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1RX0
Asym. Unit
Info
Asym.Unit (285 KB)
Biol.Unit 1 (277 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ISOBUTYRYL-COA DEHYDROGENASE COMPLEXED WITH SUBSTRATE/LIGAND.
Authors
:
K. P. Battaile, T. V. Nguyen, J. Vockley, J. J. Kim
Date
:
18 Dec 03 (Deposition) - 20 Apr 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.77
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Flavoprotein, Dehydrogenase, Coenzyme A, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. P. Battaile, T. V. Nguyen, J. Vockley, J. J. Kim
Structures Of Isobutyryl-Coa Dehydrogenase And Enzyme-Product Complex: Comparison With Isovaleryl- And Short-Chain Acyl-Coa Dehydrogenases.
J. Biol. Chem. V. 279 16526 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 24)
Info
All Hetero Components
1a: METHACRYLYL-COENZYME A (2MCa)
1b: METHACRYLYL-COENZYME A (2MCb)
2a: ACETIC ACID (ACYa)
2b: ACETIC ACID (ACYb)
2c: ACETIC ACID (ACYc)
2d: ACETIC ACID (ACYd)
2e: ACETIC ACID (ACYe)
2f: ACETIC ACID (ACYf)
2g: ACETIC ACID (ACYg)
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)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
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
2MC
2
Ligand/Ion
METHACRYLYL-COENZYME A
2
ACY
7
Ligand/Ion
ACETIC ACID
3
EDO
11
Ligand/Ion
1,2-ETHANEDIOL
4
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:9289
BINDING SITE FOR RESIDUE EDO A 2001
02
AC2
SOFTWARE
PHE C:31
BINDING SITE FOR RESIDUE EDO C 2002
03
AC3
SOFTWARE
PHE B:169 , GLU B:211 , HOH B:9370 , TYR D:354 , LEU D:357 , HOH D:9255 , HOH D:9339
BINDING SITE FOR RESIDUE EDO B 2003
04
AC4
SOFTWARE
ILE B:193 , PHE B:244 , ALA B:247
BINDING SITE FOR RESIDUE EDO B 2004
05
AC5
SOFTWARE
ARG C:249 , GLU C:321 , ARG C:322 , HOH C:9149
BINDING SITE FOR RESIDUE EDO C 2005
06
AC6
SOFTWARE
PRO B:15
BINDING SITE FOR RESIDUE EDO B 2006
07
AC7
SOFTWARE
HIS B:276 , TYR B:360 , HOH B:9021 , HOH B:9391
BINDING SITE FOR RESIDUE EDO B 2007
08
AC8
SOFTWARE
PRO A:141 , TYR C:354 , TYR C:360
BINDING SITE FOR RESIDUE EDO C 2008
09
AC9
SOFTWARE
THR D:92
BINDING SITE FOR RESIDUE EDO D 2009
10
BC1
SOFTWARE
HOH B:9319 , PHE D:283 , GLY D:284 , HOH D:9254
BINDING SITE FOR RESIDUE EDO D 2010
11
BC2
SOFTWARE
LYS A:156 , ARG A:236 , HOH A:9009
BINDING SITE FOR RESIDUE EDO A 2011
12
BC3
SOFTWARE
TYR A:136 , LEU A:138 , THR A:139 , GLY A:144 , SER A:145 , PHE A:169 , ILE A:170 , SER A:171 , TRP A:216 , VAL A:371 , LEU A:375 , SER A:378 , GLU A:380 , HOH A:9118 , HOH A:9123 , HOH A:9209 , HOH A:9210 , GLN B:291 , ARG C:280 , PHE C:283 , ASN C:290 , LEU C:293 , GLN C:349 , MET C:350 , GLY C:353 , TYR C:354 , HOH C:9082 , HOH C:9083
BINDING SITE FOR RESIDUE FAD A 399
13
BC4
SOFTWARE
GLN A:291 , TYR B:136 , LEU B:138 , THR B:139 , GLY B:144 , SER B:145 , PHE B:169 , ILE B:170 , SER B:171 , TRP B:216 , VAL B:371 , LEU B:375 , SER B:378 , GLU B:380 , HOH B:9326 , HOH B:9381 , HOH B:9402 , ARG D:280 , PHE D:283 , ASN D:290 , LEU D:293 , GLN D:349 , MET D:350 , GLY D:352 , GLY D:353 , TYR D:354 , ACY D:9002 , HOH D:9273 , HOH D:9274
BINDING SITE FOR RESIDUE FAD B 399
14
BC5
SOFTWARE
ARG A:280 , PHE A:283 , ASN A:290 , LEU A:293 , GLN A:349 , MET A:350 , GLY A:352 , GLY A:353 , TYR A:354 , HOH A:9361 , TYR C:136 , LEU C:138 , THR C:139 , GLY C:144 , SER C:145 , PHE C:169 , ILE C:170 , SER C:171 , VAL C:371 , LEU C:375 , SER C:378 , GLU C:380 , 2MC C:400 , HOH C:9137 , HOH C:9270 , HOH C:9271 , HOH C:9329 , GLN D:291
BINDING SITE FOR RESIDUE FAD C 399
15
BC6
SOFTWARE
ARG B:280 , PHE B:283 , ASN B:290 , LEU B:293 , GLN B:349 , MET B:350 , GLY B:352 , GLY B:353 , TYR B:354 , ACY B:9001 , HOH B:9390 , GLN C:291 , TYR D:136 , LEU D:138 , THR D:139 , GLY D:144 , SER D:145 , PHE D:169 , ILE D:170 , SER D:171 , VAL D:371 , ILE D:374 , LEU D:375 , SER D:378 , GLU D:380 , 2MC D:400 , HOH D:9334 , HOH D:9346 , HOH D:9347
BINDING SITE FOR RESIDUE FAD D 399
16
BC7
SOFTWARE
ILE C:103 , TYR C:136 , THR C:139 , SER C:145 , ALA C:147 , PHE C:244 , VAL C:248 , LEU C:251 , ASN C:252 , ARG C:255 , VAL C:326 , LEU C:375 , GLU C:376 , GLY C:377 , LEU C:385 , ARG C:388 , FAD C:399 , HOH C:9202 , HOH C:9203 , HOH C:9269 , HOH C:9349 , HOH C:9350
BINDING SITE FOR RESIDUE 2MC C 400
17
BC8
SOFTWARE
ILE D:103 , TYR D:136 , THR D:139 , SER D:145 , ALA D:147 , PHE D:244 , VAL D:248 , LEU D:251 , ASN D:252 , ARG D:255 , VAL D:326 , LEU D:375 , GLU D:376 , GLY D:377 , LEU D:385 , ARG D:388 , FAD D:399 , HOH D:9128 , HOH D:9129 , HOH D:9130 , HOH D:9333
BINDING SITE FOR RESIDUE 2MC D 400
18
BC9
SOFTWARE
HOH B:9141 , FAD D:399
BINDING SITE FOR RESIDUE ACY B 9001
19
CC1
SOFTWARE
FAD B:399
BINDING SITE FOR RESIDUE ACY D 9002
20
CC2
SOFTWARE
LEU D:62 , PHE D:64
BINDING SITE FOR RESIDUE ACY D 9003
21
CC3
SOFTWARE
GLY C:142 , SER C:143 , SER C:149 , HOH C:9267
BINDING SITE FOR RESIDUE ACY C 9004
22
CC4
SOFTWARE
TYR A:68 , LEU A:78 , ARG A:80 , TRP A:109 , HOH A:9088 , HOH A:9089 , HOH A:9090
BINDING SITE FOR RESIDUE ACY A 9005
23
CC5
SOFTWARE
GLN B:61 , LEU B:62 , GLY B:63 , HOH B:9118
BINDING SITE FOR RESIDUE ACY B 9006
24
CC6
SOFTWARE
ARG D:312 , HOH D:9312
BINDING SITE FOR RESIDUE ACY D 9007
[
close Site info
]
SAPs(SNPs)/Variants
(9, 36)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_035071 (M106I, chain A/B/C/D, )
2: VAR_035072 (D112Y, chain A/B/C/D, )
3: VAR_035073 (G115R, chain A/B/C/D, )
4: VAR_035074 (M130T, chain A/B/C/D, )
5: VAR_035075 (V181I, chain A/B/C/D, )
6: VAR_035076 (R280Q, chain A/B/C/D, )
7: VAR_035077 (A298T, chain A/B/C/D, )
8: VAR_035078 (R312C, chain A/B/C/D, )
9: VAR_035079 (Q363R, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_035071
M
128
I
ACAD8_HUMAN
Disease (IBDD)
---
A/B/C/D
M
106
I
2
UniProt
VAR_035072
D
134
Y
ACAD8_HUMAN
Disease (IBDD)
---
A/B/C/D
D
112
Y
3
UniProt
VAR_035073
G
137
R
ACAD8_HUMAN
Disease (IBDD)
---
A/B/C/D
G
115
R
4
UniProt
VAR_035074
M
152
T
ACAD8_HUMAN
Disease (IBDD)
---
A/B/C/D
M
130
T
5
UniProt
VAR_035075
V
203
I
ACAD8_HUMAN
Disease (IBDD)
---
A/B/C/D
V
181
I
6
UniProt
VAR_035076
R
302
Q
ACAD8_HUMAN
Disease (IBDD)
---
A/B/C/D
R
280
Q
7
UniProt
VAR_035077
A
320
T
ACAD8_HUMAN
Disease (IBDD)
---
A/B/C/D
A
298
T
8
UniProt
VAR_035078
R
334
C
ACAD8_HUMAN
Disease (IBDD)
---
A/B/C/D
R
312
C
9
UniProt
VAR_035079
Q
385
R
ACAD8_HUMAN
Disease (IBDD)
---
A/B/C/D
Q
363
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ACYL_COA_DH_1 (A:137-149,B:137-149,C:137-149,D:13...)
;
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.
ACAD8_HUMAN
159-171
4
A:137-149
B:137-149
C:137-149
D:137-149
[
close PROSITE info
]
Exons
(11, 44)
Info
All Exons
Exon 1.1a (A:10-15 | B:10-15 | C:11-15 | D:10...)
Exon 1.2a (A:15-48 | B:15-48 | C:15-48 | D:15...)
Exon 1.3 (A:49-105 | B:49-105 | C:49-105 | D...)
Exon 1.4b (A:105-142 | B:105-142 | C:105-142 ...)
Exon 1.5b (A:142-167 | B:142-167 | C:142-167 ...)
Exon 1.5e (A:168-213 | B:168-213 | C:168-213 ...)
Exon 1.5l (A:214-259 | B:214-259 | C:214-259 ...)
Exon 1.6 (A:259-291 | B:259-291 | C:259-291 ...)
Exon 1.7c (A:292-342 | B:292-342 | C:292-342 ...)
Exon 1.8e (A:343-377 | B:343-377 | C:343-377 ...)
Exon 1.9b (A:377-393 | B:377-393 | C:377-393 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2a
03: Boundary 1.2a/1.3
04: Boundary 1.3/1.4b
05: Boundary 1.4b/1.5b
06: Boundary 1.5b/1.5e
07: Boundary 1.5e/1.5l
08: Boundary 1.5l/1.6
09: Boundary 1.6/1.7c
10: Boundary 1.7c/1.8e
11: Boundary 1.8e/1.9b
12: Boundary 1.9b/-
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
1.1a
ENST00000281182
1a
ENSE00000999980
chr11:
134123389-134123603
215
ACAD8_HUMAN
1-37
37
4
A:10-15
B:10-15
C:11-15
D:10-15
6
6
5
6
1.2a
ENST00000281182
2a
ENSE00001099807
chr11:
134126442-134126542
101
ACAD8_HUMAN
37-70
34
4
A:15-48
B:15-48
C:15-48
D:15-48
34
34
34
34
1.3
ENST00000281182
3
ENSE00001099805
chr11:
134126982-134127151
170
ACAD8_HUMAN
71-127
57
4
A:49-105
B:49-105
C:49-105
D:49-105
57
57
57
57
1.4b
ENST00000281182
4b
ENSE00001099804
chr11:
134128409-134128518
110
ACAD8_HUMAN
127-164
38
4
A:105-142
B:105-142
C:105-142
D:105-142
38
38
38
38
1.5b
ENST00000281182
5b
ENSE00001099809
chr11:
134128902-134128978
77
ACAD8_HUMAN
164-189
26
4
A:142-167
B:142-167
C:142-167
D:142-167
26
26
26
26
1.5e
ENST00000281182
5e
ENSE00001099810
chr11:
134129502-134129639
138
ACAD8_HUMAN
190-235
46
4
A:168-213
B:168-213
C:168-213
D:168-213
46
46
46
46
1.5l
ENST00000281182
5l
ENSE00001099814
chr11:
134130938-134131073
136
ACAD8_HUMAN
236-281
46
4
A:214-259
B:214-259
C:214-259
D:214-259
46
46
46
46
1.6
ENST00000281182
6
ENSE00001099803
chr11:
134131169-134131266
98
ACAD8_HUMAN
281-313
33
4
A:259-291
B:259-291
C:259-291
D:259-291
33
33
33
33
1.7c
ENST00000281182
7c
ENSE00001099812
chr11:
134131632-134131784
153
ACAD8_HUMAN
314-364
51
4
A:292-342
B:292-342
C:292-342
D:292-342
51
51
51
51
1.8e
ENST00000281182
8e
ENSE00001099808
chr11:
134132414-134132516
103
ACAD8_HUMAN
365-399
35
4
A:343-377
B:343-377
C:343-377
D:343-377
35
35
35
35
1.9b
ENST00000281182
9b
ENSE00002140309
chr11:
134134802-134135749
948
ACAD8_HUMAN
399-415
17
4
A:377-393
B:377-393
C:377-393
D:377-393
17
17
17
17
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1rx0a1 (A:241-393)
1b: SCOP_d1rx0b1 (B:241-393)
1c: SCOP_d1rx0c1 (C:241-393)
1d: SCOP_d1rx0d1 (D:241-393)
2a: SCOP_d1rx0a2 (A:10-240)
2b: SCOP_d1rx0b2 (B:10-240)
2c: SCOP_d1rx0c2 (C:11-240)
2d: SCOP_d1rx0d2 (D:10-240)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
Acyl-CoA dehydrogenase C-terminal domain-like
(61)
Family
:
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain
(29)
Protein domain
:
Isobutyryl-CoA dehydrogenase
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1rx0a1
A:241-393
1b
d1rx0b1
B:241-393
1c
d1rx0c1
C:241-393
1d
d1rx0d1
D:241-393
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
:
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains
(32)
Protein domain
:
Isobutyryl-CoA dehydrogenase
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d1rx0a2
A:10-240
2b
d1rx0b2
B:10-240
2c
d1rx0c2
C:11-240
2d
d1rx0d2
D:10-240
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1rx0C01 (C:11-133)
1b: CATH_1rx0A01 (A:10-133)
1c: CATH_1rx0B01 (B:10-133)
1d: CATH_1rx0D01 (D:10-133)
2a: CATH_1rx0A03 (A:239-393)
2b: CATH_1rx0B03 (B:239-393)
2c: CATH_1rx0C03 (C:239-393)
2d: CATH_1rx0D03 (D:239-393)
3a: CATH_1rx0A02 (A:134-238)
3b: CATH_1rx0B02 (B:134-238)
3c: CATH_1rx0C02 (C:134-238)
3d: CATH_1rx0D02 (D:134-238)
View:
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Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Butyryl-Coa Dehydrogenase, subunit A; domain 1
(28)
Homologous Superfamily
:
Butyryl-Coa Dehydrogenase, subunit A, domain 1
(28)
Human (Homo sapiens)
(10)
1a
1rx0C01
C:11-133
1b
1rx0A01
A:10-133
1c
1rx0B01
B:10-133
1d
1rx0D01
D:10-133
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)
2a
1rx0A03
A:239-393
2b
1rx0B03
B:239-393
2c
1rx0C03
C:239-393
2d
1rx0D03
D:239-393
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)
3a
1rx0A02
A:134-238
3b
1rx0B02
B:134-238
3c
1rx0C02
C:134-238
3d
1rx0D02
D:134-238
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_Acyl_CoA_dh_1_1rx0D01 (D:241-391)
1b: PFAM_Acyl_CoA_dh_1_1rx0D02 (D:241-391)
1c: PFAM_Acyl_CoA_dh_1_1rx0D03 (D:241-391)
1d: PFAM_Acyl_CoA_dh_1_1rx0D04 (D:241-391)
2a: PFAM_Acyl_CoA_dh_M_1rx0D05 (D:135-187)
2b: PFAM_Acyl_CoA_dh_M_1rx0D06 (D:135-187)
2c: PFAM_Acyl_CoA_dh_M_1rx0D07 (D:135-187)
2d: PFAM_Acyl_CoA_dh_M_1rx0D08 (D:135-187)
3a: PFAM_Acyl_CoA_dh_N_1rx0D09 (D:20-131)
3b: PFAM_Acyl_CoA_dh_N_1rx0D10 (D:20-131)
3c: PFAM_Acyl_CoA_dh_N_1rx0D11 (D:20-131)
3d: PFAM_Acyl_CoA_dh_N_1rx0D12 (D:20-131)
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Clan
:
Acyl-CoA_dh
(32)
Family
:
Acyl-CoA_dh_1
(24)
Homo sapiens (Human)
(10)
1a
Acyl-CoA_dh_1-1rx0D01
D:241-391
1b
Acyl-CoA_dh_1-1rx0D02
D:241-391
1c
Acyl-CoA_dh_1-1rx0D03
D:241-391
1d
Acyl-CoA_dh_1-1rx0D04
D:241-391
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-1rx0D05
D:135-187
2b
Acyl-CoA_dh_M-1rx0D06
D:135-187
2c
Acyl-CoA_dh_M-1rx0D07
D:135-187
2d
Acyl-CoA_dh_M-1rx0D08
D:135-187
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-1rx0D09
D:20-131
3b
Acyl-CoA_dh_N-1rx0D10
D:20-131
3c
Acyl-CoA_dh_N-1rx0D11
D:20-131
3d
Acyl-CoA_dh_N-1rx0D12
D:20-131
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