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2OFW
Asym. Unit
Info
Asym.Unit (285 KB)
Biol.Unit 1 (73 KB)
Biol.Unit 2 (74 KB)
Biol.Unit 3 (73 KB)
Biol.Unit 4 (71 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE APSK DOMAIN OF HUMAN PAPSS1 COMPLEXED WITH 2 APS MOLECULES
Authors
:
N Sekulic, A Lavie
Date
:
04 Jan 07 (Deposition) - 10 Apr 07 (Release) - 22 Sep 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Keywords
:
Nucleotide Kinase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Sekulic, K. Dietrich, I. Paarmann, S. Ort, M. Konrad, A. Lavie
Elucidation Of The Active Conformation Of The Aps-Kinase Domain Of Human Paps Synthetase 1.
J. Mol. Biol. V. 367 488 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 22)
Info
All Hetero Components
1a: ADENOSINE-5'-PHOSPHOSULFATE (ADXa)
1b: ADENOSINE-5'-PHOSPHOSULFATE (ADXb)
1c: ADENOSINE-5'-PHOSPHOSULFATE (ADXc)
1d: ADENOSINE-5'-PHOSPHOSULFATE (ADXd)
1e: ADENOSINE-5'-PHOSPHOSULFATE (ADXe)
1f: ADENOSINE-5'-PHOSPHOSULFATE (ADXf)
1g: ADENOSINE-5'-PHOSPHOSULFATE (ADXg)
1h: ADENOSINE-5'-PHOSPHOSULFATE (ADXh)
1i: ADENOSINE-5'-PHOSPHOSULFATE (ADXi)
1j: ADENOSINE-5'-PHOSPHOSULFATE (ADXj)
1k: ADENOSINE-5'-PHOSPHOSULFATE (ADXk)
1l: ADENOSINE-5'-PHOSPHOSULFATE (ADXl)
1m: ADENOSINE-5'-PHOSPHOSULFATE (ADXm)
1n: ADENOSINE-5'-PHOSPHOSULFATE (ADXn)
1o: ADENOSINE-5'-PHOSPHOSULFATE (ADXo)
1p: ADENOSINE-5'-PHOSPHOSULFATE (ADXp)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADX
16
Ligand/Ion
ADENOSINE-5'-PHOSPHOSULFATE
2
MG
6
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(22, 22)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR B:66 , ADX B:1201 , HOH B:1202 , HOH B:1203 , HOH B:1204 , HOH B:1290
BINDING SITE FOR RESIDUE MG B 1002
02
AC2
SOFTWARE
THR C:66 , ADX C:1301 , HOH C:1302 , HOH C:1303 , HOH C:1304 , HOH D:1402
BINDING SITE FOR RESIDUE MG C 1003
03
AC3
SOFTWARE
THR D:66 , ADX D:1401 , HOH D:1403 , HOH D:1404 , HOH D:1405 , HOH D:1406
BINDING SITE FOR RESIDUE MG D 1004
04
AC4
SOFTWARE
THR E:66 , ADX E:1501 , HOH E:1502 , HOH E:1503 , HOH E:1504
BINDING SITE FOR RESIDUE MG E 1005
05
AC5
SOFTWARE
THR F:66 , ADX F:1601 , HOH F:1602 , HOH F:1603 , HOH F:1604 , HOH F:1605
BINDING SITE FOR RESIDUE MG F 1006
06
AC6
SOFTWARE
THR H:66 , ADX H:1801 , HOH H:1802 , HOH H:1803 , HOH H:1805 , HOH H:1903
BINDING SITE FOR RESIDUE MG H 1008
07
AC7
SOFTWARE
SER A:61 , ASP A:89 , ARG A:92 , PHE A:101 , ARG A:106 , ASN A:109 , PHE A:131 , ILE A:132 , SER A:133 , PRO A:134 , LEU A:173 , GLY A:184 , PHE A:185 , THR A:186 , HOH A:1115 , HOH A:1150
BINDING SITE FOR RESIDUE ADX A 1100
08
AC8
SOFTWARE
ASN A:27 , VAL A:28 , ASP B:89 , ARG B:92 , PHE B:101 , ARG B:106 , ASN B:109 , PHE B:131 , ILE B:132 , SER B:133 , PRO B:134 , LYS B:171 , LEU B:173 , LYS B:183 , GLY B:184 , PHE B:185 , THR B:186 , HOH B:1205 , HOH B:1229 , HOH B:1243 , HOH B:1261 , HOH B:1271 , HOH B:1276 , HOH B:1290
BINDING SITE FOR RESIDUE ADX B 1200
09
AC9
SOFTWARE
ASP C:89 , ARG C:92 , PHE C:101 , ARG C:106 , ASN C:109 , PHE C:131 , ILE C:132 , SER C:133 , PRO C:134 , LEU C:173 , LYS C:183 , GLY C:184 , PHE C:185 , THR C:186 , HOH C:1302 , HOH C:1333 , HOH C:1374 , HOH C:1385 , HOH C:1389 , THR D:26 , ASN D:27
BINDING SITE FOR RESIDUE ADX C 1300
10
BC1
SOFTWARE
THR C:26 , ASN C:27 , GLY D:88 , ASP D:89 , ARG D:92 , PHE D:101 , ARG D:106 , ASN D:109 , PHE D:131 , ILE D:132 , SER D:133 , PRO D:134 , LEU D:173 , LYS D:183 , GLY D:184 , PHE D:185 , THR D:186 , HOH D:1430 , HOH D:1442 , HOH D:1474 , HOH D:1481 , HOH D:1502
BINDING SITE FOR RESIDUE ADX D 1400
11
BC2
SOFTWARE
ASP E:89 , ARG E:92 , PHE E:101 , ARG E:106 , ASN E:109 , PHE E:131 , ILE E:132 , SER E:133 , PRO E:134 , LEU E:173 , LYS E:183 , GLY E:184 , PHE E:185 , THR E:186 , HOH E:1504 , HOH E:1521 , HOH E:1534 , THR F:26 , ASN F:27
BINDING SITE FOR RESIDUE ADX E 1500
12
BC3
SOFTWARE
THR E:26 , ASN E:27 , VAL E:28 , HOH E:1526 , ASP F:89 , ARG F:92 , PHE F:101 , ARG F:106 , ASN F:109 , PHE F:131 , ILE F:132 , SER F:133 , PRO F:134 , LEU F:173 , GLY F:184 , PHE F:185 , THR F:186 , HOH F:1605 , HOH F:1607 , HOH F:1669 , HOH F:1692
BINDING SITE FOR RESIDUE ADX F 1600
13
BC4
SOFTWARE
ARG G:92 , PHE G:101 , ARG G:106 , ASN G:109 , PHE G:131 , ILE G:132 , SER G:133 , PRO G:134 , LEU G:173 , GLY G:184 , PHE G:185 , THR G:186 , HOH G:1758 , HOH G:1765 , HOH G:1794
BINDING SITE FOR RESIDUE ADX G 1700
14
BC5
SOFTWARE
ASN G:27 , VAL G:28 , ASP H:89 , ARG H:92 , PHE H:101 , ARG H:106 , ASN H:109 , PHE H:131 , ILE H:132 , SER H:133 , PRO H:134 , LEU H:173 , LYS H:183 , GLY H:184 , PHE H:185 , THR H:186 , HOH H:1803 , HOH H:1804 , HOH H:1835 , HOH H:1901
BINDING SITE FOR RESIDUE ADX H 1800
15
BC6
SOFTWARE
GLY A:62 , ALA A:63 , GLY A:64 , LYS A:65 , THR A:66 , THR A:67 , ARG A:168 , THR A:204 , CYS A:207 , VAL A:209 , HOH A:1190 , HOH A:1206
BINDING SITE FOR RESIDUE ADX A 1101
16
BC7
SOFTWARE
LEU B:60 , GLY B:62 , ALA B:63 , GLY B:64 , LYS B:65 , THR B:66 , THR B:67 , ARG B:168 , THR B:204 , CYS B:207 , ASP B:208 , VAL B:209 , CYS B:212 , MG B:1002 , HOH B:1202 , HOH B:1211 , HOH B:1283 , HOH B:1290
BINDING SITE FOR RESIDUE ADX B 1201
17
BC8
SOFTWARE
LEU C:60 , GLY C:62 , ALA C:63 , GLY C:64 , LYS C:65 , THR C:66 , THR C:67 , ARG C:168 , THR C:204 , CYS C:207 , ASP C:208 , VAL C:209 , CYS C:212 , MG C:1003 , HOH C:1347 , HOH C:1364 , HOH C:1390 , HOH D:1402
BINDING SITE FOR RESIDUE ADX C 1301
18
BC9
SOFTWARE
LEU D:60 , GLY D:62 , ALA D:63 , GLY D:64 , LYS D:65 , THR D:66 , THR D:67 , ARG D:168 , THR D:204 , CYS D:207 , ASP D:208 , VAL D:209 , CYS D:212 , MG D:1004 , HOH D:1404 , HOH D:1406 , HOH D:1442 , HOH D:1483
BINDING SITE FOR RESIDUE ADX D 1401
19
CC1
SOFTWARE
LEU E:60 , GLY E:62 , ALA E:63 , GLY E:64 , LYS E:65 , THR E:66 , THR E:67 , ARG E:168 , VAL E:170 , THR E:204 , CYS E:207 , CYS E:212 , MG E:1005 , HOH E:1502 , HOH E:1504 , HOH E:1582 , HOH E:1591
BINDING SITE FOR RESIDUE ADX E 1501
20
CC2
SOFTWARE
LEU F:60 , GLY F:62 , ALA F:63 , GLY F:64 , LYS F:65 , THR F:66 , THR F:67 , ARG F:168 , THR F:204 , CYS F:207 , ASP F:208 , VAL F:209 , CYS F:212 , MG F:1006 , HOH F:1604 , HOH F:1605 , HOH F:1634
BINDING SITE FOR RESIDUE ADX F 1601
21
CC3
SOFTWARE
LEU G:60 , GLY G:62 , ALA G:63 , GLY G:64 , LYS G:65 , THR G:66 , THR G:67 , ARG G:168 , VAL G:170 , THR G:204 , CYS G:207 , ASP G:208 , VAL G:209 , CYS G:212 , HOH G:1702 , HOH G:1703 , HOH G:1704 , HOH G:1784
BINDING SITE FOR RESIDUE ADX G 1701
22
CC4
SOFTWARE
SER H:61 , GLY H:62 , ALA H:63 , GLY H:64 , LYS H:65 , THR H:66 , THR H:67 , ARG H:168 , THR H:204 , CYS H:207 , ASP H:208 , VAL H:209 , CYS H:212 , MG H:1008 , HOH H:1803 , HOH H:1805 , HOH H:1812
BINDING SITE FOR RESIDUE ADX H 1801
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(5, 40)
Info
All Exons
Exon 1.3 (A:27-59 | B:35-59 | C:24-59 | D:24...)
Exon 1.4c (A:59-137 | B:59-137 | C:59-137 | D...)
Exon 1.5c (A:138-184 (gaps) | B:138-184 | C:1...)
Exon 1.6 (A:184-223 | B:184-223 | C:184-223 ...)
Exon 1.7b (A:224-227 | B:224-227 | C:224-227 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1a/1.3
2: Boundary 1.3/1.4c
3: Boundary 1.4c/1.5c
4: Boundary 1.5c/1.6
5: Boundary 1.6/1.7b
6: Boundary 1.7b/1.8
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
ENST00000265174
1a
ENSE00000935008
chr4:
108641608-108641276
333
PAPS1_HUMAN
1-20
20
0
-
-
1.3
ENST00000265174
3
ENSE00000935007
chr4:
108622441-108622327
115
PAPS1_HUMAN
21-59
39
8
A:27-59
B:35-59
C:24-59
D:24-59
E:25-59
F:24-59
G:27-59
H:35-59
33
25
36
36
35
36
33
25
1.4c
ENST00000265174
4c
ENSE00000736237
chr4:
108615162-108614927
236
PAPS1_HUMAN
59-137
79
8
A:59-137
B:59-137
C:59-137
D:59-137
E:59-137
F:59-137
G:59-137
H:59-137
79
79
79
79
79
79
79
79
1.5c
ENST00000265174
5c
ENSE00000736234
chr4:
108608333-108608195
139
PAPS1_HUMAN
138-184
47
8
A:138-184 (gaps)
B:138-184
C:138-184
D:138-184
E:138-184
F:138-184
G:138-184
H:138-184
47
47
47
47
47
47
47
47
1.6
ENST00000265174
6
ENSE00000736231
chr4:
108603289-108603171
119
PAPS1_HUMAN
184-223
40
8
A:184-223
B:184-223
C:184-223
D:184-223
E:184-223
F:184-223
G:184-223
H:184-223
40
40
40
40
40
40
40
40
1.7b
ENST00000265174
7b
ENSE00000841651
chr4:
108581228-108581115
114
PAPS1_HUMAN
224-261
38
8
A:224-227
B:224-227
C:224-227
D:224-227
E:224-227
F:224-227
G:224-227
H:224-227
4
4
4
4
4
4
4
4
1.8
ENST00000265174
8
ENSE00000841650
chr4:
108578163-108578052
112
PAPS1_HUMAN
262-299
38
0
-
-
1.9
ENST00000265174
9
ENSE00000841649
chr4:
108576056-108575851
206
PAPS1_HUMAN
299-367
69
0
-
-
1.10b
ENST00000265174
10b
ENSE00001217423
chr4:
108574782-108574647
136
PAPS1_HUMAN
368-413
46
0
-
-
1.11
ENST00000265174
11
ENSE00001217417
chr4:
108566226-108565958
269
PAPS1_HUMAN
413-502
90
0
-
-
1.12a
ENST00000265174
12a
ENSE00001217412
chr4:
108553016-108552787
230
PAPS1_HUMAN
503-579
77
0
-
-
1.13
ENST00000265174
13
ENSE00001217468
chr4:
108535543-108534822
722
PAPS1_HUMAN
579-624
46
0
-
-
[
close EXON info
]
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d2ofwa_ (A:)
1b: SCOP_d2ofwb_ (B:)
1c: SCOP_d2ofwc_ (C:)
1d: SCOP_d2ofwd_ (D:)
1e: SCOP_d2ofwe_ (E:)
1f: SCOP_d2ofwf_ (F:)
1g: SCOP_d2ofwg_ (G:)
1h: SCOP_d2ofwh_ (H:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
automated matches
(303)
Protein domain
:
automated matches
(303)
Human (Homo sapiens) [TaxId: 9606]
(86)
1a
d2ofwa_
A:
1b
d2ofwb_
B:
1c
d2ofwc_
C:
1d
d2ofwd_
D:
1e
d2ofwe_
E:
1f
d2ofwf_
F:
1g
d2ofwg_
G:
1h
d2ofwh_
H:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_2ofwC00 (C:24-227)
1b: CATH_2ofwD00 (D:24-227)
1c: CATH_2ofwF00 (F:24-227)
1d: CATH_2ofwE00 (E:25-227)
1e: CATH_2ofwG00 (G:27-227)
1f: CATH_2ofwA00 (A:27-227)
1g: CATH_2ofwB00 (B:35-227)
1h: CATH_2ofwH00 (H:35-227)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Human (Homo sapiens)
(413)
1a
2ofwC00
C:24-227
1b
2ofwD00
D:24-227
1c
2ofwF00
F:24-227
1d
2ofwE00
E:25-227
1e
2ofwG00
G:27-227
1f
2ofwA00
A:27-227
1g
2ofwB00
B:35-227
1h
2ofwH00
H:35-227
[
close CATH info
]
Pfam Domains
(2, 16)
Info
all PFAM domains
1a: PFAM_APS_kinase_2ofwH01 (H:51-209)
1b: PFAM_APS_kinase_2ofwH02 (H:51-209)
1c: PFAM_APS_kinase_2ofwH03 (H:51-209)
1d: PFAM_APS_kinase_2ofwH04 (H:51-209)
1e: PFAM_APS_kinase_2ofwH05 (H:51-209)
1f: PFAM_APS_kinase_2ofwH06 (H:51-209)
1g: PFAM_APS_kinase_2ofwH07 (H:51-209)
1h: PFAM_APS_kinase_2ofwH08 (H:51-209)
2a: PFAM_PUA_2_2ofwH09 (H:225-225)
2b: PFAM_PUA_2_2ofwH10 (H:225-225)
2c: PFAM_PUA_2_2ofwH11 (H:225-225)
2d: PFAM_PUA_2_2ofwH12 (H:225-225)
2e: PFAM_PUA_2_2ofwH13 (H:225-225)
2f: PFAM_PUA_2_2ofwH14 (H:225-225)
2g: PFAM_PUA_2_2ofwH15 (H:225-225)
2h: PFAM_PUA_2_2ofwH16 (H:225-225)
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Families
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Organisms
(
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(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
APS_kinase
(10)
Homo sapiens (Human)
(7)
1a
APS_kinase-2ofwH01
H:51-209
1b
APS_kinase-2ofwH02
H:51-209
1c
APS_kinase-2ofwH03
H:51-209
1d
APS_kinase-2ofwH04
H:51-209
1e
APS_kinase-2ofwH05
H:51-209
1f
APS_kinase-2ofwH06
H:51-209
1g
APS_kinase-2ofwH07
H:51-209
1h
APS_kinase-2ofwH08
H:51-209
Clan
:
PUA
(42)
Family
:
PUA_2
(11)
Homo sapiens (Human)
(6)
2a
PUA_2-2ofwH09
H:225-225
2b
PUA_2-2ofwH10
H:225-225
2c
PUA_2-2ofwH11
H:225-225
2d
PUA_2-2ofwH12
H:225-225
2e
PUA_2-2ofwH13
H:225-225
2f
PUA_2-2ofwH14
H:225-225
2g
PUA_2-2ofwH15
H:225-225
2h
PUA_2-2ofwH16
H:225-225
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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)
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Asym.Unit (285 KB)
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