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2JIF
Asym. Unit
Info
Asym.Unit (273 KB)
Biol.Unit 1 (263 KB)
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(1)
Title
:
STRUCTURE OF HUMAN SHORT-BRANCHED CHAIN ACYL-COA DEHYDROGENASE (ACADSB)
Authors
:
A. C. W. Pike, V. Hozjan, C. Smee, F. H. Niesen, K. L. Kavanagh, C. Umeano, A. P. Turnbull, F. Von Delft, J. Weigelt, A. Edwards, C. H. Arrowsmith M. Sundstrom, U. Oppermann
Date
:
28 Feb 07 (Deposition) - 03 Apr 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Mitochondrion, Oxidoreductase, Transit Peptide, Fatty Acid Metabolism, Fad, Flavoprotein, Disease Mutation, Lipid Metabolism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. C. W. Pike, V. Hozjan, C. Smee, F. H. Niesen, K. L. Kavanagh, C. Umeano A. P. Turnbull, F. Von Delft, J. Weigelt, A. Edwards, C. H. Arrowsmith M. Sundstrom, U. Oppermann
Crystal Structure Of Human Short-Branched Chain Acyl-Coa Dehydrogenase
To Be Published
[
close entry info
]
Hetero Components
(4, 25)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
1j: CHLORIDE ION (CLj)
2a: COENZYME A PERSULFIDE (COSa)
2b: COENZYME A PERSULFIDE (COSb)
2c: COENZYME A PERSULFIDE (COSc)
2d: COENZYME A PERSULFIDE (COSd)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
4a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
4b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
4c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
4d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
10
Ligand/Ion
CHLORIDE ION
2
COS
4
Ligand/Ion
COENZYME A PERSULFIDE
3
EDO
7
Ligand/Ion
1,2-ETHANEDIOL
4
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(25, 25)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:108 , ARG A:151
BINDING SITE FOR RESIDUE CL A1436
02
AC2
SOFTWARE
HIS A:213 , SER A:259
BINDING SITE FOR RESIDUE CL A1437
03
AC3
SOFTWARE
ASP B:108 , ARG B:151
BINDING SITE FOR RESIDUE CL B1436
04
AC4
SOFTWARE
HIS B:213 , SER B:259
BINDING SITE FOR RESIDUE CL B1437
05
AC5
SOFTWARE
TYR A:373 , TYR B:373
BINDING SITE FOR RESIDUE CL B1438
06
AC6
SOFTWARE
ASP C:108 , ARG C:151
BINDING SITE FOR RESIDUE CL C1436
07
AC7
SOFTWARE
SER C:259 , HOH C:2141
BINDING SITE FOR RESIDUE CL C1437
08
AC8
SOFTWARE
ASP D:108 , ARG D:151
BINDING SITE FOR RESIDUE CL D1439
09
AC9
SOFTWARE
HIS D:213 , SER D:259
BINDING SITE FOR RESIDUE CL D1440
10
BC1
SOFTWARE
TYR C:373 , TYR D:373
BINDING SITE FOR RESIDUE CL D1441
11
BC2
SOFTWARE
PHE A:174 , LEU A:176 , SER A:177 , GLY A:182 , SER A:183 , TRP A:207 , SER A:209 , THR A:260 , ILE A:409 , ILE A:412 , ALA A:416 , ASN A:418 , ILE A:419 , ASN A:422 , COS A:1434 , HOH A:2182 , HOH A:2195 , HOH A:2196 , HOH A:2197 , HOH A:2198 , HOH A:2199 , GLN B:330 , ARG C:319 , GLN C:321 , PHE C:322 , LEU C:326 , PHE C:329 , LEU C:332 , GLU C:387 , TRP C:388 , GLY C:391 , HOH C:2203
BINDING SITE FOR RESIDUE FAD A1433
12
BC3
SOFTWARE
SER A:183 , SER A:185 , TYR A:229 , LYS A:230 , TYR A:283 , ILE A:287 , LEU A:290 , ASN A:291 , ARG A:294 , TYR A:413 , GLU A:414 , GLY A:415 , ILE A:419 , FAD A:1433 , HOH A:2062 , HOH A:2185 , HOH A:2201 , HOH A:2202 , PHE C:322
BINDING SITE FOR RESIDUE COS A1434
13
BC4
SOFTWARE
VAL A:131 , PRO A:399 , TYR A:403 , HOH A:2203 , HOH A:2204
BINDING SITE FOR RESIDUE EDO A1435
14
BC5
SOFTWARE
GLN A:330 , PHE B:174 , LEU B:176 , SER B:177 , GLY B:182 , SER B:183 , TRP B:207 , SER B:209 , LYS B:252 , THR B:260 , ILE B:409 , ILE B:412 , ALA B:416 , ASN B:418 , ASN B:422 , COS B:1434 , HOH B:2181 , HOH B:2193 , HOH B:2194 , HOH B:2195 , HOH B:2196 , HOH B:2197 , HOH B:2198 , ARG D:319 , GLN D:321 , PHE D:322 , LEU D:326 , PHE D:329 , LEU D:332 , GLU D:387 , TRP D:388 , GLY D:391 , HOH D:2227
BINDING SITE FOR RESIDUE FAD B1433
15
BC6
SOFTWARE
SER B:183 , SER B:185 , PHE B:186 , TYR B:229 , TYR B:283 , ILE B:287 , LEU B:290 , ASN B:291 , ARG B:294 , TYR B:413 , GLU B:414 , GLY B:415 , ILE B:419 , FAD B:1433 , HOH B:2200 , HOH B:2201 , HOH B:2202 , PHE D:322
BINDING SITE FOR RESIDUE COS B1434
16
BC7
SOFTWARE
ARG B:256 , HOH B:2203 , HOH B:2204 , ARG D:256 , HOH D:2030 , HOH D:2231
BINDING SITE FOR RESIDUE EDO B1435
17
BC8
SOFTWARE
ARG A:319 , GLN A:321 , PHE A:322 , LEU A:326 , PHE A:329 , LEU A:332 , GLU A:387 , TRP A:388 , GLY A:391 , HOH A:2166 , PHE C:174 , LEU C:176 , SER C:177 , GLY C:182 , SER C:183 , TRP C:207 , SER C:209 , THR C:260 , ILE C:409 , ILE C:412 , ALA C:416 , ASN C:418 , ASN C:422 , COS C:1434 , HOH C:2113 , HOH C:2226 , HOH C:2227 , HOH C:2228 , HOH C:2229 , HOH C:2230 , GLN D:330
BINDING SITE FOR RESIDUE FAD C1433
18
BC9
SOFTWARE
SER C:183 , SER C:185 , PHE C:186 , TYR C:229 , LYS C:230 , TYR C:283 , ILE C:287 , ASN C:291 , ARG C:294 , TYR C:413 , GLU C:414 , GLY C:415 , ILE C:419 , FAD C:1433 , HOH C:2089 , HOH C:2220 , HOH C:2221 , HOH C:2231 , HOH C:2232 , HOH C:2233 , HOH C:2234
BINDING SITE FOR RESIDUE COS C1434
19
CC1
SOFTWARE
VAL C:131 , PRO C:399 , TYR C:403 , HOH C:2235 , HOH C:2236
BINDING SITE FOR RESIDUE EDO C1435
20
CC2
SOFTWARE
ARG B:319 , PHE B:322 , LEU B:326 , PHE B:329 , LEU B:332 , GLU B:387 , TRP B:388 , GLY B:391 , HOH B:2165 , GLN C:330 , PHE D:174 , LEU D:176 , SER D:177 , GLY D:182 , SER D:183 , TRP D:207 , ILE D:208 , SER D:209 , ILE D:409 , ILE D:412 , ALA D:416 , ASN D:418 , ILE D:419 , ASN D:422 , COS D:1434 , HOH D:2241 , HOH D:2243 , HOH D:2255 , HOH D:2256 , HOH D:2257 , HOH D:2258 , HOH D:2259
BINDING SITE FOR RESIDUE FAD D1433
21
CC3
SOFTWARE
SER D:183 , SER D:185 , PHE D:186 , TYR D:229 , TYR D:283 , ILE D:287 , LEU D:290 , ASN D:291 , ARG D:294 , ILE D:364 , TYR D:413 , GLU D:414 , GLY D:415 , ILE D:419 , FAD D:1433 , EDO D:1437 , HOH D:2097 , HOH D:2261 , HOH D:2262 , HOH D:2263 , HOH D:2264 , HOH D:2265 , HOH D:2267
BINDING SITE FOR RESIDUE COS D1434
22
CC4
SOFTWARE
LYS C:88 , GLN D:158 , TYR D:162 , LEU D:236 , ALA D:273 , ASN D:274
BINDING SITE FOR RESIDUE EDO D1435
23
CC5
SOFTWARE
LYS C:91 , VAL D:237 , ASP D:238 , THR D:241 , ASN D:274
BINDING SITE FOR RESIDUE EDO D1436
24
CC6
SOFTWARE
PHE B:322 , ILE D:419 , ASN D:422 , COS D:1434 , HOH D:2267
BINDING SITE FOR RESIDUE EDO D1437
25
CC7
SOFTWARE
VAL D:131 , PRO D:399 , TYR D:403 , HOH D:2269
BINDING SITE FOR RESIDUE EDO D1438
[
close Site info
]
SAPs(SNPs)/Variants
(4, 16)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_014749 (S209G, chain A/B/C/D, )
2: VAR_013010 (L255F, chain A/B/C/D, )
3: VAR_048178 (I316V, chain A/B/C/D, )
4: VAR_048179 (E376G, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_014749
S
209
G
ACDSB_HUMAN
Polymorphism
1799823
A/B/C/D
S
209
G
2
UniProt
VAR_013010
L
255
F
ACDSB_HUMAN
Disease (SBCADD)
---
A/B/C/D
L
255
F
3
UniProt
VAR_048178
I
316
V
ACDSB_HUMAN
Polymorphism
1131430
A/B/C/D
I
316
V
4
UniProt
VAR_048179
E
376
G
ACDSB_HUMAN
Polymorphism
12357783
A/B/C/D
E
376
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ACYL_COA_DH_1 (A:175-187,B:175-187,C:175-187,D:17...)
2: ACYL_COA_DH_2 (A:387-406,B:387-406,C:387-406,D:38...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ACYL_COA_DH_1
PS00072
Acyl-CoA dehydrogenases signature 1.
ACDSB_HUMAN
175-187
4
A:175-187
B:175-187
C:175-187
D:175-187
2
ACYL_COA_DH_2
PS00073
Acyl-CoA dehydrogenases signature 2.
ACDSB_HUMAN
387-406
4
A:387-406
B:387-406
C:387-406
D:387-406
[
close PROSITE info
]
Exons
(10, 40)
Info
All Exons
Exon 1.3a (A:52-68 | B:56-68 | C:56-68 | D:52...)
Exon 1.4 (A:68-101 | B:68-101 | C:68-101 | D...)
Exon 1.5b (A:102-170 | B:102-170 | C:102-170 ...)
Exon 1.6 (A:171-227 | B:171-227 | C:171-227 ...)
Exon 1.7b (A:228-269 | B:228-269 | C:228-269 ...)
Exon 1.8a (A:270-300 | B:270-300 | C:270-300 ...)
Exon 1.9b (A:301-330 | B:301-330 | C:301-330 ...)
Exon 1.10 (A:331-376 | B:331-376 | C:331-376 ...)
Exon 1.11 (A:377-410 | B:377-410 | C:377-410 ...)
Exon 1.12 (A:410-432 | B:410-432 | C:410-432 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1/1.3a
02: Boundary 1.3a/1.4
03: Boundary 1.4/1.5b
04: Boundary 1.5b/1.6
05: Boundary 1.6/1.7b
06: Boundary 1.7b/1.8a
07: Boundary 1.8a/1.9b
08: Boundary 1.9b/1.10
09: Boundary 1.10/1.11
10: Boundary 1.11/1.12
11: Boundary 1.12/-
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
ENST00000358776
1
ENSE00001448198
chr10:
124768532-124768587
56
ACDSB_HUMAN
1-14
14
0
-
-
1.3a
ENST00000358776
3a
ENSE00001205631
chr10:
124793872-124794031
160
ACDSB_HUMAN
15-68
54
4
A:52-68
B:56-68
C:56-68
D:52-68
17
13
13
17
1.4
ENST00000358776
4
ENSE00001205603
chr10:
124797263-124797363
101
ACDSB_HUMAN
68-101
34
4
A:68-101
B:68-101
C:68-101
D:68-101
34
34
34
34
1.5b
ENST00000358776
5b
ENSE00002174786
chr10:
124799982-124800188
207
ACDSB_HUMAN
102-170
69
4
A:102-170
B:102-170
C:102-170
D:102-170
69
69
69
69
1.6
ENST00000358776
6
ENSE00001613421
chr10:
124800725-124800895
171
ACDSB_HUMAN
171-227
57
4
A:171-227
B:171-227
C:171-227
D:171-227
57
57
57
57
1.7b
ENST00000358776
7b
ENSE00001747360
chr10:
124802562-124802687
126
ACDSB_HUMAN
228-269
42
4
A:228-269
B:228-269
C:228-269
D:228-269
42
42
42
42
1.8a
ENST00000358776
8a
ENSE00001708357
chr10:
124803909-124804001
93
ACDSB_HUMAN
270-300
31
4
A:270-300
B:270-300
C:270-300
D:270-300
31
31
31
31
1.9b
ENST00000358776
9b
ENSE00001724008
chr10:
124806725-124806814
90
ACDSB_HUMAN
301-330
30
4
A:301-330
B:301-330
C:301-330
D:301-330
30
30
30
30
1.10
ENST00000358776
10
ENSE00001661123
chr10:
124810565-124810702
138
ACDSB_HUMAN
331-376
46
4
A:331-376
B:331-376
C:331-376
D:331-376
46
46
46
46
1.11
ENST00000358776
11
ENSE00001766561
chr10:
124812577-124812676
100
ACDSB_HUMAN
377-410
34
4
A:377-410
B:377-410
C:377-410
D:377-410
34
34
34
34
1.12
ENST00000358776
12
ENSE00001399396
chr10:
124813211-124817827
4617
ACDSB_HUMAN
410-432
23
4
A:410-432
B:410-432
C:410-432
D:410-432
23
23
23
23
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2jifa2 (A:280-432)
1b: SCOP_d2jifc2 (C:280-432)
1c: SCOP_d2jifd2 (D:280-432)
1d: SCOP_d2jifb2 (B:280-432)
2a: SCOP_d2jifa1 (A:52-279)
2b: SCOP_d2jifb1 (B:56-279)
2c: SCOP_d2jifc1 (C:56-279)
2d: SCOP_d2jifd1 (D:52-279)
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Superfamilies
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)
Families
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
Acyl-CoA dehydrogenase C-terminal domain-like
(61)
Family
:
automated matches
(29)
Protein domain
:
automated matches
(29)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d2jifa2
A:280-432
1b
d2jifc2
C:280-432
1c
d2jifd2
D:280-432
1d
d2jifb2
B:280-432
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Superfamily
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Family
:
automated matches
(26)
Protein domain
:
automated matches
(26)
Human (Homo sapiens) [TaxId: 9606]
(2)
2a
d2jifa1
A:52-279
2b
d2jifb1
B:56-279
2c
d2jifc1
C:56-279
2d
d2jifd1
D:52-279
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2jifA03 (A:279-432)
1b: CATH_2jifB03 (B:279-432)
1c: CATH_2jifC03 (C:279-432)
1d: CATH_2jifD03 (D:279-432)
2a: CATH_2jifA02 (A:170-278)
2b: CATH_2jifB02 (B:170-278)
2c: CATH_2jifC02 (C:170-278)
2d: CATH_2jifD02 (D:170-278)
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Architectures
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Topologies
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Butyryl-CoA Dehydrogenase, subunit A; domain 3
(76)
Homologous Superfamily
:
Butyryl-CoA Dehydrogenase, subunit A, domain 3
(37)
Human (Homo sapiens)
(13)
1a
2jifA03
A:279-432
1b
2jifB03
B:279-432
1c
2jifC03
C:279-432
1d
2jifD03
D:279-432
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Butyryl-CoA Dehydrogenase, subunit A; domain 2
(35)
Homologous Superfamily
:
Butyryl-CoA Dehydrogenase, subunit A, domain 2
(35)
Human (Homo sapiens)
(14)
2a
2jifA02
A:170-278
2b
2jifB02
B:170-278
2c
2jifC02
C:170-278
2d
2jifD02
D:170-278
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_Acyl_CoA_dh_1_2jifD01 (D:280-428)
1b: PFAM_Acyl_CoA_dh_1_2jifD02 (D:280-428)
1c: PFAM_Acyl_CoA_dh_1_2jifD03 (D:280-428)
1d: PFAM_Acyl_CoA_dh_1_2jifD04 (D:280-428)
2a: PFAM_Acyl_CoA_dh_M_2jifD05 (D:173-224)
2b: PFAM_Acyl_CoA_dh_M_2jifD06 (D:173-224)
2c: PFAM_Acyl_CoA_dh_M_2jifD07 (D:173-224)
2d: PFAM_Acyl_CoA_dh_M_2jifD08 (D:173-224)
3a: PFAM_Acyl_CoA_dh_N_2jifD09 (D:58-170)
3b: PFAM_Acyl_CoA_dh_N_2jifD10 (D:58-170)
3c: PFAM_Acyl_CoA_dh_N_2jifD11 (D:58-170)
3d: PFAM_Acyl_CoA_dh_N_2jifD12 (D:58-170)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Acyl-CoA_dh
(32)
Family
:
Acyl-CoA_dh_1
(24)
Homo sapiens (Human)
(10)
1a
Acyl-CoA_dh_1-2jifD01
D:280-428
1b
Acyl-CoA_dh_1-2jifD02
D:280-428
1c
Acyl-CoA_dh_1-2jifD03
D:280-428
1d
Acyl-CoA_dh_1-2jifD04
D:280-428
Clan
:
no clan defined [family: Acyl-CoA_dh_M]
(24)
Family
:
Acyl-CoA_dh_M
(24)
Homo sapiens (Human)
(10)
2a
Acyl-CoA_dh_M-2jifD05
D:173-224
2b
Acyl-CoA_dh_M-2jifD06
D:173-224
2c
Acyl-CoA_dh_M-2jifD07
D:173-224
2d
Acyl-CoA_dh_M-2jifD08
D:173-224
Clan
:
no clan defined [family: Acyl-CoA_dh_N]
(23)
Family
:
Acyl-CoA_dh_N
(23)
Homo sapiens (Human)
(10)
3a
Acyl-CoA_dh_N-2jifD09
D:58-170
3b
Acyl-CoA_dh_N-2jifD10
D:58-170
3c
Acyl-CoA_dh_N-2jifD11
D:58-170
3d
Acyl-CoA_dh_N-2jifD12
D:58-170
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