH D:630 , HOH D:637 , HOH D:679 , HOH D:721
BINDING SITE FOR RESIDUE AKG D 412
09
AC9
SOFTWARE
ARG C:60 , SER C:61 , CYS C:83 , ILE C:84 , ASN C:108 , HOH C:439 , HOH C:501 , HOH C:503 , HOH C:520 , HOH C:585 , HOH C:625 , HOH C:636 , LYS D:141
BINDING SITE FOR RESIDUE AKG C 412
10
BC1
SOFTWARE
TYR A:180 , GLN A:195 , HIS A:196 , LEU A:197 , SER A:198 , HOH A:598 , HOH A:645
BINDING SITE FOR RESIDUE UNL A 414
11
BC2
SOFTWARE
TYR B:180 , HIS B:196 , LEU B:197 , SER B:198
BINDING SITE FOR RESIDUE UNL B 413
12
BC3
SOFTWARE
TYR C:180 , GLN C:195 , HIS C:196 , LEU C:197 , SER C:198 , HOH C:654
BINDING SITE FOR RESIDUE UNL C 413
13
BC4
SOFTWARE
LYS B:39 , TYR D:180 , HIS D:196 , LEU D:197 , SER D:198 , HOH D:550 , HOH D:589 , HOH D:763
BINDING SITE FOR RESIDUE UNL D 413
14
BC5
SOFTWARE
HIS A:38 , LYS A:39 , GLY A:40 , ALA A:41 , LEU A:42 , HOH A:678
BINDING SITE FOR RESIDUE UNL A 415
15
BC6
SOFTWARE
HIS C:38 , LYS C:39 , GLY C:40
BINDING SITE FOR RESIDUE UNL C 414
16
BC7
SOFTWARE
HIS D:38 , LYS D:39 , GLY D:40 , ALA D:41
BINDING SITE FOR RESIDUE UNL D 414
17
BC8
SOFTWARE
ILE A:84 , PHE A:106 , VAL A:112 , GLY A:158 , TYR A:159 , GLY A:160 , HIS A:161 , ILE A:162 , ASP A:181 , ILE A:182 , LYS A:185 , HIS A:210 , VAL A:211 , PRO A:212 , SER A:216 , THR A:217 , MSE A:220 , ALA A:238 , SER A:239 , ARG A:240 , ASP A:264 , HIS A:292 , GLY A:294 , GLY A:295 , HOH A:433 , HOH A:445 , HOH A:450 , HOH A:500 , HOH A:521
BINDING SITE FOR RESIDUE NAD A 416
18
BC9
SOFTWARE
ILE B:84 , PHE B:106 , VAL B:112 , GLY B:158 , TYR B:159 , GLY B:160 , HIS B:161 , ILE B:162 , TYR B:180 , ASP B:181 , ILE B:182 , LYS B:185 , HIS B:210 , VAL B:211 , PRO B:212 , SER B:216 , THR B:217 , MSE B:220 , ALA B:238 , SER B:239 , ARG B:240 , ASP B:264 , HIS B:292 , GLY B:294 , GLY B:295 , HOH B:442 , HOH B:454 , HOH B:517 , HOH B:548 , HOH B:549 , HOH B:569 , HOH B:590 , HOH B:737
BINDING SITE FOR RESIDUE NAD B 414
19
CC1
SOFTWARE
ILE C:84 , PHE C:106 , VAL C:112 , GLY C:158 , TYR C:159 , GLY C:160 , HIS C:161 , ILE C:162 , ASP C:181 , ILE C:182 , LYS C:185 , HIS C:210 , VAL C:211 , PRO C:212 , SER C:216 , THR C:217 , ALA C:238 , SER C:239 , ARG C:240 , ASP C:264 , HIS C:292 , GLY C:294 , GLY C:295 , HOH C:421 , HOH C:450 , HOH C:469 , HOH C:471 , HOH C:662
BINDING SITE FOR RESIDUE NAD C 415
20
CC2
SOFTWARE
ASN D:108 , GLY D:158 , TYR D:159 , GLY D:160 , HIS D:161 , ILE D:162 , TYR D:180 , ASP D:181 , ILE D:182 , GLU D:183 , LYS D:185 , HIS D:210 , VAL D:211 , PRO D:212 , SER D:216 , THR D:217 , ALA D:238 , SER D:239 , ARG D:240 , ASP D:264 , HIS D:292 , GLY D:294 , GLY D:295 , AKG D:412 , HOH D:416 , HOH D:417 , HOH D:482 , HOH D:498 , HOH D:570 , HOH D:660 , HOH D:701 , HOH D:726 , HOH D:769
BINDING SITE FOR RESIDUE NAD D 415
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 16)
Info
All PROSITE Patterns/Profiles
1: D_2_HYDROXYACID_DH_1 (A:154-181,B:154-181,C:154-181,D:15...)
2: D_2_HYDROXYACID_DH_2 (A:200-222,B:200-222,C:200-222,D:20...)
3: D_2_HYDROXYACID_DH_3 (A:229-245,B:229-245,C:229-245,D:22...)
4: ACT (A:339-410,B:339-410,C:339-410,D:33...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
D_2_HYDROXYACID_DH_1
PS00065
D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.
SERA_ECO57
154-181
4
A:154-181
B:154-181
C:154-181
D:154-181
SERA_ECOL6
154-181
4
A:154-181
B:154-181
C:154-181
D:154-181
SERA_ECOLI
154-181
4
A:154-181
B:154-181
C:154-181
D:154-181
SERA_SHIFL
154-181
4
A:154-181
B:154-181
C:154-181
D:154-181
2
D_2_HYDROXYACID_DH_2
PS00670
D-isomer specific 2-hydroxyacid dehydrogenases signature 2.
SERA_ECO57
200-222
4
A:200-222
B:200-222
C:200-222
D:200-222
SERA_ECOL6
200-222
4
A:200-222
B:200-222
C:200-222
D:200-222
SERA_ECOLI
200-222
4
A:200-222
B:200-222
C:200-222
D:200-222
SERA_SHIFL
200-222
4
A:200-222
B:200-222
C:200-222
D:200-222
3
D_2_HYDROXYACID_DH_3
PS00671
D-isomer specific 2-hydroxyacid dehydrogenases signature 3.
SERA_ECO57
229-245
4
A:229-245
B:229-245
C:229-245
D:229-245
SERA_ECOL6
229-245
4
A:229-245
B:229-245
C:229-245
D:229-245
SERA_ECOLI
229-245
4
A:229-245
B:229-245
C:229-245
D:229-245
SERA_SHIFL
229-245
4
A:229-245
B:229-245
C:229-245
D:229-245
4
ACT
PS51671
ACT domain profile.
SERA_ECO57
339-410
4
A:339-410
B:339-410
C:339-410
D:339-410
SERA_ECOL6
339-410
4
A:339-410
B:339-410
C:339-410
D:339-410
SERA_ECOLI
339-410
4
A:339-410
B:339-410
C:339-410
D:339-410
SERA_SHIFL
339-410
4
A:339-410
B:339-410
C:339-410
D:339-410
[
close PROSITE info
]
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
(3, 12)
Info
All SCOP Domains
1a: SCOP_d1ybaa3 (A:327-410)
1b: SCOP_d1ybab3 (B:327-410)
1c: SCOP_d1ybac3 (C:327-410)
1d: SCOP_d1ybad3 (D:327-410)
2a: SCOP_d1ybaa2 (A:7-107,A:296-326)
2b: SCOP_d1ybab2 (B:7-107,B:296-326)
2c: SCOP_d1ybac2 (C:7-107,C:296-326)
2d: SCOP_d1ybad2 (D:7-107,D:296-326)
3a: SCOP_d1ybaa1 (A:108-295)
3b: SCOP_d1ybab1 (B:108-295)
3c: SCOP_d1ybac1 (C:108-295)
3d: SCOP_d1ybad1 (D:108-295)
View:
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)
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Folds
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Families
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
ACT-like
(63)
Family
:
Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
(9)
Protein domain
:
Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
(9)
Escherichia coli [TaxId: 562]
(7)
1a
d1ybaa3
A:327-410
1b
d1ybab3
B:327-410
1c
d1ybac3
C:327-410
1d
d1ybad3
D:327-410
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Formate/glycerate dehydrogenase catalytic domain-like
(49)
Family
:
Formate/glycerate dehydrogenases, substrate-binding domain
(21)
Protein domain
:
Phosphoglycerate dehydrogenase
(9)
Escherichia coli [TaxId: 562]
(7)
2a
d1ybaa2
A:7-107,A:296-326
2b
d1ybab2
B:7-107,B:296-326
2c
d1ybac2
C:7-107,C:296-326
2d
d1ybad2
D:7-107,D:296-326
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Formate/glycerate dehydrogenases, NAD-domain
(49)
Protein domain
:
Phosphoglycerate dehydrogenase
(9)
Escherichia coli [TaxId: 562]
(7)
3a
d1ybaa1
A:108-295
3b
d1ybab1
B:108-295
3c
d1ybac1
C:108-295
3d
d1ybad1
D:108-295
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1ybaA03 (A:328-409)
1b: CATH_1ybaB03 (B:328-409)
1c: CATH_1ybaC03 (C:328-409)
1d: CATH_1ybaD03 (D:328-409)
2a: CATH_1ybaA02 (A:109-297)
2b: CATH_1ybaD01 (D:5-108,D:298-326)
2c: CATH_1ybaB02 (B:109-297)
2d: CATH_1ybaC02 (C:109-297)
2e: CATH_1ybaD02 (D:109-297)
2f: CATH_1ybaA01 (A:5-108,A:298-326)
2g: CATH_1ybaB01 (B:5-108,B:298-326)
2h: CATH_1ybaC01 (C:5-108,C:298-326)
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Architectures
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Topologies
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.260, no name defined]
(34)
Escherichia coli. Organism_taxid: 562.
(7)
1a
1ybaA03
A:328-409
1b
1ybaB03
B:328-409
1c
1ybaC03
C:328-409
1d
1ybaD03
D:328-409
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Escherichia coli. Organism_taxid: 562.
(48)
2a
1ybaA02
A:109-297
2b
1ybaD01
D:5-108,D:298-326
2c
1ybaB02
B:109-297
2d
1ybaC02
C:109-297
2e
1ybaD02
D:109-297
2f
1ybaA01
A:5-108,A:298-326
2g
1ybaB01
B:5-108,B:298-326
2h
1ybaC01
C:5-108,C:298-326
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_ACT_1ybaD01 (D:339-402)
1b: PFAM_ACT_1ybaD02 (D:339-402)
1c: PFAM_ACT_1ybaD03 (D:339-402)
1d: PFAM_ACT_1ybaD04 (D:339-402)
2a: PFAM_2_Hacid_dh_1ybaD05 (D:13-326)
2b: PFAM_2_Hacid_dh_1ybaD06 (D:13-326)
2c: PFAM_2_Hacid_dh_1ybaD07 (D:13-326)
2d: PFAM_2_Hacid_dh_1ybaD08 (D:13-326)
3a: PFAM_2_Hacid_dh_C_1ybaD09 (D:117-294)
3b: PFAM_2_Hacid_dh_C_1ybaD10 (D:117-294)
3c: PFAM_2_Hacid_dh_C_1ybaD11 (D:117-294)
3d: PFAM_2_Hacid_dh_C_1ybaD12 (D:117-294)
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Organisms
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Clan
:
ACT
(34)
Family
:
ACT
(19)
Escherichia coli O157:H7
(1)
1a
ACT-1ybaD01
D:339-402
1b
ACT-1ybaD02
D:339-402
1c
ACT-1ybaD03
D:339-402
1d
ACT-1ybaD04
D:339-402
Clan
:
Form_Glyc_dh
(56)
Family
:
2-Hacid_dh
(21)
Escherichia coli O157:H7
(1)
2a
2-Hacid_dh-1ybaD05
D:13-326
2b
2-Hacid_dh-1ybaD06
D:13-326
2c
2-Hacid_dh-1ybaD07
D:13-326
2d
2-Hacid_dh-1ybaD08
D:13-326
Clan
:
NADP_Rossmann
(1239)
Family
:
2-Hacid_dh_C
(23)
Escherichia coli O157:H7
(1)
3a
2-Hacid_dh_C-1ybaD09
D:117-294
3b
2-Hacid_dh_C-1ybaD10
D:117-294
3c
2-Hacid_dh_C-1ybaD11
D:117-294
3d
2-Hacid_dh_C-1ybaD12
D:117-294
[
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]
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select :A, :C
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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set label size to 20 (allowed range: 1-58)
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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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In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
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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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