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2BVC
Biol. Unit 1
Info
Asym.Unit (475 KB)
Biol.Unit 1 (922 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS GLUTAMINE SYNTHETASE IN COMPLEX WITH A TRANSITION STATE MIMIC
Authors
:
W. W. Krajewski, T. A. Jones, S. L. Mowbray
Date
:
23 Jun 05 (Deposition) - 07 Jul 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (2x)
Keywords
:
Ligase, Transition State Mimic, Synthetase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. W. Krajewski, T. A. Jones, S. L. Mowbray
Structure Of Mycobacterium Tuberculosis Glutamine Synthetase In Complex With A Transition-State Mimic Provides Functional Insights.
Proc. Natl. Acad. Sci. Usa V. 102 10499 2005
[
close entry info
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Hetero Components
(2, 24)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
1e: ADENOSINE-5'-DIPHOSPHATE (ADPe)
1f: ADENOSINE-5'-DIPHOSPHATE (ADPf)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
12
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
P3S
12
Ligand/Ion
L-METHIONINE-S-SULFOXIMINE PHOSPHATE
[
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
GLU A:135 , GLU A:219 , GLU A:227 , P3S A:500 , HOH A:2028
BINDING SITE FOR RESIDUE MG A 502
02
AC2
SOFTWARE
GLU A:133 , HIS A:276 , GLU A:366 , P3S A:500 , ADP A:501
BINDING SITE FOR RESIDUE MG A 503
03
AC3
SOFTWARE
GLU A:133 , GLU A:227 , P3S A:500 , ADP A:501 , HOH A:2067
BINDING SITE FOR RESIDUE MG A 504
04
AC4
SOFTWARE
SER F:424
BINDING SITE FOR RESIDUE CL A 505
05
AC5
SOFTWARE
GLU B:135 , GLU B:219 , GLU B:227 , P3S B:500 , HOH B:2091
BINDING SITE FOR RESIDUE MG B 502
06
AC6
SOFTWARE
GLU B:133 , HIS B:276 , GLU B:366 , ARG B:368 , P3S B:500 , ADP B:501
BINDING SITE FOR RESIDUE MG B 503
07
AC7
SOFTWARE
GLU B:133 , GLU B:227 , P3S B:500 , ADP B:501 , HOH B:2057
BINDING SITE FOR RESIDUE MG B 504
08
AC8
SOFTWARE
SER E:424
BINDING SITE FOR RESIDUE CL B 505
09
AC9
SOFTWARE
GLU C:135 , GLU C:219 , GLU C:227 , P3S C:500 , HOH C:2087
BINDING SITE FOR RESIDUE MG C 502
10
BC1
SOFTWARE
GLU C:133 , HIS C:276 , GLU C:366 , ARG C:368 , P3S C:500 , ADP C:501
BINDING SITE FOR RESIDUE MG C 503
11
BC2
SOFTWARE
GLU C:133 , GLU C:227 , P3S C:500 , ADP C:501 , HOH C:2053
BINDING SITE FOR RESIDUE MG C 504
12
BC3
SOFTWARE
SER A:424 , HOH A:2109
BINDING SITE FOR RESIDUE CL C 505
13
BC4
SOFTWARE
GLU D:135 , GLU D:219 , GLU D:227 , P3S D:500 , HOH D:2063
BINDING SITE FOR RESIDUE MG D 502
14
BC5
SOFTWARE
GLU D:133 , HIS D:276 , GLU D:366 , ARG D:368 , P3S D:500 , ADP D:501
BINDING SITE FOR RESIDUE MG D 503
15
BC6
SOFTWARE
GLU D:133 , GLU D:227 , P3S D:500 , ADP D:501 , HOH D:2059
BINDING SITE FOR RESIDUE MG D 504
16
BC7
SOFTWARE
SER B:424
BINDING SITE FOR RESIDUE CL D 505
17
BC8
SOFTWARE
GLU E:135 , GLU E:219 , GLU E:227 , P3S E:500 , MG E:504 , HOH E:2073
BINDING SITE FOR RESIDUE MG E 502
18
BC9
SOFTWARE
GLU E:133 , HIS E:276 , GLU E:366 , P3S E:500 , ADP E:501
BINDING SITE FOR RESIDUE MG E 503
19
CC1
SOFTWARE
GLU E:133 , GLU E:227 , P3S E:500 , ADP E:501 , MG E:502 , HOH E:2074
BINDING SITE FOR RESIDUE MG E 504
20
CC2
SOFTWARE
SER C:424
BINDING SITE FOR RESIDUE CL E 505
21
CC3
SOFTWARE
GLU F:135 , GLU F:219 , GLU F:227 , P3S F:500 , MG F:504 , HOH F:2027
BINDING SITE FOR RESIDUE MG F 502
22
CC4
SOFTWARE
GLU F:133 , HIS F:276 , GLU F:366 , P3S F:500 , ADP F:501
BINDING SITE FOR RESIDUE MG F 503
23
CC5
SOFTWARE
GLU F:133 , GLU F:227 , P3S F:500 , ADP F:501 , MG F:502 , HOH F:2105
BINDING SITE FOR RESIDUE MG F 504
24
CC6
SOFTWARE
SER D:424
BINDING SITE FOR RESIDUE CL F 505
25
CC7
SOFTWARE
GLU A:133 , GLU A:135 , GLU A:219 , GLU A:227 , GLY A:272 , HIS A:276 , ARG A:329 , TYR A:334 , GLU A:335 , ARG A:347 , GLU A:366 , ARG A:368 , ADP A:501 , MG A:502 , MG A:503 , MG A:504 , HOH A:2028 , HOH A:2047 , HOH A:2067 , HOH A:2116 , HOH A:2117 , ASP F:54
BINDING SITE FOR RESIDUE P3S A 500
26
CC8
SOFTWARE
GLU A:133 , GLU A:214 , LYS A:215 , GLU A:227 , ASN A:229 , TYR A:230 , GLN A:231 , PHE A:232 , HIS A:278 , SER A:280 , ARG A:347 , ARG A:352 , LYS A:361 , ARG A:364 , GLU A:366 , P3S A:500 , MG A:503 , MG A:504 , HOH A:2025 , HOH A:2067 , HOH A:2094 , HOH A:2118 , HOH A:2119
BINDING SITE FOR RESIDUE ADP A 501
27
CC9
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 , ADP B:501 , MG B:502 , MG B:503 , MG B:504 , HOH B:2038 , HOH B:2076 , HOH B:2091 , HOH B:2092
BINDING SITE FOR RESIDUE P3S B 500
28
DC1
SOFTWARE
GLU B:133 , GLU B:214 , LYS B:215 , GLU B:227 , ASN B:229 , TYR B:230 , GLN B:231 , PHE B:232 , HIS B:278 , SER B:280 , ARG B:347 , ARG B:352 , LYS B:361 , ARG B:364 , GLU B:366 , P3S B:500 , MG B:503 , MG B:504 , HOH B:2014 , HOH B:2055 , HOH B:2057
BINDING SITE FOR RESIDUE ADP B 501
29
DC2
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 , ADP C:501 , MG C:502 , MG C:503 , MG C:504 , HOH C:2038 , HOH C:2053 , HOH C:2069 , HOH C:2086 , HOH C:2087
BINDING SITE FOR RESIDUE P3S C 500
30
DC3
SOFTWARE
GLU C:133 , GLU C:214 , LYS C:215 , GLU C:227 , ASN C:229 , TYR C:230 , GLN C:231 , PHE C:232 , HIS C:278 , SER C:280 , ARG C:347 , ARG C:352 , LYS C:361 , ARG C:364 , GLU C:366 , P3S C:500 , MG C:503 , MG C:504 , HOH C:2015 , HOH C:2053
BINDING SITE FOR RESIDUE ADP C 501
31
DC4
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 , ADP D:501 , MG D:502 , MG D:503 , MG D:504 , HOH D:2059 , HOH D:2061 , HOH D:2063 , HOH D:2078 , HOH D:2096
BINDING SITE FOR RESIDUE P3S D 500
32
DC5
SOFTWARE
GLU D:133 , GLU D:214 , LYS D:215 , GLU D:227 , ASN D:229 , TYR D:230 , GLN D:231 , PHE D:232 , HIS D:278 , SER D:280 , ARG D:347 , ARG D:352 , LYS D:361 , ARG D:364 , GLU D:366 , P3S D:500 , MG D:503 , MG D:504 , HOH D:2024 , HOH D:2058 , HOH D:2059
BINDING SITE FOR RESIDUE ADP D 501
33
DC6
SOFTWARE
ASP D:54 , GLU E:133 , GLU E:135 , GLU E:219 , GLU E:227 , GLY E:272 , GLY E:274 , HIS E:276 , ARG E:329 , GLU E:335 , ARG E:347 , GLU E:366 , ARG E:368 , ADP E:501 , MG E:502 , MG E:503 , MG E:504 , HOH E:2051 , HOH E:2072 , HOH E:2073 , HOH E:2074 , HOH E:2094
BINDING SITE FOR RESIDUE P3S E 500
34
DC7
SOFTWARE
GLY E:131 , GLU E:133 , GLU E:214 , LYS E:215 , GLU E:227 , ASN E:229 , TYR E:230 , GLN E:231 , PHE E:232 , HIS E:278 , SER E:280 , ARG E:347 , ARG E:352 , LYS E:361 , ARG E:364 , GLU E:366 , P3S E:500 , MG E:503 , MG E:504 , HOH E:2074 , HOH E:2101 , HOH E:2121
BINDING SITE FOR RESIDUE ADP E 501
35
DC8
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 , ADP F:501 , MG F:502 , MG F:503 , MG F:504 , HOH F:2027 , HOH F:2065 , HOH F:2081 , HOH F:2105 , HOH F:2106
BINDING SITE FOR RESIDUE P3S F 500
36
DC9
SOFTWARE
GLU F:133 , GLU F:214 , LYS F:215 , GLU F:227 , ASN F:229 , TYR F:230 , GLN F:231 , PHE F:232 , HIS F:278 , SER F:280 , ARG F:347 , ARG F:352 , LYS F:361 , ARG F:364 , GLU F:366 , P3S F:500 , MG F:503 , MG F:504 , HOH F:2025 , HOH F:2105
BINDING SITE FOR RESIDUE ADP F 501
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
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PROSITE Patterns/Profiles
(3, 72)
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...)
;
View:
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Label:
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
12
A:53-71
B:53-71
C:53-71
D:53-71
E: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
12
A:265-280
B:265-280
C:265-280
D:265-280
E: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
12
A:394-406
B:394-406
C:394-406
D:394-406
E: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
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_d2bvca1 (A:4-104)
1b: SCOP_d2bvce1 (E:4-104)
1c: SCOP_d2bvcf1 (F:4-104)
1d: SCOP_d2bvcb1 (B:4-104)
1e: SCOP_d2bvcc1 (C:4-104)
1f: SCOP_d2bvcd1 (D:4-104)
2a: SCOP_d2bvca2 (A:105-478)
2b: SCOP_d2bvce2 (E:105-478)
2c: SCOP_d2bvcf2 (F:105-478)
2d: SCOP_d2bvcb2 (B:105-478)
2e: SCOP_d2bvcc2 (C:105-478)
2f: SCOP_d2bvcd2 (D:105-478)
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Protein Domains
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(
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Organisms
(
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(
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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
d2bvca1
A:4-104
1b
d2bvce1
E:4-104
1c
d2bvcf1
F:4-104
1d
d2bvcb1
B:4-104
1e
d2bvcc1
C:4-104
1f
d2bvcd1
D: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
d2bvca2
A:105-478
2b
d2bvce2
E:105-478
2c
d2bvcf2
F:105-478
2d
d2bvcb2
B:105-478
2e
d2bvcc2
C:105-478
2f
d2bvcd2
D:105-478
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2bvcA02 (A:108-466)
1b: CATH_2bvcB02 (B:108-466)
1c: CATH_2bvcC02 (C:108-466)
1d: CATH_2bvcD02 (D:108-466)
1e: CATH_2bvcE02 (E:108-466)
1f: CATH_2bvcF02 (F:108-466)
2a: CATH_2bvcA01 (A:5-107)
2b: CATH_2bvcB01 (B:5-107)
2c: CATH_2bvcC01 (C:5-107)
2d: CATH_2bvcD01 (D:5-107)
2e: CATH_2bvcE01 (E:5-107)
2f: CATH_2bvcF01 (F:5-107)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Creatine Kinase; Chain A, domain 2
(27)
Homologous Superfamily
:
Creatine Kinase; Chain
(27)
Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv.
(1)
1a
2bvcA02
A:108-466
1b
2bvcB02
B:108-466
1c
2bvcC02
C:108-466
1d
2bvcD02
D:108-466
1e
2bvcE02
E:108-466
1f
2bvcF02
F:108-466
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.70, no name defined]
(11)
Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv.
(1)
2a
2bvcA01
A:5-107
2b
2bvcB01
B:5-107
2c
2bvcC01
C:5-107
2d
2bvcD01
D:5-107
2e
2bvcE01
E:5-107
2f
2bvcF01
F:5-107
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Atom Selection
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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'
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select non-helix/non-sheet protein parts
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set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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show bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (475 KB)
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Biol.Unit 1 (922 KB)
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