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1T3Q
Asym. Unit
Info
Asym.Unit (439 KB)
Biol.Unit 1 (429 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF QUINOLINE 2-OXIDOREDUCTASE FROM PSEUDOMONAS PUTIDA 86
Authors
:
I. Bonin, B. M. Martins, V. Purvanov, S. Fetzner, R. Huber, H. Dobbek
Date
:
27 Apr 04 (Deposition) - 14 Sep 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Qor, Molybdenum, Mcd, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Bonin, B. M. Martins, V. Purvanov, S. Fetzner, R. Huber, H. Dobbek
Active Site Geometry And Substrate Recognition Of The Molybdenum Hydroxylase Quinoline 2-Oxidoreductase.
Structure V. 12 1425 2004
[
close entry info
]
Hetero Components
(6, 27)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2a: FE2/S2 (INORGANIC) CLUSTER (FESa)
2b: FE2/S2 (INORGANIC) CLUSTER (FESb)
2c: FE2/S2 (INORGANIC) CLUSTER (FESc)
2d: FE2/S2 (INORGANIC) CLUSTER (FESd)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
4a: PTERIN CYTOSINE DINUCLEOTIDE (MCNa)
4b: PTERIN CYTOSINE DINUCLEOTIDE (MCNb)
5a: DIOXOSULFIDOMOLYBDENUM(VI) ION (SMOa)
5b: DIOXOSULFIDOMOLYBDENUM(VI) ION (SMOb)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
6e: SULFATE ION (SO4e)
6f: SULFATE ION (SO4f)
6g: SULFATE ION (SO4g)
6h: SULFATE ION (SO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
FES
4
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
3
GOL
9
Ligand/Ion
GLYCEROL
4
MCN
2
Ligand/Ion
PTERIN CYTOSINE DINUCLEOTIDE
5
SMO
2
Ligand/Ion
DIOXOSULFIDOMOLYBDENUM(VI) ION
6
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(27, 27)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER B:17 , PRO B:672 , MET B:673 , GLU B:676 , HOH B:5352 , HOH B:5414
BINDING SITE FOR RESIDUE SO4 B 3100
02
AC2
SOFTWARE
ARG B:168 , ARG B:318
BINDING SITE FOR RESIDUE SO4 B 3101
03
AC3
SOFTWARE
VAL B:165 , ARG B:168 , HOH B:5210 , HOH B:5425
BINDING SITE FOR RESIDUE SO4 B 3102
04
AC4
SOFTWARE
PRO E:102 , ARG E:110 , HOH E:5109 , HOH E:5114 , HOH E:5423
BINDING SITE FOR RESIDUE SO4 E 3103
05
AC5
SOFTWARE
ARG E:168 , ARG E:318 , ILE E:358
BINDING SITE FOR RESIDUE SO4 E 3104
06
AC6
SOFTWARE
HOH A:5021 , PRO B:102 , ASN B:106 , ARG B:110 , HOH B:5242 , HOH B:5397
BINDING SITE FOR RESIDUE SO4 B 3105
07
AC7
SOFTWARE
ARG E:21 , HOH E:5360
BINDING SITE FOR RESIDUE SO4 E 3106
08
AC8
SOFTWARE
PRO E:525 , ALA E:526 , SER E:527 , HOH E:5039 , HOH E:5129 , HOH E:5503 , HOH E:5680
BINDING SITE FOR RESIDUE SO4 E 3107
09
AC9
SOFTWARE
GLN A:106 , CYS A:107 , GLY A:108 , CYS A:110 , CYS A:142 , ARG A:143 , CYS A:144 , MET B:201
BINDING SITE FOR RESIDUE FES A 4907
10
BC1
SOFTWARE
GLY A:47 , CYS A:48 , GLU A:49 , GLY A:51 , VAL A:52 , CYS A:53 , GLY A:54 , CYS A:56 , ARG A:66 , CYS A:68
BINDING SITE FOR RESIDUE FES A 4908
11
BC2
SOFTWARE
GLN D:106 , CYS D:107 , GLY D:108 , CYS D:110 , CYS D:142 , ARG D:143 , CYS D:144 , MET E:201
BINDING SITE FOR RESIDUE FES D 4909
12
BC3
SOFTWARE
GLY D:47 , CYS D:48 , GLU D:49 , GLY D:51 , VAL D:52 , CYS D:53 , GLY D:54 , SER D:55 , CYS D:56 , CYS D:68
BINDING SITE FOR RESIDUE FES D 4910
13
BC4
SOFTWARE
GLN A:50 , GLY A:51 , LEU A:69 , ILE C:29 , ALA C:31 , GLY C:32 , GLY C:33 , GLN C:34 , SER C:35 , LEU C:36 , LEU C:53 , ALA C:73 , HIS C:77 , ALA C:101 , GLY C:109 , THR C:110 , GLY C:113 , SER C:114 , ALA C:116 , HIS C:117 , ALA C:122 , GLU C:123 , LEU C:160 , LEU C:166 , GLY C:188 , TYR C:190 , HOH C:4932 , HOH C:4935 , HOH C:4937 , HOH C:4940 , HOH C:4981 , HOH C:5127 , HOH C:5188
BINDING SITE FOR RESIDUE FAD C 4931
14
BC5
SOFTWARE
GLN D:50 , GLY D:51 , VAL D:52 , LEU D:69 , ILE F:29 , ALA F:31 , GLY F:32 , GLY F:33 , GLN F:34 , SER F:35 , LEU F:36 , LEU F:53 , ALA F:73 , HIS F:77 , ALA F:101 , GLY F:109 , THR F:110 , GLY F:113 , SER F:114 , ALA F:116 , HIS F:117 , ALA F:122 , GLU F:123 , LEU F:160 , LEU F:166 , GLY F:188 , TYR F:190 , HOH F:4934 , HOH F:4938 , HOH F:4940 , HOH F:4948 , HOH F:4995 , HOH F:5006 , HOH F:5010 , HOH F:5214
BINDING SITE FOR RESIDUE FAD F 4932
15
BC6
SOFTWARE
GLN D:106 , CYS D:144 , GLY E:254 , PHE E:255 , GLY E:256 , ARG E:371 , SER E:506 , GLY E:507 , GLN E:508 , HIS E:510 , THR E:513 , TYR E:545 , ALA E:546 , SER E:547 , ARG E:548 , GLY E:549 , ALA E:550 , CYS E:666 , THR E:668 , ILE E:670 , ASN E:671 , VAL E:675 , GLN E:678 , LYS E:739 , GLY E:740 , MET E:741 , GLY E:742 , SMO E:4922 , HOH E:4928 , HOH E:5061
BINDING SITE FOR RESIDUE MCN E 4920
16
BC7
SOFTWARE
GLN A:106 , CYS A:144 , GLY B:253 , GLY B:254 , PHE B:255 , GLY B:256 , ARG B:371 , SER B:506 , GLY B:507 , GLN B:508 , HIS B:510 , THR B:513 , TYR B:545 , ALA B:546 , SER B:547 , ARG B:548 , GLY B:549 , ALA B:550 , CYS B:666 , THR B:668 , ILE B:670 , ASN B:671 , ILE B:674 , VAL B:675 , GLN B:678 , LYS B:739 , GLY B:740 , MET B:741 , GLY B:742 , SMO B:4923 , HOH B:4945 , HOH B:5040
BINDING SITE FOR RESIDUE MCN B 4921
17
BC8
SOFTWARE
GLN E:224 , GLY E:256 , TYR E:370 , ARG E:371 , TYR E:545 , ALA E:546 , GLU E:743 , MCN E:4920 , HOH E:5252
BINDING SITE FOR RESIDUE SMO E 4922
18
BC9
SOFTWARE
GLN B:224 , PHE B:255 , GLY B:256 , TYR B:370 , ARG B:371 , TYR B:545 , ALA B:546 , GLU B:743 , GOL B:3902 , MCN B:4921
BINDING SITE FOR RESIDUE SMO B 4923
19
CC1
SOFTWARE
TRP B:220 , ARG B:247 , ARG E:247
BINDING SITE FOR RESIDUE GOL E 3901
20
CC2
SOFTWARE
ALA B:369 , VAL B:373 , PHE B:375 , ALA B:546 , GLU B:743 , SMO B:4923
BINDING SITE FOR RESIDUE GOL B 3902
21
CC3
SOFTWARE
ALA D:63 , PRO D:64 , SER D:120 , PHE F:78 , GLN F:103 , ASN F:107 , HOH F:5079 , HOH F:5120
BINDING SITE FOR RESIDUE GOL F 3903
22
CC4
SOFTWARE
HOH D:4934 , LEU E:708 , TYR E:711 , LEU E:712 , ILE E:713 , ARG F:186
BINDING SITE FOR RESIDUE GOL E 3904
23
CC5
SOFTWARE
LEU E:692 , ILE E:696 , HOH E:5000 , HOH E:5347 , ARG F:185 , ILE F:257 , HIS F:258 , HOH F:4993
BINDING SITE FOR RESIDUE GOL E 3905
24
CC6
SOFTWARE
ARG B:567 , GLN B:570 , ASP B:621 , HOH B:4970 , HOH B:5141
BINDING SITE FOR RESIDUE GOL B 3906
25
CC7
SOFTWARE
MET A:65 , GLY C:32 , ASN C:107 , ARG C:108 , THR C:110 , HOH C:4941 , HOH C:4946 , HOH C:4992 , HOH C:5149
BINDING SITE FOR RESIDUE GOL C 3907
26
CC8
SOFTWARE
VAL C:143 , ARG C:168
BINDING SITE FOR RESIDUE GOL C 3908
27
CC9
SOFTWARE
SER A:129 , ARG A:130 , HOH A:4923 , HOH A:4999
BINDING SITE FOR RESIDUE GOL A 3909
[
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
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(6, 12)
Info
All SCOP Domains
1a: SCOP_d1t3qa1 (A:88-168)
1b: SCOP_d1t3qd1 (D:88-168)
2a: SCOP_d1t3qb1 (B:1-165)
2b: SCOP_d1t3qe1 (E:1-165)
3a: SCOP_d1t3qa2 (A:7-87)
3b: SCOP_d1t3qd2 (D:7-87)
4a: SCOP_d1t3qc1 (C:177-285)
4b: SCOP_d1t3qf1 (F:177-285)
5a: SCOP_d1t3qc2 (C:1-176)
5b: SCOP_d1t3qf2 (F:1-176)
6a: SCOP_d1t3qb2 (B:166-786)
6b: SCOP_d1t3qe2 (E:166-786)
View:
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Classes
(
)
(
)
Folds
(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
CO dehydrogenase ISP C-domain like
(45)
Superfamily
:
CO dehydrogenase ISP C-domain like
(45)
Family
:
CO dehydrogenase ISP C-domain like
(42)
Protein domain
:
Quinoline 2-oxidoreductase small subunit QorS, C-domain
(1)
Pseudomonas putida [TaxId: 303]
(1)
1a
d1t3qa1
A:88-168
1b
d1t3qd1
D:88-168
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
alpha/beta-Hammerhead
(191)
Superfamily
:
CO dehydrogenase molybdoprotein N-domain-like
(44)
Family
:
CO dehydrogenase molybdoprotein N-domain-like
(34)
Protein domain
:
Quinoline 2-oxidoreductase large subunit QorL, N-domain
(1)
Pseudomonas putida [TaxId: 303]
(1)
2a
d1t3qb1
B:1-165
2b
d1t3qe1
E:1-165
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
2Fe-2S ferredoxin-like
(174)
Family
:
2Fe-2S ferredoxin domains from multidomain proteins
(82)
Protein domain
:
Quinoline 2-oxidoreductase small subunit QorS, N-domain
(1)
Pseudomonas putida [TaxId: 303]
(1)
3a
d1t3qa2
A:7-87
3b
d1t3qd2
D:7-87
Fold
:
CO dehydrogenase flavoprotein C-domain-like
(111)
Superfamily
:
CO dehydrogenase flavoprotein C-terminal domain-like
(35)
Family
:
CO dehydrogenase flavoprotein C-terminal domain-like
(23)
Protein domain
:
Quinoline 2-oxidoreductase medium subunit QorM
(1)
Pseudomonas putida [TaxId: 303]
(1)
4a
d1t3qc1
C:177-285
4b
d1t3qf1
F:177-285
Fold
:
FAD-binding/transporter-associated domain-like
(99)
Superfamily
:
FAD-binding/transporter-associated domain-like
(99)
Family
:
CO dehydrogenase flavoprotein N-terminal domain-like
(33)
Protein domain
:
Quinoline 2-oxidoreductase medium subunit QorM
(1)
Pseudomonas putida [TaxId: 303]
(1)
5a
d1t3qc2
C:1-176
5b
d1t3qf2
F:1-176
Fold
:
Molybdenum cofactor-binding domain
(44)
Superfamily
:
Molybdenum cofactor-binding domain
(44)
Family
:
Molybdenum cofactor-binding domain
(44)
Protein domain
:
Quinoline 2-oxidoreductase large subunit QorL
(1)
Pseudomonas putida [TaxId: 303]
(1)
6a
d1t3qb2
B:166-786
6b
d1t3qe2
E:166-786
[
close SCOP info
]
CATH Domains
(5, 10)
Info
all CATH domains
1a: CATH_1t3qC03 (C:175-285)
1b: CATH_1t3qF03 (F:175-285)
2a: CATH_1t3qC01 (C:1-56)
2b: CATH_1t3qF01 (F:1-56)
3a: CATH_1t3qC02 (C:57-174)
3b: CATH_1t3qF02 (F:57-174)
4a: CATH_1t3qA01 (A:7-87)
4b: CATH_1t3qD01 (D:7-87)
5a: CATH_1t3qA02 (A:88-168)
5b: CATH_1t3qD02 (D:88-168)
View:
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Topologies
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Enolase-like; domain 1
(252)
Homologous Superfamily
:
[code=3.30.390.50, no name defined]
(22)
Pseudomonas putida. Organism_taxid: 303. Strain: 86. Pseudomonas putida. Organism_taxid: 303. Strain: 86.
(1)
1a
1t3qC03
C:175-285
1b
1t3qF03
F:175-285
Topology
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
(50)
Homologous Superfamily
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
(50)
Pseudomonas putida. Organism_taxid: 303. Strain: 86. Pseudomonas putida. Organism_taxid: 303. Strain: 86.
(1)
2a
1t3qC01
C:1-56
2b
1t3qF01
F:1-56
Topology
:
Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
(63)
Homologous Superfamily
:
[code=3.30.465.10, no name defined]
(63)
Pseudomonas putida. Organism_taxid: 303. Strain: 86. Pseudomonas putida. Organism_taxid: 303. Strain: 86.
(1)
3a
1t3qC02
C:57-174
3b
1t3qF02
F:57-174
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.30, no name defined]
(153)
Pseudomonas putida. Organism_taxid: 303. Strain: 86. Pseudomonas putida. Organism_taxid: 303. Strain: 86.
(1)
4a
1t3qA01
A:7-87
4b
1t3qD01
D:7-87
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
[code=1.10.150.120, no name defined]
(29)
Pseudomonas putida. Organism_taxid: 303. Strain: 86. Pseudomonas putida. Organism_taxid: 303. Strain: 86.
(1)
5a
1t3qA02
A:88-168
5b
1t3qD02
D:88-168
[
close CATH info
]
Pfam Domains
(6, 12)
Info
all PFAM domains
1a: PFAM_FAD_binding_5_1t3qF01 (F:4-174)
1b: PFAM_FAD_binding_5_1t3qF02 (F:4-174)
2a: PFAM_Fer2_1t3qD01 (D:14-85)
2b: PFAM_Fer2_1t3qD02 (D:14-85)
3a: PFAM_Fer2_2_1t3qD03 (D:82-156)
3b: PFAM_Fer2_2_1t3qD04 (D:82-156)
4a: PFAM_Ald_Xan_dh_C2_1t3qE01 (E:150-720)
4b: PFAM_Ald_Xan_dh_C2_1t3qE02 (E:150-720)
5a: PFAM_Ald_Xan_dh_C_1t3qE03 (E:28-142)
5b: PFAM_Ald_Xan_dh_C_1t3qE04 (E:28-142)
6a: PFAM_CO_deh_flav_C_1t3qF03 (F:178-279)
6b: PFAM_CO_deh_flav_C_1t3qF04 (F:178-279)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FAD_PCMH
(53)
Family
:
FAD_binding_5
(22)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(1)
1a
FAD_binding_5-1t3qF01
F:4-174
1b
FAD_binding_5-1t3qF02
F:4-174
Clan
:
Fer2
(69)
Family
:
Fer2
(60)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(9)
2a
Fer2-1t3qD01
D:14-85
2b
Fer2-1t3qD02
D:14-85
Family
:
Fer2_2
(24)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(1)
3a
Fer2_2-1t3qD03
D:82-156
3b
Fer2_2-1t3qD04
D:82-156
Clan
:
no clan defined [family: Ald_Xan_dh_C2]
(24)
Family
:
Ald_Xan_dh_C2
(24)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(1)
4a
Ald_Xan_dh_C2-1t3qE01
E:150-720
4b
Ald_Xan_dh_C2-1t3qE02
E:150-720
Clan
:
no clan defined [family: Ald_Xan_dh_C]
(24)
Family
:
Ald_Xan_dh_C
(24)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(1)
5a
Ald_Xan_dh_C-1t3qE03
E:28-142
5b
Ald_Xan_dh_C-1t3qE04
E:28-142
Clan
:
no clan defined [family: CO_deh_flav_C]
(22)
Family
:
CO_deh_flav_C
(22)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(1)
6a
CO_deh_flav_C-1t3qF03
F:178-279
6b
CO_deh_flav_C-1t3qF04
F:178-279
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
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Protein
Nucleic
Backbone
Sidechain
Hetero
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
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Chain B
Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
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(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)
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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") .
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Asym.Unit (439 KB)
Header - Asym.Unit
Biol.Unit 1 (429 KB)
Header - Biol.Unit 1
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