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1S20
Asym. Unit
Info
Asym.Unit (468 KB)
Biol.Unit 1 (120 KB)
Biol.Unit 2 (118 KB)
Biol.Unit 3 (119 KB)
Biol.Unit 4 (121 KB)
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(1)
Title
:
A NOVEL NAD BINDING PROTEIN REVEALED BY THE CRYSTAL STRUCTURE OF E. COLI 2,3-DIKETOGULONATE REDUCTASE (YIAK) NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER82
Authors
:
F. Forouhar, I. Lee, J. Benach, K. Kulkarni, R. Xiao, T. B. Acton, G. T. Montelione, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date
:
07 Jan 04 (Deposition) - 20 Jan 04 (Release) - 14 Apr 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Keywords
:
Alpha Beta Dimeric Protein, Oxidoreductase, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Forouhar, I. Lee, J. Benach, K. Kulkarni, R. Xiao, T. B. Acton, G. T. Montelione, L. Tong
A Novel Nad-Binding Protein Revealed By The Crystal Structure Of 2, 3-Diketo-L-Gulonate Reductase (Yiak).
J. Biol. Chem. V. 279 13148 2004
[
close entry info
]
Hetero Components
(3, 132)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1aa: SELENOMETHIONINE (MSEaa)
1ab: SELENOMETHIONINE (MSEab)
1ac: SELENOMETHIONINE (MSEac)
1ad: SELENOMETHIONINE (MSEad)
1ae: SELENOMETHIONINE (MSEae)
1af: SELENOMETHIONINE (MSEaf)
1ag: SELENOMETHIONINE (MSEag)
1ah: SELENOMETHIONINE (MSEah)
1ai: SELENOMETHIONINE (MSEai)
1aj: SELENOMETHIONINE (MSEaj)
1ak: SELENOMETHIONINE (MSEak)
1al: SELENOMETHIONINE (MSEal)
1am: SELENOMETHIONINE (MSEam)
1an: SELENOMETHIONINE (MSEan)
1ao: SELENOMETHIONINE (MSEao)
1ap: SELENOMETHIONINE (MSEap)
1aq: SELENOMETHIONINE (MSEaq)
1ar: SELENOMETHIONINE (MSEar)
1as: SELENOMETHIONINE (MSEas)
1at: SELENOMETHIONINE (MSEat)
1au: SELENOMETHIONINE (MSEau)
1av: SELENOMETHIONINE (MSEav)
1aw: SELENOMETHIONINE (MSEaw)
1ax: SELENOMETHIONINE (MSEax)
1ay: SELENOMETHIONINE (MSEay)
1az: SELENOMETHIONINE (MSEaz)
1b: SELENOMETHIONINE (MSEb)
1ba: SELENOMETHIONINE (MSEba)
1bb: SELENOMETHIONINE (MSEbb)
1bc: SELENOMETHIONINE (MSEbc)
1bd: SELENOMETHIONINE (MSEbd)
1be: SELENOMETHIONINE (MSEbe)
1bf: SELENOMETHIONINE (MSEbf)
1bg: SELENOMETHIONINE (MSEbg)
1bh: SELENOMETHIONINE (MSEbh)
1bi: SELENOMETHIONINE (MSEbi)
1bj: SELENOMETHIONINE (MSEbj)
1bk: SELENOMETHIONINE (MSEbk)
1bl: SELENOMETHIONINE (MSEbl)
1bm: SELENOMETHIONINE (MSEbm)
1bn: SELENOMETHIONINE (MSEbn)
1bo: SELENOMETHIONINE (MSEbo)
1bp: SELENOMETHIONINE (MSEbp)
1bq: SELENOMETHIONINE (MSEbq)
1br: SELENOMETHIONINE (MSEbr)
1bs: SELENOMETHIONINE (MSEbs)
1bt: SELENOMETHIONINE (MSEbt)
1bu: SELENOMETHIONINE (MSEbu)
1bv: SELENOMETHIONINE (MSEbv)
1bw: SELENOMETHIONINE (MSEbw)
1bx: SELENOMETHIONINE (MSEbx)
1by: SELENOMETHIONINE (MSEby)
1bz: SELENOMETHIONINE (MSEbz)
1c: SELENOMETHIONINE (MSEc)
1ca: SELENOMETHIONINE (MSEca)
1cb: SELENOMETHIONINE (MSEcb)
1cc: SELENOMETHIONINE (MSEcc)
1cd: SELENOMETHIONINE (MSEcd)
1ce: SELENOMETHIONINE (MSEce)
1cf: SELENOMETHIONINE (MSEcf)
1cg: SELENOMETHIONINE (MSEcg)
1ch: SELENOMETHIONINE (MSEch)
1ci: SELENOMETHIONINE (MSEci)
1cj: SELENOMETHIONINE (MSEcj)
1ck: SELENOMETHIONINE (MSEck)
1cl: SELENOMETHIONINE (MSEcl)
1cm: SELENOMETHIONINE (MSEcm)
1cn: SELENOMETHIONINE (MSEcn)
1co: SELENOMETHIONINE (MSEco)
1cp: SELENOMETHIONINE (MSEcp)
1cq: SELENOMETHIONINE (MSEcq)
1cr: SELENOMETHIONINE (MSEcr)
1cs: SELENOMETHIONINE (MSEcs)
1ct: SELENOMETHIONINE (MSEct)
1cu: SELENOMETHIONINE (MSEcu)
1cv: SELENOMETHIONINE (MSEcv)
1cw: SELENOMETHIONINE (MSEcw)
1cx: SELENOMETHIONINE (MSEcx)
1cy: SELENOMETHIONINE (MSEcy)
1cz: SELENOMETHIONINE (MSEcz)
1d: SELENOMETHIONINE (MSEd)
1da: SELENOMETHIONINE (MSEda)
1db: SELENOMETHIONINE (MSEdb)
1dc: SELENOMETHIONINE (MSEdc)
1dd: SELENOMETHIONINE (MSEdd)
1de: SELENOMETHIONINE (MSEde)
1df: SELENOMETHIONINE (MSEdf)
1dg: SELENOMETHIONINE (MSEdg)
1dh: SELENOMETHIONINE (MSEdh)
1di: SELENOMETHIONINE (MSEdi)
1dj: SELENOMETHIONINE (MSEdj)
1dk: SELENOMETHIONINE (MSEdk)
1dl: SELENOMETHIONINE (MSEdl)
1dm: SELENOMETHIONINE (MSEdm)
1dn: SELENOMETHIONINE (MSEdn)
1do: SELENOMETHIONINE (MSEdo)
1dp: SELENOMETHIONINE (MSEdp)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
1m: SELENOMETHIONINE (MSEm)
1n: SELENOMETHIONINE (MSEn)
1o: SELENOMETHIONINE (MSEo)
1p: SELENOMETHIONINE (MSEp)
1q: SELENOMETHIONINE (MSEq)
1r: SELENOMETHIONINE (MSEr)
1s: SELENOMETHIONINE (MSEs)
1t: SELENOMETHIONINE (MSEt)
1u: SELENOMETHIONINE (MSEu)
1v: SELENOMETHIONINE (MSEv)
1w: SELENOMETHIONINE (MSEw)
1x: SELENOMETHIONINE (MSEx)
1y: SELENOMETHIONINE (MSEy)
1z: SELENOMETHIONINE (MSEz)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
2d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
2e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
2f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
3a: L(+)-TARTARIC ACID (TLAa)
3b: L(+)-TARTARIC ACID (TLAb)
3c: L(+)-TARTARIC ACID (TLAc)
3d: L(+)-TARTARIC ACID (TLAd)
3e: L(+)-TARTARIC ACID (TLAe)
3f: L(+)-TARTARIC ACID (TLAf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
120
Mod. Amino Acid
SELENOMETHIONINE
2
NAD
6
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
TLA
6
Ligand/Ion
L(+)-TARTARIC 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
HIS A:44 , ARG A:48 , HIS A:116 , SER A:179 , TYR A:180 , GLY A:181 , NAD A:401 , HOH A:1555 , HOH A:1928
BINDING SITE FOR RESIDUE TLA A 501
02
AC2
SOFTWARE
HIS B:44 , ARG B:48 , HIS B:116 , SER B:179 , TYR B:180 , GLY B:181 , NAD B:402 , HOH B:2210
BINDING SITE FOR RESIDUE TLA B 502
03
AC3
SOFTWARE
HIS D:44 , ARG D:48 , HIS D:116 , SER D:179 , TYR D:180 , GLY D:181 , NAD D:404 , HOH D:2372 , HOH D:2373
BINDING SITE FOR RESIDUE TLA D 504
04
AC4
SOFTWARE
HIS F:44 , ARG F:48 , HIS F:116 , SER F:179 , TYR F:180 , GLY F:181 , NAD F:406 , HOH F:1752 , HOH F:1843 , HOH F:2398
BINDING SITE FOR RESIDUE TLA F 506
05
AC5
SOFTWARE
HIS G:44 , ARG G:48 , HIS G:116 , SER G:179 , TYR G:180 , GLY G:181 , NAD G:407 , HOH G:1169 , HOH G:1508 , HOH G:2319
BINDING SITE FOR RESIDUE TLA G 507
06
AC6
SOFTWARE
HIS H:44 , ARG H:48 , HIS H:116 , SER H:179 , TYR H:180 , GLY H:181 , NAD H:408 , HOH H:2119
BINDING SITE FOR RESIDUE TLA H 508
07
AC7
SOFTWARE
HIS A:44 , HIS A:116 , THR A:156 , PRO A:158 , MSE A:170 , VAL A:171 , ASP A:172 , MSE A:173 , SER A:174 , ARG A:301 , GLY A:304 , GLU A:306 , TLA A:501 , HOH A:1075 , HOH A:1282 , HOH A:1289 , HOH A:1637 , HOH A:2133 , HOH A:2134 , HOH A:2368 , TRP B:147 , TRP B:224 , LYS B:225
BINDING SITE FOR RESIDUE NAD A 401
08
AC8
SOFTWARE
TRP A:224 , LYS A:225 , HIS B:44 , HIS B:116 , TRP B:117 , THR B:156 , PRO B:158 , MSE B:170 , VAL B:171 , ASP B:172 , MSE B:173 , SER B:174 , ARG B:301 , GLY B:304 , GLU B:306 , TLA B:502 , HOH B:1044 , HOH B:1112 , HOH B:1293 , HOH B:1393 , HOH B:1530 , HOH B:1564 , HOH B:1947 , HOH B:2147 , HOH B:2369
BINDING SITE FOR RESIDUE NAD B 402
09
AC9
SOFTWARE
TRP C:224 , LYS C:225 , HIS D:44 , HIS D:116 , TRP D:117 , THR D:138 , THR D:156 , PRO D:158 , MSE D:170 , VAL D:171 , ASP D:172 , MSE D:173 , SER D:174 , GLY D:304 , GLU D:306 , TLA D:504 , HOH D:1033 , HOH D:1134 , HOH D:1440 , HOH D:2376 , HOH D:2380
BINDING SITE FOR RESIDUE NAD D 404
10
BC1
SOFTWARE
TRP E:224 , LYS E:225 , HOH E:1470 , HIS F:44 , HIS F:116 , TRP F:117 , THR F:156 , PRO F:158 , MSE F:170 , VAL F:171 , ASP F:172 , MSE F:173 , SER F:174 , ARG F:301 , PRO F:303 , GLY F:304 , GLU F:306 , TLA F:506 , HOH F:1090 , HOH F:1443 , HOH F:1686
BINDING SITE FOR RESIDUE NAD F 406
11
BC2
SOFTWARE
HIS G:44 , HIS G:116 , THR G:156 , PRO G:158 , MSE G:170 , VAL G:171 , ASP G:172 , MSE G:173 , SER G:174 , ARG G:301 , GLY G:304 , GLU G:306 , TLA G:507 , HOH G:1061 , HOH G:1109 , HOH G:1152 , HOH G:1246 , HOH G:1338 , HOH G:2100 , TRP H:147 , TRP H:224 , LYS H:225 , HOH H:1630
BINDING SITE FOR RESIDUE NAD G 407
12
BC3
SOFTWARE
TRP G:147 , TRP G:224 , LYS G:225 , HIS H:44 , HIS H:116 , TRP H:117 , THR H:138 , THR H:156 , PRO H:158 , MSE H:170 , VAL H:171 , ASP H:172 , MSE H:173 , SER H:174 , ARG H:301 , GLY H:304 , GLU H:306 , TLA H:508 , HOH H:1144 , HOH H:1748 , HOH H:1850 , HOH H:2148 , HOH H:2378
BINDING SITE FOR RESIDUE NAD H 408
[
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]
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1s20a_ (A:)
1b: SCOP_d1s20b_ (B:)
1c: SCOP_d1s20c_ (C:)
1d: SCOP_d1s20d_ (D:)
1e: SCOP_d1s20e_ (E:)
1f: SCOP_d1s20f_ (F:)
1g: SCOP_d1s20g_ (G:)
1h: SCOP_d1s20h_ (H:)
View:
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Classes
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)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
L-sulfolactate dehydrogenase-like
(12)
Superfamily
:
L-sulfolactate dehydrogenase-like
(12)
Family
:
L-sulfolactate dehydrogenase-like
(7)
Protein domain
:
2,3-diketogulonate oxidoreductase (YiaK)
(2)
Escherichia coli [TaxId: 562]
(2)
1a
d1s20a_
A:
1b
d1s20b_
B:
1c
d1s20c_
C:
1d
d1s20d_
D:
1e
d1s20e_
E:
1f
d1s20f_
F:
1g
d1s20g_
G:
1h
d1s20h_
H:
[
close SCOP info
]
CATH Domains
(3, 24)
Info
all CATH domains
1a: CATH_1s20A02 (A:65-164,A:222-270)
1b: CATH_1s20B02 (B:65-164,B:222-270)
1c: CATH_1s20C02 (C:65-164,C:222-270)
1d: CATH_1s20D02 (D:65-164,D:222-270)
1e: CATH_1s20E02 (E:65-164,E:222-270)
1f: CATH_1s20F02 (F:65-164,F:222-270)
1g: CATH_1s20G02 (G:65-164,G:222-270)
1h: CATH_1s20H02 (H:65-164,H:222-270)
2a: CATH_1s20A03 (A:181-220)
2b: CATH_1s20B03 (B:181-220)
2c: CATH_1s20C03 (C:181-220)
2d: CATH_1s20D03 (D:181-220)
2e: CATH_1s20E03 (E:181-220)
2f: CATH_1s20F03 (F:181-220)
2g: CATH_1s20G03 (G:181-220)
2h: CATH_1s20H03 (H:181-220)
3a: CATH_1s20G01 (G:2-64,G:317-335)
3b: CATH_1s20A01 (A:2-64,A:317-334)
3c: CATH_1s20B01 (B:2-64,B:317-334)
3d: CATH_1s20C01 (C:2-64,C:317-334)
3e: CATH_1s20D01 (D:2-64,D:317-334)
3f: CATH_1s20E01 (E:2-64,E:317-334)
3g: CATH_1s20H01 (H:2-64,H:317-334)
3h: CATH_1s20F01 (F:2-64,F:317-333)
View:
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Classes
(
)
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)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Ribosomal Protein S8; Chain: A, domain 1
(139)
Homologous Superfamily
:
Hypothetical oxidoreductase yiak; domain 2
(3)
Escherichia coli. Organism_taxid: 562.
(2)
1a
1s20A02
A:65-164,A:222-270
1b
1s20B02
B:65-164,B:222-270
1c
1s20C02
C:65-164,C:222-270
1d
1s20D02
D:65-164,D:222-270
1e
1s20E02
E:65-164,E:222-270
1f
1s20F02
F:65-164,F:222-270
1g
1s20G02
G:65-164,G:222-270
1h
1s20H02
H:65-164,H:222-270
Topology
:
Wheat Germ Agglutinin (Isolectin 2); domain 1
(140)
Homologous Superfamily
:
Hypothetical oxidoreductase yiak; domain 3
(2)
Escherichia coli. Organism_taxid: 562.
(2)
2a
1s20A03
A:181-220
2b
1s20B03
B:181-220
2c
1s20C03
C:181-220
2d
1s20D03
D:181-220
2e
1s20E03
E:181-220
2f
1s20F03
F:181-220
2g
1s20G03
G:181-220
2h
1s20H03
H:181-220
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
(3)
Homologous Superfamily
:
[code=1.10.1530.10, no name defined]
(3)
Escherichia coli. Organism_taxid: 562.
(2)
3a
1s20G01
G:2-64,G:317-335
3b
1s20A01
A:2-64,A:317-334
3c
1s20B01
B:2-64,B:317-334
3d
1s20C01
C:2-64,C:317-334
3e
1s20D01
D:2-64,D:317-334
3f
1s20E01
E:2-64,E:317-334
3g
1s20H01
H:2-64,H:317-334
3h
1s20F01
F:2-64,F:317-333
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Ldh_2_1s20H01 (H:1-332)
1b: PFAM_Ldh_2_1s20H02 (H:1-332)
1c: PFAM_Ldh_2_1s20H03 (H:1-332)
1d: PFAM_Ldh_2_1s20H04 (H:1-332)
1e: PFAM_Ldh_2_1s20H05 (H:1-332)
1f: PFAM_Ldh_2_1s20H06 (H:1-332)
1g: PFAM_Ldh_2_1s20H07 (H:1-332)
1h: PFAM_Ldh_2_1s20H08 (H:1-332)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Ldh_2]
(7)
Family
:
Ldh_2
(7)
Escherichia coli (strain K12)
(3)
1a
Ldh_2-1s20H01
H:1-332
1b
Ldh_2-1s20H02
H:1-332
1c
Ldh_2-1s20H03
H:1-332
1d
Ldh_2-1s20H04
H:1-332
1e
Ldh_2-1s20H05
H:1-332
1f
Ldh_2-1s20H06
H:1-332
1g
Ldh_2-1s20H07
H:1-332
1h
Ldh_2-1s20H08
H:1-332
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select :A, :C
select chains 'A' and '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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select non-helix/non-sheet protein parts
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set label size to 20 (allowed range: 1-58)
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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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