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3ZXR
Biol. Unit 1
Info
Asym.Unit (496 KB)
Biol.Unit 1 (959 KB)
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Title
:
CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS GLUTAMINE SYNTHETASE IN COMPLEX WITH TRI-SUBSTITUTED IMIDAZOLE INHIBITOR (3-(2-TERT-BUTYL-5-(PYRIDIN-4-YL)-1H-IMIDAZOL-4-YL)QUINOLINE) AND L-METHIONINE-S-SULFOXIMINE PHOSPHATE.
Authors
:
M. T. Nilsson, S. L. Mowbray
Date
:
15 Aug 11 (Deposition) - 04 Apr 12 (Release) - 04 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (2x)
Keywords
:
Ligase, Nucleotide-Binding, Taut State, Rv2220, Mt2278, Glna1
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Gising, M. T. Nilsson, L. R. Odell, S. Yahiaoui, M. Lindh, H. Iyer, A. M. Sinha, B. R. Srinivasa, M. Larhed, S. L. Mowbray, A. Karlen
Trisubstituted Imidazoles As Mycobacterium Tuberculosis Glutamine Synthetase Inhibitors.
J. Med. Chem. V. 55 2894 2012
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 36)
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)
2a: 3-(2-TERT-BUTYL-5-(PYRIDIN-4-YL)-1... (IQ1a)
2b: 3-(2-TERT-BUTYL-5-(PYRIDIN-4-YL)-1... (IQ1b)
2c: 3-(2-TERT-BUTYL-5-(PYRIDIN-4-YL)-1... (IQ1c)
2d: 3-(2-TERT-BUTYL-5-(PYRIDIN-4-YL)-1... (IQ1d)
2e: 3-(2-TERT-BUTYL-5-(PYRIDIN-4-YL)-1... (IQ1e)
2f: 3-(2-TERT-BUTYL-5-(PYRIDIN-4-YL)-1... (IQ1f)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
3k: MAGNESIUM ION (MGk)
3l: MAGNESIUM ION (MGl)
3m: MAGNESIUM ION (MGm)
3n: MAGNESIUM ION (MGn)
3o: MAGNESIUM ION (MGo)
3p: MAGNESIUM ION (MGp)
3q: MAGNESIUM ION (MGq)
3r: MAGNESIUM ION (MGr)
4a: L-METHIONINE-S-SULFOXIMINE PHOSPHA... (P3Sa)
4b: L-METHIONINE-S-SULFOXIMINE PHOSPHA... (P3Sb)
4c: L-METHIONINE-S-SULFOXIMINE PHOSPHA... (P3Sc)
4d: L-METHIONINE-S-SULFOXIMINE PHOSPHA... (P3Sd)
4e: L-METHIONINE-S-SULFOXIMINE PHOSPHA... (P3Se)
4f: L-METHIONINE-S-SULFOXIMINE PHOSPHA... (P3Sf)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
5c: PHOSPHATE ION (PO4c)
5d: PHOSPHATE ION (PO4d)
5e: PHOSPHATE ION (PO4e)
5f: PHOSPHATE ION (PO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
IQ1
12
Ligand/Ion
3-(2-TERT-BUTYL-5-(PYRIDIN-4-YL)-1H-IMIDAZOL-4-YL)QUINOLINE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
P3S
12
Ligand/Ion
L-METHIONINE-S-SULFOXIMINE PHOSPHATE
5
PO4
12
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(42, 42)
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)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:129 , GLY A:131 , GLU A:214 , TYR A:230 , PHE A:232 , HIS A:278 , SER A:280 , ARG A:364 , PO4 A:506 , HOH A:2165
BINDING SITE FOR RESIDUE IQ1 A 501
02
AC2
SOFTWARE
GLU A:135 , GLU A:219 , GLU A:227 , MG A:504 , P3S A:505 , HOH A:2091
BINDING SITE FOR RESIDUE MG A 502
03
AC3
SOFTWARE
GLU A:133 , HIS A:276 , GLU A:366 , MG A:504 , P3S A:505 , PO4 A:506
BINDING SITE FOR RESIDUE MG A 503
04
AC4
SOFTWARE
GLU A:133 , GLU A:227 , MG A:502 , MG A:503 , P3S A:505 , PO4 A:506 , HOH A:2092 , HOH A:2168
BINDING SITE FOR RESIDUE MG A 504
05
AC5
SOFTWARE
GLU A:133 , GLU A:135 , GLU A:219 , GLU A:227 , GLY A:272 , HIS A:276 , ARG A:329 , GLU A:335 , ARG A:347 , GLU A:366 , ARG A:368 , MG A:502 , MG A:503 , MG A:504 , PO4 A:506 , HOH A:2091 , HOH A:2136 , HOH A:2168 , HOH A:2171 , HOH A:2192 , ASP F:54
BINDING SITE FOR RESIDUE P3S A 505
06
AC6
SOFTWARE
GLU A:133 , HIS A:278 , ARG A:347 , ARG A:352 , GLU A:366 , IQ1 A:501 , MG A:503 , MG A:504 , P3S A:505 , HOH A:2092 , HOH A:2168 , HOH A:2169 , HOH A:2227
BINDING SITE FOR RESIDUE PO4 A 506
07
AC7
SOFTWARE
SER A:424 , HOH A:2237 , HOH A:2249
BINDING SITE FOR RESIDUE CL A 507
08
AC8
SOFTWARE
TYR B:129 , GLY B:131 , GLU B:214 , TYR B:230 , PHE B:232 , HIS B:278 , SER B:280 , ALA B:362 , ARG B:364 , PO4 B:506 , HOH B:2149 , LYS E:14
BINDING SITE FOR RESIDUE IQ1 B 501
09
AC9
SOFTWARE
GLU B:135 , GLU B:219 , GLU B:227 , MG B:504 , P3S B:505 , HOH B:2089
BINDING SITE FOR RESIDUE MG B 502
10
BC1
SOFTWARE
GLU B:133 , HIS B:276 , GLU B:366 , MG B:504 , P3S B:505 , PO4 B:506
BINDING SITE FOR RESIDUE MG B 503
11
BC2
SOFTWARE
GLU B:133 , GLU B:227 , MG B:502 , MG B:503 , P3S B:505 , PO4 B:506 , HOH B:2088 , HOH B:2152
BINDING SITE FOR RESIDUE MG B 504
12
BC3
SOFTWARE
ASP A:54 , GLU B:133 , GLU B:135 , GLU B:219 , GLU B:227 , GLY B:272 , HIS B:276 , ARG B:329 , GLU B:335 , ARG B:347 , GLU B:366 , ARG B:368 , MG B:502 , MG B:503 , MG B:504 , PO4 B:506 , HOH B:2089 , HOH B:2130 , HOH B:2152 , HOH B:2153 , HOH B:2174
BINDING SITE FOR RESIDUE P3S B 505
13
BC4
SOFTWARE
GLU B:133 , HIS B:278 , ARG B:347 , ARG B:352 , GLU B:366 , IQ1 B:501 , MG B:503 , MG B:504 , P3S B:505 , HOH B:2088 , HOH B:2152 , HOH B:2202 , HOH B:2206
BINDING SITE FOR RESIDUE PO4 B 506
14
BC5
SOFTWARE
SER B:424 , HOH B:2226
BINDING SITE FOR RESIDUE CL B 507
15
BC6
SOFTWARE
TYR C:129 , GLY C:131 , GLU C:214 , TYR C:230 , PHE C:232 , HIS C:278 , SER C:280 , ARG C:364 , PO4 C:506 , HOH C:2150
BINDING SITE FOR RESIDUE IQ1 C 501
16
BC7
SOFTWARE
GLU C:135 , GLU C:219 , GLU C:227 , MG C:504 , P3S C:505 , HOH C:2090
BINDING SITE FOR RESIDUE MG C 502
17
BC8
SOFTWARE
GLU C:133 , HIS C:276 , GLU C:366 , MG C:504 , P3S C:505 , PO4 C:506
BINDING SITE FOR RESIDUE MG C 503
18
BC9
SOFTWARE
GLU C:133 , GLU C:227 , MG C:502 , MG C:503 , P3S C:505 , PO4 C:506 , HOH C:2089 , HOH C:2154
BINDING SITE FOR RESIDUE MG C 504
19
CC1
SOFTWARE
ASP B:54 , GLU C:133 , GLU C:135 , GLU C:219 , GLU C:227 , GLY C:272 , HIS C:276 , ARG C:329 , GLU C:335 , ARG C:347 , GLU C:366 , ARG C:368 , MG C:502 , MG C:503 , MG C:504 , PO4 C:506 , HOH C:2090 , HOH C:2131 , HOH C:2154 , HOH C:2155 , HOH C:2176
BINDING SITE FOR RESIDUE P3S C 505
20
CC2
SOFTWARE
GLU C:133 , HIS C:278 , ARG C:347 , ARG C:352 , GLU C:366 , IQ1 C:501 , MG C:503 , MG C:504 , P3S C:505 , HOH C:2089 , HOH C:2153 , HOH C:2154 , HOH C:2207
BINDING SITE FOR RESIDUE PO4 C 506
21
CC3
SOFTWARE
SER C:424
BINDING SITE FOR RESIDUE CL C 507
22
CC4
SOFTWARE
TYR D:129 , GLY D:131 , GLU D:214 , TYR D:230 , PHE D:232 , HIS D:278 , SER D:280 , ARG D:364 , PO4 D:506 , HOH D:2149
BINDING SITE FOR RESIDUE IQ1 D 501
23
CC5
SOFTWARE
GLU D:135 , GLU D:219 , GLU D:227 , MG D:504 , P3S D:505 , HOH D:2087
BINDING SITE FOR RESIDUE MG D 502
24
CC6
SOFTWARE
GLU D:133 , HIS D:276 , GLU D:366 , MG D:504 , P3S D:505 , PO4 D:506
BINDING SITE FOR RESIDUE MG D 503
25
CC7
SOFTWARE
GLU D:133 , GLU D:227 , MG D:502 , MG D:503 , P3S D:505 , PO4 D:506 , HOH D:2088 , HOH D:2152
BINDING SITE FOR RESIDUE MG D 504
26
CC8
SOFTWARE
ASP C:54 , GLU D:133 , GLU D:135 , GLU D:219 , GLU D:227 , GLY D:272 , HIS D:276 , ARG D:329 , GLU D:335 , ARG D:347 , GLU D:366 , ARG D:368 , MG D:502 , MG D:503 , MG D:504 , PO4 D:506 , HOH D:2087 , HOH D:2129 , HOH D:2152 , HOH D:2153 , HOH D:2174
BINDING SITE FOR RESIDUE P3S D 505
27
CC9
SOFTWARE
GLU D:133 , HIS D:278 , ARG D:347 , ARG D:352 , GLU D:366 , IQ1 D:501 , MG D:503 , MG D:504 , P3S D:505 , HOH D:2088 , HOH D:2151 , HOH D:2152 , HOH D:2205
BINDING SITE FOR RESIDUE PO4 D 506
28
DC1
SOFTWARE
SER D:424 , HOH D:2226
BINDING SITE FOR RESIDUE CL D 507
29
DC2
SOFTWARE
TYR E:129 , GLY E:131 , GLU E:214 , TYR E:230 , PHE E:232 , HIS E:278 , SER E:280 , ARG E:364 , PO4 E:506 , HOH E:2147
BINDING SITE FOR RESIDUE IQ1 E 501
30
DC3
SOFTWARE
GLU E:135 , GLU E:219 , GLU E:227 , MG E:504 , P3S E:505 , HOH E:2087
BINDING SITE FOR RESIDUE MG E 502
31
DC4
SOFTWARE
GLU E:133 , HIS E:276 , GLU E:366 , ARG E:368 , P3S E:505 , PO4 E:506
BINDING SITE FOR RESIDUE MG E 503
32
DC5
SOFTWARE
GLU E:133 , GLU E:227 , MG E:502 , P3S E:505 , PO4 E:506 , HOH E:2086 , HOH E:2149
BINDING SITE FOR RESIDUE MG E 504
33
DC6
SOFTWARE
ASP D:54 , GLU E:133 , GLU E:135 , GLU E:219 , GLU E:227 , GLY E:272 , HIS E:276 , ARG E:329 , GLU E:335 , ALA E:336 , ARG E:347 , GLU E:366 , ARG E:368 , MG E:502 , MG E:503 , MG E:504 , PO4 E:506 , HOH E:2087 , HOH E:2127 , HOH E:2149 , HOH E:2151 , HOH E:2173
BINDING SITE FOR RESIDUE P3S E 505
34
DC7
SOFTWARE
GLU E:133 , HIS E:278 , ARG E:347 , ARG E:352 , GLU E:366 , IQ1 E:501 , MG E:503 , MG E:504 , P3S E:505 , HOH E:2086 , HOH E:2149 , HOH E:2150 , HOH E:2203
BINDING SITE FOR RESIDUE PO4 E 506
35
DC8
SOFTWARE
SER E:424 , HOH E:2225
BINDING SITE FOR RESIDUE CL E 507
36
DC9
SOFTWARE
GLY F:131 , GLU F:214 , TYR F:230 , PHE F:232 , HIS F:278 , SER F:280 , ARG F:364 , PO4 F:506 , HOH F:2129
BINDING SITE FOR RESIDUE IQ1 F 501
37
EC1
SOFTWARE
GLU F:135 , GLU F:219 , GLU F:227 , MG F:504 , P3S F:505 , HOH F:2069
BINDING SITE FOR RESIDUE MG F 502
38
EC2
SOFTWARE
GLU F:133 , HIS F:276 , GLU F:366 , MG F:504 , P3S F:505 , PO4 F:506
BINDING SITE FOR RESIDUE MG F 503
39
EC3
SOFTWARE
GLU F:133 , GLU F:227 , MG F:502 , MG F:503 , P3S F:505 , PO4 F:506 , HOH F:2070 , HOH F:2132
BINDING SITE FOR RESIDUE MG F 504
40
EC4
SOFTWARE
ASP E:54 , GLU F:133 , GLU F:135 , GLU F:219 , GLU F:227 , GLY F:272 , HIS F:276 , ARG F:329 , GLU F:335 , ARG F:347 , GLU F:366 , ARG F:368 , MG F:502 , MG F:503 , MG F:504 , PO4 F:506 , HOH F:2069 , HOH F:2109 , HOH F:2132 , HOH F:2133 , HOH F:2153
BINDING SITE FOR RESIDUE P3S F 505
41
EC5
SOFTWARE
GLU F:133 , HIS F:278 , ARG F:347 , ARG F:352 , GLU F:366 , IQ1 F:501 , MG F:503 , MG F:504 , P3S F:505 , HOH F:2070 , HOH F:2131 , HOH F:2132 , HOH F:2184
BINDING SITE FOR RESIDUE PO4 F 506
42
EC6
SOFTWARE
SER F:424 , HOH F:2193 , HOH F:2204
BINDING SITE FOR RESIDUE CL F 507
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 60)
Info
All PROSITE Patterns/Profiles
1: GLNA_1 (A:53-71,B:53-71,C:53-71,D:53-71,E:...)
2: GLNA_ATP (A:265-280,B:265-280,C:265-280,D:26...)
3: GLNA_ADENYLATION (A:394-406,B:394-406,C:394-406,D:39...)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLNA_1
PS00180
Glutamine synthetase signature 1.
GLN1B_MYCTO
53-71
8
A:53-71
B:53-71
C:53-71
F:53-71
GLN1B_MYCTU
53-71
12
A:53-71
B:53-71
C:53-71
D:53-71
E:53-71
F:53-71
2
GLNA_ATP
PS00181
Glutamine synthetase putative ATP-binding region signature.
GLN1B_MYCTO
265-280
8
A:265-280
B:265-280
C:265-280
F:265-280
GLN1B_MYCTU
265-280
12
A:265-280
B:265-280
C:265-280
D:265-280
E:265-280
F:265-280
3
GLNA_ADENYLATION
PS00182
Glutamine synthetase class-I adenylation site.
GLN1B_MYCTO
394-406
8
A:394-406
B:394-406
C:394-406
F:394-406
GLN1B_MYCTU
394-406
12
A:394-406
B:394-406
C:394-406
D:394-406
E:394-406
F:394-406
[
close PROSITE info
]
Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d3zxra1 (A:4-104)
1b: SCOP_d3zxrb1 (B:4-104)
1c: SCOP_d3zxrc1 (C:4-104)
1d: SCOP_d3zxrd1 (D:4-104)
1e: SCOP_d3zxre1 (E:4-104)
1f: SCOP_d3zxrf1 (F:4-104)
2a: SCOP_d3zxra2 (A:105-478)
2b: SCOP_d3zxrb2 (B:105-478)
2c: SCOP_d3zxrc2 (C:105-478)
2d: SCOP_d3zxrd2 (D:105-478)
2e: SCOP_d3zxre2 (E:105-478)
2f: SCOP_d3zxrf2 (F:105-478)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
Glutamine synthetase, N-terminal domain
(20)
Family
:
automated matches
(12)
Protein domain
:
automated matches
(12)
Mycobacterium tuberculosis [TaxId: 83332]
(6)
1a
d3zxra1
A:4-104
1b
d3zxrb1
B:4-104
1c
d3zxrc1
C:4-104
1d
d3zxrd1
D:4-104
1e
d3zxre1
E:4-104
1f
d3zxrf1
F:4-104
Fold
:
Glutamine synthetase/guanido kinase
(68)
Superfamily
:
Glutamine synthetase/guanido kinase
(68)
Family
:
automated matches
(18)
Protein domain
:
automated matches
(18)
Mycobacterium tuberculosis [TaxId: 83332]
(6)
2a
d3zxra2
A:105-478
2b
d3zxrb2
B:105-478
2c
d3zxrc2
C:105-478
2d
d3zxrd2
D:105-478
2e
d3zxre2
E:105-478
2f
d3zxrf2
F:105-478
[
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
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Atom Selection
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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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 (496 KB)
Header - Asym.Unit
Biol.Unit 1 (959 KB)
Header - Biol.Unit 1
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