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1SOJ
Asym. Unit
Info
Asym.Unit (741 KB)
Biol.Unit 1 (129 KB)
Biol.Unit 2 (129 KB)
Biol.Unit 3 (129 KB)
Biol.Unit 4 (129 KB)
Biol.Unit 5 (129 KB)
Biol.Unit 6 (129 KB)
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(1)
Title
:
CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B IN COMPLEX WITH IBMX
Authors
:
G. Scapin, S. B. Patel, C. Chung, J. P. Varnerin, S. D. Edmondson, A. Mastracchio, E. R. Parmee, J. W. Becker, S. B. Singh, L. H. Van Der Ploeg, M. R. Tota
Date
:
15 Mar 04 (Deposition) - 11 May 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Biol. Unit 5: I,J (1x)
Biol. Unit 6: K,L (1x)
Keywords
:
Pde3B Phosphodiesterase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Scapin, S. B. Patel, C. Chung, J. P. Varnerin, S. D. Edmondson, A. Mastracchio, E. R. Parmee, S. B. Singh, J. W. Becker, L. H. Van Der Ploeg, M. R. Tota
Crystal Structure Of Human Phosphodiesterase 3B: Atomic Basis For Substrate And Inhibitor Specificity
Biochemistry V. 43 6091 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 36)
Info
All Hetero Components
1a: 3-ISOBUTYL-1-METHYLXANTHINE (IBMa)
1b: 3-ISOBUTYL-1-METHYLXANTHINE (IBMb)
1c: 3-ISOBUTYL-1-METHYLXANTHINE (IBMc)
1d: 3-ISOBUTYL-1-METHYLXANTHINE (IBMd)
1e: 3-ISOBUTYL-1-METHYLXANTHINE (IBMe)
1f: 3-ISOBUTYL-1-METHYLXANTHINE (IBMf)
1g: 3-ISOBUTYL-1-METHYLXANTHINE (IBMg)
1h: 3-ISOBUTYL-1-METHYLXANTHINE (IBMh)
1i: 3-ISOBUTYL-1-METHYLXANTHINE (IBMi)
1j: 3-ISOBUTYL-1-METHYLXANTHINE (IBMj)
1k: 3-ISOBUTYL-1-METHYLXANTHINE (IBMk)
1l: 3-ISOBUTYL-1-METHYLXANTHINE (IBMl)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
2i: MAGNESIUM ION (MGi)
2j: MAGNESIUM ION (MGj)
2k: MAGNESIUM ION (MGk)
2l: MAGNESIUM ION (MGl)
2m: MAGNESIUM ION (MGm)
2n: MAGNESIUM ION (MGn)
2o: MAGNESIUM ION (MGo)
2p: MAGNESIUM ION (MGp)
2q: MAGNESIUM ION (MGq)
2r: MAGNESIUM ION (MGr)
2s: MAGNESIUM ION (MGs)
2t: MAGNESIUM ION (MGt)
2u: MAGNESIUM ION (MGu)
2v: MAGNESIUM ION (MGv)
2w: MAGNESIUM ION (MGw)
2x: MAGNESIUM ION (MGx)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IBM
12
Ligand/Ion
3-ISOBUTYL-1-METHYLXANTHINE
2
MG
24
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(36, 36)
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)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:11 , HOH A:16 , HIS A:741 , HIS A:821 , ASP A:822 , ASP A:937
BINDING SITE FOR RESIDUE MG A 2123
02
AC2
SOFTWARE
HOH A:11 , HOH A:12 , HOH A:13 , HOH A:14 , HOH A:15 , ASP A:822
BINDING SITE FOR RESIDUE MG A 2124
03
AC3
SOFTWARE
HOH B:21 , HOH B:25 , HIS B:741 , HIS B:821 , ASP B:822 , ASP B:937
BINDING SITE FOR RESIDUE MG B 2125
04
AC4
SOFTWARE
HOH B:21 , HOH B:22 , HOH B:23 , HOH B:24 , HOH B:26 , ASP B:822
BINDING SITE FOR RESIDUE MG B 2126
05
AC5
SOFTWARE
HOH C:31 , HOH C:36 , HIS C:741 , HIS C:821 , ASP C:822 , ASP C:937
BINDING SITE FOR RESIDUE MG C 2127
06
AC6
SOFTWARE
HOH C:31 , HOH C:32 , HOH C:33 , HOH C:34 , HOH C:35 , ASP C:822
BINDING SITE FOR RESIDUE MG C 2128
07
AC7
SOFTWARE
HOH D:41 , HOH D:45 , HIS D:741 , HIS D:821 , ASP D:822 , ASP D:937
BINDING SITE FOR RESIDUE MG D 2129
08
AC8
SOFTWARE
HOH D:41 , HOH D:42 , HOH D:43 , HOH D:44 , HOH D:46 , ASP D:822
BINDING SITE FOR RESIDUE MG D 2130
09
AC9
SOFTWARE
HOH E:51 , HOH E:56 , HIS E:741 , HIS E:821 , ASP E:822 , ASP E:937
BINDING SITE FOR RESIDUE MG E 2131
10
BC1
SOFTWARE
HOH E:51 , HOH E:52 , HOH E:53 , HOH E:54 , HOH E:55 , ASP E:822
BINDING SITE FOR RESIDUE MG E 2132
11
BC2
SOFTWARE
HOH F:61 , HOH F:65 , HIS F:741 , HIS F:821 , ASP F:822 , ASP F:937
BINDING SITE FOR RESIDUE MG F 2133
12
BC3
SOFTWARE
HOH F:61 , HOH F:62 , HOH F:63 , HOH F:64 , HOH F:66 , ASP F:822
BINDING SITE FOR RESIDUE MG F 2134
13
BC4
SOFTWARE
HOH G:71 , HOH G:76 , HIS G:741 , HIS G:821 , ASP G:822 , ASP G:937
BINDING SITE FOR RESIDUE MG G 2135
14
BC5
SOFTWARE
HOH G:71 , HOH G:72 , HOH G:73 , HOH G:74 , HOH G:75 , ASP G:822
BINDING SITE FOR RESIDUE MG G 2136
15
BC6
SOFTWARE
HOH H:81 , HOH H:85 , HIS H:741 , HIS H:821 , ASP H:822 , ASP H:937
BINDING SITE FOR RESIDUE MG H 2137
16
BC7
SOFTWARE
HOH H:81 , HOH H:82 , HOH H:83 , HOH H:84 , HOH H:86 , ASP H:822
BINDING SITE FOR RESIDUE MG H 2138
17
BC8
SOFTWARE
HOH I:91 , HOH I:96 , HIS I:741 , HIS I:821 , ASP I:822 , ASP I:937
BINDING SITE FOR RESIDUE MG I 2139
18
BC9
SOFTWARE
HOH I:91 , HOH I:92 , HOH I:93 , HOH I:94 , HOH I:95 , ASP I:822
BINDING SITE FOR RESIDUE MG I 2140
19
CC1
SOFTWARE
HOH J:101 , HOH J:105 , HIS J:741 , HIS J:821 , ASP J:822 , ASP J:937
BINDING SITE FOR RESIDUE MG J 2141
20
CC2
SOFTWARE
HOH J:101 , HOH J:102 , HOH J:103 , HOH J:104 , HOH J:106 , ASP J:822
BINDING SITE FOR RESIDUE MG J 2142
21
CC3
SOFTWARE
HOH K:111 , HOH K:116 , HIS K:741 , HIS K:821 , ASP K:822 , ASP K:937
BINDING SITE FOR RESIDUE MG K 2143
22
CC4
SOFTWARE
HOH K:111 , HOH K:112 , HOH K:113 , HOH K:114 , HOH K:115 , ASP K:822
BINDING SITE FOR RESIDUE MG K 2144
23
CC5
SOFTWARE
HOH L:121 , HOH L:125 , HIS L:741 , HIS L:821 , ASP L:822 , ASP L:937 , MG L:2146
BINDING SITE FOR RESIDUE MG L 2145
24
CC6
SOFTWARE
HOH L:121 , HOH L:122 , HOH L:123 , HOH L:124 , HOH L:126 , ASP L:822 , MG L:2145
BINDING SITE FOR RESIDUE MG L 2146
25
CC7
SOFTWARE
TYR A:736 , ILE A:938 , ILE A:955 , GLN A:988 , PHE A:991 , HOH A:1125
BINDING SITE FOR RESIDUE IBM A 2111
26
CC8
SOFTWARE
TYR B:736 , ILE B:938 , ILE B:955 , GLN B:988 , PHE B:991 , HOH B:1130
BINDING SITE FOR RESIDUE IBM B 2112
27
CC9
SOFTWARE
TYR C:736 , ILE C:938 , PRO C:941 , GLN C:988 , PHE C:991 , HOH C:1225
BINDING SITE FOR RESIDUE IBM C 2113
28
DC1
SOFTWARE
TYR D:736 , PRO D:941 , ILE D:955 , GLN D:988 , PHE D:991 , HOH D:1230
BINDING SITE FOR RESIDUE IBM D 2114
29
DC2
SOFTWARE
TYR E:736 , ILE E:938 , PRO E:941 , GLN E:988 , PHE E:991 , HOH E:1325
BINDING SITE FOR RESIDUE IBM E 2115
30
DC3
SOFTWARE
TYR F:736 , ILE F:938 , ILE F:955 , GLN F:988 , PHE F:991 , HOH F:1330
BINDING SITE FOR RESIDUE IBM F 2116
31
DC4
SOFTWARE
ILE G:938 , ILE G:955 , GLN G:988 , PHE G:991 , HOH G:1425
BINDING SITE FOR RESIDUE IBM G 2117
32
DC5
SOFTWARE
TYR H:736 , ILE H:938 , ILE H:955 , GLN H:988 , PHE H:991 , HOH H:1430
BINDING SITE FOR RESIDUE IBM H 2118
33
DC6
SOFTWARE
TYR I:736 , ILE I:938 , PRO I:941 , ILE I:955 , GLN I:988 , PHE I:991 , HOH I:1525
BINDING SITE FOR RESIDUE IBM I 2119
34
DC7
SOFTWARE
TYR J:736 , ILE J:938 , PRO J:941 , ILE J:955 , GLN J:988 , PHE J:991 , HOH J:1530
BINDING SITE FOR RESIDUE IBM J 2120
35
DC8
SOFTWARE
TYR K:736 , ILE K:938 , GLN K:988 , PHE K:991 , HOH K:1625
BINDING SITE FOR RESIDUE IBM K 2121
36
DC9
SOFTWARE
TYR L:736 , ILE L:938 , ILE L:955 , GLN L:988 , PHE L:991 , HOH L:1630
BINDING SITE FOR RESIDUE IBM L 2122
[
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
(1, 12)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (A:821-832,B:821-832,C:821-832,D:82...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PDEASE_I
PS00126
3'5'-cyclic nucleotide phosphodiesterases signature.
PDE3B_HUMAN
821-832
12
A:821-832
B:821-832
C:821-832
D:821-832
E:821-832
F:821-832
G:821-832
H:821-832
I:821-832
J:821-832
K:821-832
L:821-832
[
close PROSITE info
]
Exons
(8, 96)
Info
All Exons
Exon 1.11 (A:659-698 | B:656-698 | C:659-698 ...)
Exon 1.12 (A:699-736 | B:699-736 | C:699-736 ...)
Exon 1.13 (A:736-766 | B:736-766 | C:736-766 ...)
Exon 1.14 (A:783-840 | B:776-840 | C:783-840 ...)
Exon 1.15 (A:841-908 | B:841-908 | C:841-908 ...)
Exon 1.16 (A:909-962 | B:909-962 | C:909-962 ...)
Exon 1.17 (A:963-1017 | B:963-1024 | C:963-10...)
Exon 1.18b (A:1053-1073 | B:1053-1073 | C:1053...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.10/1.11
2: Boundary 1.11/1.12
3: Boundary 1.12/1.13
4: Boundary 1.13/1.14
5: Boundary 1.14/1.15
6: Boundary 1.15/1.16
7: Boundary 1.16/1.17
8: Boundary 1.17/1.18b
9: Boundary 1.18b/-
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
ENST00000282096
1a
ENSE00001262747
chr11:
14665269-14666599
1331
PDE3B_HUMAN
1-326
326
0
-
-
1.4a
ENST00000282096
4a
ENSE00001004419
chr11:
14793483-14793533
51
PDE3B_HUMAN
327-343
17
0
-
-
1.5b
ENST00000282096
5b
ENSE00001004407
chr11:
14807983-14808231
249
PDE3B_HUMAN
344-426
83
0
-
-
1.6b
ENST00000282096
6b
ENSE00001004406
chr11:
14810652-14810788
137
PDE3B_HUMAN
427-472
46
0
-
-
1.7
ENST00000282096
7
ENSE00001004411
chr11:
14825490-14825596
107
PDE3B_HUMAN
472-508
37
0
-
-
1.8
ENST00000282096
8
ENSE00001004410
chr11:
14839729-14839939
211
PDE3B_HUMAN
508-578
71
0
-
-
1.9b
ENST00000282096
9b
ENSE00001004414
chr11:
14840682-14840755
74
PDE3B_HUMAN
578-603
26
0
-
-
1.10
ENST00000282096
10
ENSE00001004408
chr11:
14852244-14852392
149
PDE3B_HUMAN
603-652
50
0
-
-
1.11
ENST00000282096
11
ENSE00001004417
chr11:
14853186-14853323
138
PDE3B_HUMAN
653-698
46
12
A:659-698
B:656-698
C:659-698
D:656-698
E:659-698
F:656-698
G:659-698
H:656-698
I:659-698
J:656-698
K:659-698
L:656-698
40
43
40
43
40
43
40
43
40
43
40
43
1.12
ENST00000282096
12
ENSE00001004418
chr11:
14854268-14854379
112
PDE3B_HUMAN
699-736
38
12
A:699-736
B:699-736
C:699-736
D:699-736
E:699-736
F:699-736
G:699-736
H:699-736
I:699-736
J:699-736
K:699-736
L:699-736
38
38
38
38
38
38
38
38
38
38
38
38
1.13
ENST00000282096
13
ENSE00001004415
chr11:
14856528-14856641
114
PDE3B_HUMAN
736-774
39
12
A:736-766
B:736-766
C:736-766
D:736-766
E:736-766
F:736-766
G:736-766
H:736-766
I:736-766
J:736-766
K:736-766
L:736-766
31
31
31
31
31
31
31
31
31
31
31
31
1.14
ENST00000282096
14
ENSE00001004409
chr11:
14865373-14865572
200
PDE3B_HUMAN
774-840
67
12
A:783-840
B:776-840
C:783-840
D:776-840
E:783-840
F:776-840
G:783-840
H:776-840
I:783-840
J:776-840
K:783-840
L:776-840
58
65
58
65
58
65
58
65
58
65
58
65
1.15
ENST00000282096
15
ENSE00001004413
chr11:
14880589-14880792
204
PDE3B_HUMAN
841-908
68
12
A:841-908
B:841-908
C:841-908
D:841-908
E:841-908
F:841-908
G:841-908
H:841-908
I:841-908
J:841-908
K:841-908
L:841-908
68
68
68
68
68
68
68
68
68
68
68
68
1.16
ENST00000282096
16
ENSE00001004416
chr11:
14882751-14882912
162
PDE3B_HUMAN
909-962
54
12
A:909-962
B:909-962
C:909-962
D:909-962
E:909-962
F:909-962
G:909-962
H:909-962
I:909-962
J:909-962
K:909-962
L:909-962
54
54
54
54
54
54
54
54
54
54
54
54
1.17
ENST00000282096
17
ENSE00001004412
chr11:
14889052-14889304
253
PDE3B_HUMAN
963-1047
85
12
A:963-1017
B:963-1024
C:963-1017
D:963-1024
E:963-1017
F:963-1024
G:963-1017
H:963-1024
I:963-1017
J:963-1024
K:963-1017
L:963-1024
55
62
55
62
55
62
55
62
55
62
55
62
1.18b
ENST00000282096
18b
ENSE00001329007
chr11:
14891007-14892350
1344
PDE3B_HUMAN
1047-1112
66
12
A:1053-1073
B:1053-1073
C:1053-1073
D:1053-1073
E:1053-1073
F:1053-1073
G:1053-1073
H:1053-1073
I:1053-1073
J:1053-1073
K:1053-1073
L:1053-1073
21
21
21
21
21
21
21
21
21
21
21
21
[
close EXON info
]
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1soja_ (A:)
1b: SCOP_d1sojg_ (G:)
1c: SCOP_d1sojh_ (H:)
1d: SCOP_d1soji_ (I:)
1e: SCOP_d1sojj_ (J:)
1f: SCOP_d1sojk_ (K:)
1g: SCOP_d1sojl_ (L:)
1h: SCOP_d1sojb_ (B:)
1i: SCOP_d1sojc_ (C:)
1j: SCOP_d1sojd_ (D:)
1k: SCOP_d1soje_ (E:)
1l: SCOP_d1sojf_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
HD-domain/PDEase-like
(204)
Superfamily
:
HD-domain/PDEase-like
(204)
Family
:
PDEase
(118)
Protein domain
:
cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1soja_
A:
1b
d1sojg_
G:
1c
d1sojh_
H:
1d
d1soji_
I:
1e
d1sojj_
J:
1f
d1sojk_
K:
1g
d1sojl_
L:
1h
d1sojb_
B:
1i
d1sojc_
C:
1j
d1sojd_
D:
1k
d1soje_
E:
1l
d1sojf_
F:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_PDEase_I_1sojL01 (L:798-1007)
1b: PFAM_PDEase_I_1sojL02 (L:798-1007)
1c: PFAM_PDEase_I_1sojL03 (L:798-1007)
1d: PFAM_PDEase_I_1sojL04 (L:798-1007)
1e: PFAM_PDEase_I_1sojL05 (L:798-1007)
1f: PFAM_PDEase_I_1sojL06 (L:798-1007)
1g: PFAM_PDEase_I_1sojL07 (L:798-1007)
1h: PFAM_PDEase_I_1sojL08 (L:798-1007)
1i: PFAM_PDEase_I_1sojL09 (L:798-1007)
1j: PFAM_PDEase_I_1sojL10 (L:798-1007)
1k: PFAM_PDEase_I_1sojL11 (L:798-1007)
1l: PFAM_PDEase_I_1sojL12 (L:798-1007)
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HD_PDEase
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PDEase_I
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Homo sapiens (Human)
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1a
PDEase_I-1sojL01
L:798-1007
1b
PDEase_I-1sojL02
L:798-1007
1c
PDEase_I-1sojL03
L:798-1007
1d
PDEase_I-1sojL04
L:798-1007
1e
PDEase_I-1sojL05
L:798-1007
1f
PDEase_I-1sojL06
L:798-1007
1g
PDEase_I-1sojL07
L:798-1007
1h
PDEase_I-1sojL08
L:798-1007
1i
PDEase_I-1sojL09
L:798-1007
1j
PDEase_I-1sojL10
L:798-1007
1k
PDEase_I-1sojL11
L:798-1007
1l
PDEase_I-1sojL12
L:798-1007
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