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1K0U
Asym. Unit
Info
Asym.Unit (531 KB)
Biol.Unit 1 (268 KB)
Biol.Unit 2 (264 KB)
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(1)
Title
:
INHIBITION OF S-ADENOSYLHOMOCYSTEINE HYDROLASE BY "ACYCLIC SUGAR" ADENOSINE ANALOGUE D-ERITADENINE
Authors
:
F. Takusagawa, Y. Huang, J. Komoto, Y. Takata, T. Gomi, H. Ogawa, M. Fujioka, D. Powell
Date
:
20 Sep 01 (Deposition) - 17 Oct 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
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
:
S-Adenosylhomocysteine, Hydrolase, D-Eritadenine, Inhibitor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Huang, J. Komoto, Y. Takata, D. R. Powell, T. Gomi, H. Ogawa, M. Fujioka, F. Takusagawa
Inhibition Of S-Adenosylhomocysteine Hydrolase By Acyclic Sugar Adenosine Analogue D-Eritadenine. Crystal Structure Of S-Adenosylhomocysteine Hydrolase Complexed With D-Eritadenine.
J. Biol. Chem. V. 277 7477 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 16)
Info
All Hetero Components
1a: D-ERITADENINE (DEAa)
1b: D-ERITADENINE (DEAb)
1c: D-ERITADENINE (DEAc)
1d: D-ERITADENINE (DEAd)
1e: D-ERITADENINE (DEAe)
1f: D-ERITADENINE (DEAf)
1g: D-ERITADENINE (DEAg)
1h: D-ERITADENINE (DEAh)
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)
2g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
2h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DEA
8
Ligand/Ion
D-ERITADENINE
2
NAD
8
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
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
THR A:156 , THR A:157 , THR A:158 , ASN A:190 , GLY A:219 , GLY A:221 , ASP A:222 , VAL A:223 , THR A:241 , GLU A:242 , ILE A:243 , ASP A:244 , ASN A:247 , THR A:274 , THR A:275 , ILE A:280 , ILE A:298 , GLY A:299 , HIS A:300 , LEU A:343 , ASN A:345 , HIS A:352 , DEA A:1433 , HOH A:9224 , GLN B:412 , LYS B:425 , TYR B:429
BINDING SITE FOR RESIDUE NAD A 1432
02
AC2
SOFTWARE
HIS A:54 , THR A:56 , GLU A:58 , THR A:59 , ASP A:130 , GLU A:155 , THR A:156 , LYS A:185 , ASP A:189 , LEU A:346 , GLY A:351 , HIS A:352 , PHE A:361 , NAD A:1432
BINDING SITE FOR RESIDUE DEA A 1433
03
AC3
SOFTWARE
GLN A:412 , LYS A:425 , TYR A:429 , THR B:156 , THR B:157 , THR B:158 , ASN B:190 , GLY B:219 , GLY B:221 , ASP B:222 , VAL B:223 , THR B:241 , GLU B:242 , ILE B:243 , ASP B:244 , ASN B:247 , THR B:274 , THR B:275 , ILE B:280 , ILE B:298 , GLY B:299 , HIS B:300 , LEU B:343 , ASN B:345 , HIS B:352 , DEA B:2433 , HOH B:9363
BINDING SITE FOR RESIDUE NAD B 2432
04
AC4
SOFTWARE
HIS B:54 , THR B:56 , GLU B:58 , THR B:59 , ASP B:130 , GLU B:155 , THR B:156 , LYS B:185 , ASP B:189 , LEU B:346 , GLY B:351 , HIS B:352 , PHE B:361 , NAD B:2432
BINDING SITE FOR RESIDUE DEA B 2433
05
AC5
SOFTWARE
THR C:156 , THR C:157 , THR C:158 , ASN C:190 , GLY C:219 , GLY C:221 , ASP C:222 , VAL C:223 , THR C:241 , GLU C:242 , ILE C:243 , ASP C:244 , ASN C:247 , THR C:274 , THR C:275 , ILE C:280 , ILE C:298 , GLY C:299 , HIS C:300 , LEU C:343 , ASN C:345 , HIS C:352 , DEA C:3433 , GLN D:412 , LYS D:425 , TYR D:429
BINDING SITE FOR RESIDUE NAD C 3432
06
AC6
SOFTWARE
HIS C:54 , THR C:56 , GLU C:58 , THR C:59 , ASP C:130 , GLU C:155 , THR C:156 , LYS C:185 , ASP C:189 , LEU C:346 , GLY C:351 , HIS C:352 , MET C:357 , PHE C:361 , NAD C:3432
BINDING SITE FOR RESIDUE DEA C 3433
07
AC7
SOFTWARE
GLN C:412 , LYS C:425 , TYR C:429 , THR D:156 , THR D:157 , THR D:158 , ASN D:190 , GLY D:219 , GLY D:221 , ASP D:222 , VAL D:223 , THR D:241 , GLU D:242 , ILE D:243 , ASP D:244 , ASN D:247 , THR D:274 , THR D:275 , ILE D:280 , ILE D:298 , GLY D:299 , HIS D:300 , LEU D:343 , ASN D:345 , HIS D:352 , DEA D:4433
BINDING SITE FOR RESIDUE NAD D 4432
08
AC8
SOFTWARE
HIS D:54 , THR D:56 , GLU D:58 , THR D:59 , ASP D:130 , GLU D:155 , THR D:156 , LYS D:185 , ASP D:189 , LEU D:346 , GLY D:351 , HIS D:352 , MET D:357 , PHE D:361 , NAD D:4432
BINDING SITE FOR RESIDUE DEA D 4433
09
AC9
SOFTWARE
THR E:156 , THR E:157 , THR E:158 , ASN E:190 , GLY E:219 , GLY E:221 , ASP E:222 , VAL E:223 , THR E:241 , GLU E:242 , ILE E:243 , ASP E:244 , ASN E:247 , THR E:274 , THR E:275 , ILE E:280 , ILE E:298 , GLY E:299 , HIS E:300 , LEU E:343 , ASN E:345 , HIS E:352 , DEA E:5433 , HOH E:9406 , GLN F:412 , LYS F:425 , TYR F:429
BINDING SITE FOR RESIDUE NAD E 5432
10
BC1
SOFTWARE
LEU E:53 , HIS E:54 , THR E:56 , GLU E:58 , THR E:59 , ASP E:130 , GLU E:155 , THR E:156 , ASN E:180 , LYS E:185 , ASP E:189 , ASN E:345 , LEU E:346 , GLY E:351 , HIS E:352 , MET E:357 , PHE E:361 , NAD E:5432
BINDING SITE FOR RESIDUE DEA E 5433
11
BC2
SOFTWARE
LEU E:408 , GLN E:412 , LYS E:425 , TYR E:429 , THR F:156 , THR F:157 , THR F:158 , ASN F:190 , GLY F:219 , GLY F:221 , ASP F:222 , VAL F:223 , THR F:241 , GLU F:242 , ILE F:243 , ASP F:244 , ASN F:247 , THR F:274 , THR F:275 , CYS F:277 , ILE F:280 , ILE F:298 , GLY F:299 , HIS F:300 , LEU F:343 , ASN F:345 , HIS F:352 , DEA F:6433
BINDING SITE FOR RESIDUE NAD F 6432
12
BC3
SOFTWARE
HIS F:54 , THR F:56 , GLU F:58 , THR F:59 , ASP F:130 , GLU F:155 , THR F:156 , ASN F:180 , LYS F:185 , ASP F:189 , LEU F:346 , GLY F:351 , HIS F:352 , MET F:357 , NAD F:6432 , HOH F:9309
BINDING SITE FOR RESIDUE DEA F 6433
13
BC4
SOFTWARE
THR G:156 , THR G:157 , THR G:158 , ASN G:190 , GLY G:219 , GLY G:221 , ASP G:222 , VAL G:223 , THR G:241 , GLU G:242 , ILE G:243 , ASP G:244 , ASN G:247 , THR G:274 , THR G:275 , ILE G:280 , ILE G:298 , GLY G:299 , HIS G:300 , LEU G:343 , ASN G:345 , HIS G:352 , DEA G:7433 , LYS H:425 , TYR H:429
BINDING SITE FOR RESIDUE NAD G 7432
14
BC5
SOFTWARE
HIS G:54 , THR G:56 , GLU G:58 , THR G:59 , ASP G:130 , GLU G:155 , THR G:156 , LYS G:185 , ASP G:189 , ASN G:345 , LEU G:346 , MET G:350 , GLY G:351 , HIS G:352 , MET G:357 , NAD G:7432
BINDING SITE FOR RESIDUE DEA G 7433
15
BC6
SOFTWARE
GLN G:412 , LYS G:425 , TYR G:429 , THR H:156 , THR H:157 , THR H:158 , ASN H:190 , GLY H:219 , GLY H:221 , ASP H:222 , VAL H:223 , THR H:241 , GLU H:242 , ILE H:243 , ASP H:244 , ASN H:247 , THR H:274 , THR H:275 , ILE H:280 , ILE H:298 , GLY H:299 , HIS H:300 , LEU H:343 , ASN H:345 , DEA H:8433 , HOH H:9255
BINDING SITE FOR RESIDUE NAD H 8432
16
BC7
SOFTWARE
LEU H:53 , THR H:56 , GLU H:58 , THR H:59 , ASP H:130 , GLU H:155 , THR H:156 , ASN H:180 , LYS H:185 , ASP H:189 , ASN H:190 , LEU H:346 , HIS H:352 , MET H:357 , NAD H:8432
BINDING SITE FOR RESIDUE DEA H 8433
[
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
(2, 16)
Info
All PROSITE Patterns/Profiles
1: ADOHCYASE_1 (A:77-91,B:77-91,C:77-91,D:77-91,E:...)
2: ADOHCYASE_2 (A:212-228,B:212-228,C:212-228,D:21...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADOHCYASE_1
PS00738
S-adenosyl-L-homocysteine hydrolase signature 1.
SAHH_RAT
78-92
8
A:77-91
B:77-91
C:77-91
D:77-91
E:77-91
F:77-91
G:77-91
H:77-91
2
ADOHCYASE_2
PS00739
S-adenosyl-L-homocysteine hydrolase signature 2.
SAHH_RAT
213-229
8
A:212-228
B:212-228
C:212-228
D:212-228
E:212-228
F:212-228
G:212-228
H:212-228
[
close PROSITE info
]
Exons
(10, 80)
Info
All Exons
Exon 1.1 (A:2-9 | B:2-9 | C:2-9 | D:2-9 | E:...)
Exon 1.2 (A:9-72 | B:9-72 | C:9-72 | D:9-72 ...)
Exon 1.3 (A:73-98 | B:73-98 | C:73-98 | D:73...)
Exon 1.4 (A:98-148 | B:98-148 | C:98-148 | D...)
Exon 1.5 (A:148-185 | B:148-185 | C:148-185 ...)
Exon 1.6 (A:186-255 | B:186-255 | C:186-255 ...)
Exon 1.7 (A:255-284 | B:255-284 | C:255-284 ...)
Exon 1.8 (A:284-323 | B:284-323 | C:284-323 ...)
Exon 1.9 (A:324-388 | B:324-388 | C:324-388 ...)
Exon 1.10 (A:389-431 | B:389-431 | C:389-431 ...)
View:
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Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10
11: Boundary 1.10/-
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
1.1
ENSRNOT00000024310
1
ENSRNOE00000170864
chr3:
145560052-145560005
48
SAHH_RAT
1-10
10
8
A:2-9
B:2-9
C:2-9
D:2-9
E:2-9
F:2-9
G:2-9
H:2-9
8
8
8
8
8
8
8
8
1.2
ENSRNOT00000024310
2
ENSRNOE00000170967
chr3:
145553987-145553797
191
SAHH_RAT
10-73
64
8
A:9-72
B:9-72
C:9-72
D:9-72
E:9-72
F:9-72
G:9-72
H:9-72
64
64
64
64
64
64
64
64
1.3
ENSRNOT00000024310
3
ENSRNOE00000294915
chr3:
145552338-145552263
76
SAHH_RAT
74-99
26
8
A:73-98
B:73-98
C:73-98
D:73-98
E:73-98
F:73-98
G:73-98
H:73-98
26
26
26
26
26
26
26
26
1.4
ENSRNOT00000024310
4
ENSRNOE00000171132
chr3:
145550643-145550494
150
SAHH_RAT
99-149
51
8
A:98-148
B:98-148
C:98-148
D:98-148
E:98-148
F:98-148
G:98-148
H:98-148
51
51
51
51
51
51
51
51
1.5
ENSRNOT00000024310
5
ENSRNOE00000323260
chr3:
145549883-145549771
113
SAHH_RAT
149-186
38
8
A:148-185
B:148-185
C:148-185
D:148-185
E:148-185
F:148-185
G:148-185
H:148-185
38
38
38
38
38
38
38
38
1.6
ENSRNOT00000024310
6
ENSRNOE00000171339
chr3:
145549377-145549170
208
SAHH_RAT
187-256
70
8
A:186-255
B:186-255
C:186-255
D:186-255
E:186-255
F:186-255
G:186-255
H:186-255
70
70
70
70
70
70
70
70
1.7
ENSRNOT00000024310
7
ENSRNOE00000171520
chr3:
145549090-145549003
88
SAHH_RAT
256-285
30
8
A:255-284
B:255-284
C:255-284
D:255-284
E:255-284
F:255-284
G:255-284
H:255-284
30
30
30
30
30
30
30
30
1.8
ENSRNOT00000024310
8
ENSRNOE00000171706
chr3:
145548909-145548792
118
SAHH_RAT
285-324
40
8
A:284-323
B:284-323
C:284-323
D:284-323
E:284-323
F:284-323
G:284-323
H:284-323
40
40
40
40
40
40
40
40
1.9
ENSRNOT00000024310
9
ENSRNOE00000171914
chr3:
145547384-145547190
195
SAHH_RAT
325-389
65
8
A:324-388
B:324-388
C:324-388
D:324-388
E:324-388
F:324-388
G:324-388
H:324-388
65
65
65
65
65
65
65
65
1.10
ENSRNOT00000024310
10
ENSRNOE00000172116
chr3:
145545669-145544834
836
SAHH_RAT
390-432
43
8
A:389-431
B:389-431
C:389-431
D:389-431
E:389-431
F:389-431
G:389-431
H:389-431
43
43
43
43
43
43
43
43
[
close EXON info
]
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d1k0ua2 (A:2-189,A:353-431)
1b: SCOP_d1k0ug2 (G:2-189,G:353-431)
1c: SCOP_d1k0uh2 (H:2-189,H:353-431)
1d: SCOP_d1k0ub2 (B:2-189,B:353-431)
1e: SCOP_d1k0uc2 (C:2-189,C:353-431)
1f: SCOP_d1k0ud2 (D:2-189,D:353-431)
1g: SCOP_d1k0ue2 (E:2-189,E:353-431)
1h: SCOP_d1k0uf2 (F:2-189,F:353-431)
2a: SCOP_d1k0ua1 (A:190-352)
2b: SCOP_d1k0ug1 (G:190-352)
2c: SCOP_d1k0uh1 (H:190-352)
2d: SCOP_d1k0ub1 (B:190-352)
2e: SCOP_d1k0uc1 (C:190-352)
2f: SCOP_d1k0ud1 (D:190-352)
2g: SCOP_d1k0ue1 (E:190-352)
2h: SCOP_d1k0uf1 (F:190-352)
View:
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Classes
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)
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)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Formate/glycerate dehydrogenase catalytic domain-like
(49)
Family
:
S-adenosylhomocystein hydrolase
(10)
Protein domain
:
S-adenosylhomocystein hydrolase
(10)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(7)
1a
d1k0ua2
A:2-189,A:353-431
1b
d1k0ug2
G:2-189,G:353-431
1c
d1k0uh2
H:2-189,H:353-431
1d
d1k0ub2
B:2-189,B:353-431
1e
d1k0uc2
C:2-189,C:353-431
1f
d1k0ud2
D:2-189,D:353-431
1g
d1k0ue2
E:2-189,E:353-431
1h
d1k0uf2
F:2-189,F:353-431
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
:
S-adenosylhomocystein hydrolase
(10)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(7)
2a
d1k0ua1
A:190-352
2b
d1k0ug1
G:190-352
2c
d1k0uh1
H:190-352
2d
d1k0ub1
B:190-352
2e
d1k0uc1
C:190-352
2f
d1k0ud1
D:190-352
2g
d1k0ue1
E:190-352
2h
d1k0uf1
F:190-352
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1k0uA01 (A:2-191,A:352-403)
1b: CATH_1k0uB01 (B:2-191,B:352-403)
1c: CATH_1k0uC01 (C:2-191,C:352-403)
1d: CATH_1k0uD01 (D:2-191,D:352-403)
1e: CATH_1k0uE01 (E:2-191,E:352-403)
1f: CATH_1k0uF01 (F:2-191,F:352-403)
1g: CATH_1k0uG01 (G:2-191,G:352-403)
1h: CATH_1k0uH01 (H:2-191,H:352-403)
2a: CATH_1k0uA02 (A:192-351)
2b: CATH_1k0uB02 (B:192-351)
2c: CATH_1k0uC02 (C:192-351)
2d: CATH_1k0uD02 (D:192-351)
2e: CATH_1k0uE02 (E:192-351)
2f: CATH_1k0uF02 (F:192-351)
2g: CATH_1k0uG02 (G:192-351)
2h: CATH_1k0uH02 (H:192-351)
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Architectures
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Topologies
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Homologous Superfamilies
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1480, no name defined]
(11)
Norway rat (Rattus norvegicus)
(7)
1a
1k0uA01
A:2-191,A:352-403
1b
1k0uB01
B:2-191,B:352-403
1c
1k0uC01
C:2-191,C:352-403
1d
1k0uD01
D:2-191,D:352-403
1e
1k0uE01
E:2-191,E:352-403
1f
1k0uF01
F:2-191,F:352-403
1g
1k0uG01
G:2-191,G:352-403
1h
1k0uH01
H:2-191,H:352-403
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Norway rat (Rattus norvegicus)
(18)
2a
1k0uA02
A:192-351
2b
1k0uB02
B:192-351
2c
1k0uC02
C:192-351
2d
1k0uD02
D:192-351
2e
1k0uE02
E:192-351
2f
1k0uF02
F:192-351
2g
1k0uG02
G:192-351
2h
1k0uH02
H:192-351
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Asymmetric Unit 1
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