PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1PK8
Asym. Unit
Info
Asym.Unit (415 KB)
Biol.Unit 1 (206 KB)
Biol.Unit 2 (201 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF RAT SYNAPSIN I C DOMAIN COMPLEXED TO CA.ATP
Authors
:
C. A. Brautigam, Y. Chelliah, J. Deisenhofer
Date
:
05 Jun 03 (Deposition) - 23 Mar 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
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
:
Atp Binding, Atp Grasp, Calcium (Ii) Ion, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. A. Brautigam, Y. Chelliah, J. Deisenhofer
Tetramerization And Atp Binding By A Protein Comprising The A, B, And C Domains Of Rat Synapsin I.
J. Biol. Chem. V. 279 11948 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 18)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
1c: ADENOSINE-5'-TRIPHOSPHATE (ATPc)
1d: ADENOSINE-5'-TRIPHOSPHATE (ATPd)
1e: ADENOSINE-5'-TRIPHOSPHATE (ATPe)
1f: ADENOSINE-5'-TRIPHOSPHATE (ATPf)
1g: ADENOSINE-5'-TRIPHOSPHATE (ATPg)
1h: ADENOSINE-5'-TRIPHOSPHATE (ATPh)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
2h: CALCIUM ION (CAh)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
8
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
CA
8
Ligand/Ion
CALCIUM ION
3
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
[
close Hetero Component info
]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:373 , GLU A:386 , ATP A:800
BINDING SITE FOR RESIDUE CA A 817
02
AC2
SOFTWARE
GLU B:373 , GLU B:386 , ATP B:801
BINDING SITE FOR RESIDUE CA B 817
03
AC3
SOFTWARE
GLU C:373 , GLU C:386 , ATP C:802
BINDING SITE FOR RESIDUE CA C 817
04
AC4
SOFTWARE
GLU D:373 , GLU D:386 , ATP D:803
BINDING SITE FOR RESIDUE CA D 817
05
AC5
SOFTWARE
GLU E:373 , GLU E:386 , ATP E:804
BINDING SITE FOR RESIDUE CA E 817
06
AC6
SOFTWARE
GLU F:373 , GLU F:386 , ATP F:805
BINDING SITE FOR RESIDUE CA F 817
07
AC7
SOFTWARE
GLU G:373 , GLU G:386 , ATP G:806
BINDING SITE FOR RESIDUE CA G 817
08
AC8
SOFTWARE
GLU H:373 , GLU H:386 , ATP H:807 , HOH H:842
BINDING SITE FOR RESIDUE CA H 817
09
AC9
SOFTWARE
LYS A:225 , VAL A:267 , LYS A:269 , HIS A:274 , SER A:275 , GLY A:276 , LYS A:279 , GLU A:305 , PRO A:306 , ILE A:308 , ASP A:313 , ARG A:328 , TRP A:335 , LYS A:336 , THR A:337 , ASN A:338 , GLU A:373 , LEU A:375 , GLU A:386 , VAL A:388 , CA A:817 , HOH A:831 , HOH A:859 , HOH A:903 , HOH A:916 , HOH A:935
BINDING SITE FOR RESIDUE ATP A 800
10
BC1
SOFTWARE
LYS B:225 , VAL B:267 , LYS B:269 , HIS B:274 , SER B:275 , GLY B:276 , LYS B:279 , GLU B:305 , PRO B:306 , PHE B:307 , ILE B:308 , ASP B:313 , ARG B:328 , TRP B:335 , LYS B:336 , THR B:337 , ASN B:338 , GLU B:373 , LEU B:375 , ILE B:385 , GLU B:386 , VAL B:388 , CA B:817 , HOH B:842 , HOH B:890 , HOH B:900
BINDING SITE FOR RESIDUE ATP B 801
11
BC2
SOFTWARE
LYS C:225 , ILE C:247 , VAL C:267 , LYS C:269 , HIS C:274 , SER C:275 , GLY C:276 , LYS C:279 , GLU C:305 , PRO C:306 , PHE C:307 , ILE C:308 , ARG C:328 , TRP C:335 , GLU C:373 , LEU C:375 , GLU C:386 , CA C:817
BINDING SITE FOR RESIDUE ATP C 802
12
BC3
SOFTWARE
LYS D:225 , ILE D:247 , VAL D:267 , LYS D:269 , HIS D:274 , SER D:275 , GLY D:276 , LYS D:279 , GLU D:305 , PRO D:306 , PHE D:307 , ILE D:308 , ASP D:313 , ARG D:328 , TRP D:335 , LYS D:336 , THR D:337 , ASN D:338 , GLU D:373 , LEU D:375 , ILE D:385 , GLU D:386 , CA D:817 , HOH D:869 , HOH D:874 , HOH D:892
BINDING SITE FOR RESIDUE ATP D 803
13
BC4
SOFTWARE
LYS E:225 , ILE E:247 , VAL E:267 , LYS E:269 , HIS E:274 , SER E:275 , GLY E:276 , LYS E:279 , GLU E:305 , PRO E:306 , PHE E:307 , ILE E:308 , ARG E:328 , TRP E:335 , LYS E:336 , THR E:337 , GLU E:373 , LEU E:375 , GLU E:386 , CA E:817 , HOH E:870
BINDING SITE FOR RESIDUE ATP E 804
14
BC5
SOFTWARE
LYS F:225 , ILE F:247 , VAL F:267 , LYS F:269 , ALA F:273 , HIS F:274 , SER F:275 , GLY F:276 , LYS F:279 , GLU F:305 , PRO F:306 , PHE F:307 , ILE F:308 , ASP F:313 , ARG F:328 , TRP F:335 , LYS F:336 , THR F:337 , GLU F:373 , LEU F:375 , GLU F:386 , VAL F:388 , CA F:817 , HOH F:848
BINDING SITE FOR RESIDUE ATP F 805
15
BC6
SOFTWARE
LYS G:225 , ILE G:247 , VAL G:267 , LYS G:269 , HIS G:274 , SER G:275 , GLY G:276 , LYS G:279 , GLU G:305 , PRO G:306 , PHE G:307 , ILE G:308 , ASP G:313 , ARG G:328 , TRP G:335 , LYS G:336 , THR G:337 , ASN G:338 , GLU G:373 , LEU G:375 , GLU G:386 , CA G:817 , HOH G:880 , HOH G:885
BINDING SITE FOR RESIDUE ATP G 806
16
BC7
SOFTWARE
LYS H:225 , ILE H:247 , VAL H:267 , LYS H:269 , HIS H:274 , SER H:275 , GLY H:276 , LYS H:279 , GLU H:305 , PRO H:306 , PHE H:307 , ILE H:308 , ARG H:328 , TRP H:335 , GLU H:373 , LEU H:375 , GLU H:386 , VAL H:388 , CA H:817 , HOH H:842 , HOH H:855
BINDING SITE FOR RESIDUE ATP H 807
17
BC8
SOFTWARE
HIS A:217 , PHE A:364 , HOH A:879 , HOH A:902 , HIS B:217 , PHE B:364
BINDING SITE FOR RESIDUE EDO A 818
18
BC9
SOFTWARE
ASP B:120 , THR B:124 , TRP B:126 , ARG B:186 , HOH B:896
BINDING SITE FOR RESIDUE EDO B 819
[
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, 8)
Info
All PROSITE Patterns/Profiles
1: SYNAPSIN_2 (A:271-281,B:271-281,C:271-281,D:27...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SYNAPSIN_2
PS00416
Synapsins signature 2.
SYN1_RAT
271-281
8
A:271-281
B:271-281
C:271-281
D:271-281
E:271-281
F:271-281
G:271-281
H:271-281
[
close PROSITE info
]
Exons
(8, 64)
Info
All Exons
Exon 1.5 (A:112-135 | B:113-135 | C:113-135 ...)
Exon 1.6 (A:136-156 | B:136-156 | C:136-156 ...)
Exon 1.7 (A:157-204 | B:157-204 (gaps) | C:1...)
Exon 1.8 (A:204-229 | B:204-229 | C:204-229 ...)
Exon 1.9 (A:229-263 | B:229-263 | C:229-263 ...)
Exon 1.10 (A:264-310 | B:264-310 | C:264-310 ...)
Exon 1.11 (A:311-340 | B:311-340 (gaps) | C:3...)
Exon 1.12b (A:340-417 | B:340-417 | C:344-417 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.4/1.5
2: Boundary 1.5/1.6
3: Boundary 1.6/1.7
4: Boundary 1.7/1.8
5: Boundary 1.8/1.9
6: Boundary 1.9/1.10
7: Boundary 1.10/1.11
8: Boundary 1.11/1.12b
9: Boundary 1.12b/1.13
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
ENSRNOT00000014250
1
ENSRNOE00000447489
X:12512210-12512217
8
SYN1_RAT
1-3
3
0
-
-
1.2
ENSRNOT00000014250
2
ENSRNOE00000097479
X:12512244-12512301
58
SYN1_RAT
3-22
20
0
-
-
1.3
ENSRNOT00000014250
3
ENSRNOE00000097614
X:12512392-12512483
92
SYN1_RAT
23-53
31
0
-
-
1.4
ENSRNOT00000014250
4
ENSRNOE00000097742
X:12513717-12513873
157
SYN1_RAT
53-105
53
0
-
-
1.5
ENSRNOT00000014250
5
ENSRNOE00000097879
X:12515168-12515257
90
SYN1_RAT
106-135
30
8
A:112-135
B:113-135
C:113-135
D:112-135
E:112-135
F:113-135
G:112-135
H:112-135
24
23
23
24
24
23
24
24
1.6
ENSRNOT00000014250
6
ENSRNOE00000098024
X:12551213-12551275
63
SYN1_RAT
136-156
21
8
A:136-156
B:136-156
C:136-156
D:136-156
E:136-156
F:136-156
G:136-156
H:136-156
21
21
21
21
21
21
21
21
1.7
ENSRNOT00000014250
7
ENSRNOE00000098221
X:12552134-12552276
143
SYN1_RAT
157-204
48
8
A:157-204
B:157-204 (gaps)
C:157-204 (gaps)
D:157-204 (gaps)
E:157-204 (gaps)
F:157-204 (gaps)
G:157-204 (gaps)
H:157-204 (gaps)
48
48
48
48
48
48
48
48
1.8
ENSRNOT00000014250
8
ENSRNOE00000098378
X:12552359-12552433
75
SYN1_RAT
204-229
26
8
A:204-229
B:204-229
C:204-229
D:204-229
E:204-229
F:204-229
G:204-229
H:204-229
26
26
26
26
26
26
26
26
1.9
ENSRNOT00000014250
9
ENSRNOE00000098563
X:12552528-12552630
103
SYN1_RAT
229-263
35
8
A:229-263
B:229-263
C:229-263
D:229-263
E:229-263
F:229-263
G:229-263
H:229-263
35
35
35
35
35
35
35
35
1.10
ENSRNOT00000014250
10
ENSRNOE00000098754
X:12553682-12553822
141
SYN1_RAT
264-310
47
8
A:264-310
B:264-310
C:264-310
D:264-310
E:264-310
F:264-310
G:264-310
H:264-310
47
47
47
47
47
47
47
47
1.11
ENSRNOT00000014250
11
ENSRNOE00000099054
X:12554138-12554225
88
SYN1_RAT
311-340
30
8
A:311-340
B:311-340 (gaps)
C:311-336 (gaps)
D:311-340
E:311-337 (gaps)
F:311-337 (gaps)
G:311-338 (gaps)
H:311-336 (gaps)
30
30
26
30
27
27
28
26
1.12b
ENSRNOT00000014250
12b
ENSRNOE00000289921
X:12554323-12554914
592
SYN1_RAT
340-537
198
8
A:340-417
B:340-417
C:344-417
D:340-417
E:344-416
F:344-417
G:342-417
H:344-417
78
78
74
78
73
74
76
74
1.13
ENSRNOT00000014250
13
ENSRNOE00000209968
X:12555820-12556160
341
SYN1_RAT
537-581
45
0
-
-
[
close EXON info
]
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d1pk8a2 (A:214-417)
1b: SCOP_d1pk8b2 (B:214-417)
1c: SCOP_d1pk8c2 (C:214-417)
1d: SCOP_d1pk8d2 (D:214-417)
1e: SCOP_d1pk8e2 (E:214-416)
1f: SCOP_d1pk8f2 (F:214-417)
1g: SCOP_d1pk8g2 (G:214-417)
1h: SCOP_d1pk8h2 (H:214-417)
2a: SCOP_d1pk8a1 (A:112-213)
2b: SCOP_d1pk8b1 (B:113-213)
2c: SCOP_d1pk8c1 (C:113-213)
2d: SCOP_d1pk8d1 (D:112-213)
2e: SCOP_d1pk8e1 (E:112-213)
2f: SCOP_d1pk8f1 (F:113-213)
2g: SCOP_d1pk8g1 (G:112-213)
2h: SCOP_d1pk8h1 (H:112-213)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ATP-grasp
(191)
Superfamily
:
Glutathione synthetase ATP-binding domain-like
(158)
Family
:
Synapsin C-terminal domain
(7)
Protein domain
:
Synapsin
(4)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(2)
1a
d1pk8a2
A:214-417
1b
d1pk8b2
B:214-417
1c
d1pk8c2
C:214-417
1d
d1pk8d2
D:214-417
1e
d1pk8e2
E:214-416
1f
d1pk8f2
F:214-417
1g
d1pk8g2
G:214-417
1h
d1pk8h2
H:214-417
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PreATP-grasp domain
(131)
Superfamily
:
PreATP-grasp domain
(131)
Family
:
Synapsin domain
(6)
Protein domain
:
Synapsin I
(4)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(2)
2a
d1pk8a1
A:112-213
2b
d1pk8b1
B:113-213
2c
d1pk8c1
C:113-213
2d
d1pk8d1
D:112-213
2e
d1pk8e1
E:112-213
2f
d1pk8f1
F:113-213
2g
d1pk8g1
G:112-213
2h
d1pk8h1
H:112-213
[
close SCOP info
]
CATH Domains
(3, 24)
Info
all CATH domains
1a: CATH_1pk8A03 (A:215-247,A:308-393)
1b: CATH_1pk8C03 (C:215-247,C:308-393)
1c: CATH_1pk8H03 (H:215-247,H:308-393)
1d: CATH_1pk8D03 (D:215-247,D:308-393)
1e: CATH_1pk8B03 (B:215-247,B:308-393)
1f: CATH_1pk8G03 (G:215-247,G:308-393)
1g: CATH_1pk8E03 (E:215-247,E:308-393)
1h: CATH_1pk8F03 (F:215-247,F:308-393)
2a: CATH_1pk8A01 (A:248-307)
2b: CATH_1pk8G01 (G:248-307)
2c: CATH_1pk8H01 (H:248-307)
2d: CATH_1pk8B01 (B:248-307)
2e: CATH_1pk8C01 (C:248-307)
2f: CATH_1pk8D01 (D:248-307)
2g: CATH_1pk8E01 (E:248-307)
2h: CATH_1pk8F01 (F:248-307)
3a: CATH_1pk8B02 (B:113-214,B:394-406)
3b: CATH_1pk8C02 (C:113-214,C:394-406)
3c: CATH_1pk8F02 (F:113-214,F:394-406)
3d: CATH_1pk8E02 (E:112-214,E:394-406)
3e: CATH_1pk8G02 (G:112-214,G:394-406)
3f: CATH_1pk8H02 (H:112-214,H:394-406)
3g: CATH_1pk8D02 (D:112-214,D:394-406)
3h: CATH_1pk8A02 (A:112-214,A:394-406)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
D-amino Acid Aminotransferase; Chain A, domain 1
(175)
Homologous Superfamily
:
ATP-grasp fold, B domain
(118)
Norway rat (Rattus norvegicus)
(4)
1a
1pk8A03
A:215-247,A:308-393
1b
1pk8C03
C:215-247,C:308-393
1c
1pk8H03
H:215-247,H:308-393
1d
1pk8D03
D:215-247,D:308-393
1e
1pk8B03
B:215-247,B:308-393
1f
1pk8G03
G:215-247,G:308-393
1g
1pk8E03
E:215-247,E:308-393
1h
1pk8F03
F:215-247,F:308-393
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
ATP-grasp fold, A domain
(109)
Norway rat (Rattus norvegicus)
(4)
2a
1pk8A01
A:248-307
2b
1pk8G01
G:248-307
2c
1pk8H01
H:248-307
2d
1pk8B01
B:248-307
2e
1pk8C01
C:248-307
2f
1pk8D01
D:248-307
2g
1pk8E01
E:248-307
2h
1pk8F01
F:248-307
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.20, no name defined]
(85)
Norway rat (Rattus norvegicus)
(4)
3a
1pk8B02
B:113-214,B:394-406
3b
1pk8C02
C:113-214,C:394-406
3c
1pk8F02
F:113-214,F:394-406
3d
1pk8E02
E:112-214,E:394-406
3e
1pk8G02
G:112-214,G:394-406
3f
1pk8H02
H:112-214,H:394-406
3g
1pk8D02
D:112-214,D:394-406
3h
1pk8A02
A:112-214,A:394-406
[
close CATH info
]
Pfam Domains
(2, 16)
Info
all PFAM domains
1a: PFAM_Synapsin_C_1pk8H01 (H:214-416)
1b: PFAM_Synapsin_C_1pk8H02 (H:214-416)
1c: PFAM_Synapsin_C_1pk8H03 (H:214-416)
1d: PFAM_Synapsin_C_1pk8H04 (H:214-416)
1e: PFAM_Synapsin_C_1pk8H05 (H:214-416)
1f: PFAM_Synapsin_C_1pk8H06 (H:214-416)
1g: PFAM_Synapsin_C_1pk8H07 (H:214-416)
1h: PFAM_Synapsin_C_1pk8H08 (H:214-416)
2a: PFAM_Synapsin_1pk8H09 (H:112-212)
2b: PFAM_Synapsin_1pk8H10 (H:112-212)
2c: PFAM_Synapsin_1pk8H11 (H:112-212)
2d: PFAM_Synapsin_1pk8H12 (H:112-212)
2e: PFAM_Synapsin_1pk8H13 (H:112-212)
2f: PFAM_Synapsin_1pk8H14 (H:112-212)
2g: PFAM_Synapsin_1pk8H15 (H:112-212)
2h: PFAM_Synapsin_1pk8H16 (H:112-212)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
ATP-grasp
(83)
Family
:
Synapsin_C
(3)
Rattus norvegicus (Rat)
(2)
1a
Synapsin_C-1pk8H01
H:214-416
1b
Synapsin_C-1pk8H02
H:214-416
1c
Synapsin_C-1pk8H03
H:214-416
1d
Synapsin_C-1pk8H04
H:214-416
1e
Synapsin_C-1pk8H05
H:214-416
1f
Synapsin_C-1pk8H06
H:214-416
1g
Synapsin_C-1pk8H07
H:214-416
1h
Synapsin_C-1pk8H08
H:214-416
Clan
:
no clan defined [family: Synapsin]
(3)
Family
:
Synapsin
(3)
Rattus norvegicus (Rat)
(2)
2a
Synapsin-1pk8H09
H:112-212
2b
Synapsin-1pk8H10
H:112-212
2c
Synapsin-1pk8H11
H:112-212
2d
Synapsin-1pk8H12
H:112-212
2e
Synapsin-1pk8H13
H:112-212
2f
Synapsin-1pk8H14
H:112-212
2g
Synapsin-1pk8H15
H:112-212
2h
Synapsin-1pk8H16
H:112-212
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
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") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (415 KB)
Header - Asym.Unit
Biol.Unit 1 (206 KB)
Header - Biol.Unit 1
Biol.Unit 2 (201 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1PK8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help