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1G8K
Biol. Unit 5
Info
Asym.Unit (699 KB)
Biol.Unit 1 (180 KB)
Biol.Unit 2 (181 KB)
Biol.Unit 3 (182 KB)
Biol.Unit 4 (182 KB)
Biol.Unit 5 (350 KB)
Biol.Unit 6 (347 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF ARSENITE OXIDASE FROM ALCALIGENES FAECALIS
Authors
:
P. J. Ellis, T. Conrads, R. Hille, P. Kuhn
Date
:
17 Nov 00 (Deposition) - 13 Dec 00 (Release) - 05 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.64
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)
Biol. Unit 5: E,F,G,H (1x)
Biol. Unit 6: A,B,C,D (1x)
Keywords
:
Oxidase, Arsenite, Molybdopterin, [3Fe-4S] Cluster, [2Fe-2S] Cluster, Rieske, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. J. Ellis, T. Conrads, R. Hille, P. Kuhn
Crystal Structure Of The 100 Kda Arsenite Oxidase From Alcaligenes Faecalis In Two Crystal Forms At 1. 64 A And 2. 0 A.
Structure V. 9 125 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 15)
Info
All Hetero Components
1a: MOLYBDENUM(IV) ION (4MOa)
1b: MOLYBDENUM(IV) ION (4MOb)
1c: MOLYBDENUM(IV) ION (4MOc)
1d: MOLYBDENUM(IV) ION (4MOd)
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)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
4a: FE3-S4 CLUSTER (F3Sa)
4b: FE3-S4 CLUSTER (F3Sb)
4c: FE3-S4 CLUSTER (F3Sc)
4d: FE3-S4 CLUSTER (F3Sd)
5a: FE2/S2 (INORGANIC) CLUSTER (FESa)
5b: FE2/S2 (INORGANIC) CLUSTER (FESb)
5c: FE2/S2 (INORGANIC) CLUSTER (FESc)
5d: FE2/S2 (INORGANIC) CLUSTER (FESd)
6a: MERCURY (II) ION (HGa)
6b: MERCURY (II) ION (HGb)
6c: MERCURY (II) ION (HGc)
6d: MERCURY (II) ION (HGd)
6e: MERCURY (II) ION (HGe)
6f: MERCURY (II) ION (HGf)
6g: MERCURY (II) ION (HGg)
6h: MERCURY (II) ION (HGh)
6i: MERCURY (II) ION (HGi)
6j: MERCURY (II) ION (HGj)
6k: MERCURY (II) ION (HGk)
6l: MERCURY (II) ION (HGl)
7a: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDa)
7b: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDb)
7c: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDc)
7d: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDd)
7e: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDe)
7f: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDf)
7g: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDg)
7h: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDh)
8a: OXYGEN ATOM (Oa)
8b: OXYGEN ATOM (Ob)
8c: OXYGEN ATOM (Oc)
8d: OXYGEN ATOM (Od)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4MO
2
Ligand/Ion
MOLYBDENUM(IV) ION
2
CA
-1
Ligand/Ion
CALCIUM ION
3
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
4
F3S
2
Ligand/Ion
FE3-S4 CLUSTER
5
FES
2
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
6
HG
-1
Ligand/Ion
MERCURY (II) ION
7
MGD
4
Ligand/Ion
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINEDINUCLEOTIDE
8
O
-1
Ligand/Ion
OXYGEN ATOM
[
close Hetero Component info
]
Sites
(29, 29)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC2 (SOFTWARE)
06: BC3 (SOFTWARE)
07: BC8 (SOFTWARE)
08: BC9 (SOFTWARE)
09: CC1 (SOFTWARE)
10: CC2 (SOFTWARE)
11: DC6 (SOFTWARE)
12: DC7 (SOFTWARE)
13: DC8 (SOFTWARE)
14: DC9 (SOFTWARE)
15: EC1 (SOFTWARE)
16: EC2 (SOFTWARE)
17: EC3 (SOFTWARE)
18: EC4 (SOFTWARE)
19: EC5 (SOFTWARE)
20: EC6 (SOFTWARE)
21: EC7 (SOFTWARE)
22: EC8 (SOFTWARE)
23: EC9 (SOFTWARE)
24: FC1 (SOFTWARE)
25: FC2 (SOFTWARE)
26: FC3 (SOFTWARE)
27: FC6 (SOFTWARE)
28: FC7 (SOFTWARE)
29: FC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
TYR E:236 , ARG E:822 , HOH E:7484 , CYS F:95
BINDING SITE FOR RESIDUE HG F 6003
02
AC4
SOFTWARE
TYR G:236 , ARG G:822 , CYS H:95 , HOH H:6126
BINDING SITE FOR RESIDUE HG H 6004
03
AC7
SOFTWARE
GLU E:203 , CYS E:204 , TYR E:383 , GLN E:397
BINDING SITE FOR RESIDUE HG E 6007
04
AC8
SOFTWARE
GLU G:203 , CYS G:204 , TYR G:383 , GLN G:397
BINDING SITE FOR RESIDUE HG G 6008
05
BC2
SOFTWARE
CYS E:735 , LYS E:736 , VAL E:740 , HOH E:7118
BINDING SITE FOR RESIDUE HG E 6011
06
BC3
SOFTWARE
CYS G:735 , LYS G:736 , VAL G:740 , HOH G:7061
BINDING SITE FOR RESIDUE HG G 6012
07
BC8
SOFTWARE
GLY E:825 , HOH E:7882 , HOH E:7883 , HOH E:7884 , HOH E:7885 , HOH F:6164 , HOH F:6165
BINDING SITE FOR RESIDUE CA E 5207
08
BC9
SOFTWARE
GLN E:467 , SER E:754 , ASP E:783 , HOH E:7886 , ASP G:129 , HOH G:7853
BINDING SITE FOR RESIDUE CA E 5208
09
CC1
SOFTWARE
GLY G:825 , HOH G:7854 , HOH G:7855 , HOH G:7856 , HOH H:6166 , HOH H:6167 , HOH H:6168
BINDING SITE FOR RESIDUE CA G 5307
10
CC2
SOFTWARE
ASP E:129 , HOH E:7887 , GLN G:467 , SER G:754 , ASP G:783 , HOH G:7857
BINDING SITE FOR RESIDUE CA G 5308
11
DC6
SOFTWARE
GLY E:170 , HIS E:195 , ASN E:196 , LYS E:385 , TRP E:389 , HIS E:423 , GLY E:456 , CYS E:457 , ASN E:458 , THR E:462 , ILE E:513 , ASN E:514 , LEU E:515 , THR E:518 , ALA E:530 , ALA E:531 , ASP E:563 , ASN E:700 , ARG E:702 , GLN E:708 , THR E:709 , TYR E:711 , PHE E:774 , GLN E:781 , THR E:785 , TYR E:797 , LYS E:798 , MGD E:5202 , O E:5203 , 4MO E:5204 , HOH E:7044 , HOH E:7053 , HOH E:7078 , HOH E:7081 , HOH E:7102 , HOH E:7103
BINDING SITE FOR RESIDUE MGD E 5201
12
DC7
SOFTWARE
ARG E:101 , GLY E:232 , ASN E:233 , ASN E:234 , GLU E:237 , SER E:238 , GLN E:239 , VAL E:276 , ASP E:277 , PRO E:278 , ARG E:279 , THR E:281 , GLY E:304 , ASP E:306 , GLU E:384 , LYS E:385 , GLY E:386 , GLY E:422 , HIS E:423 , TRP E:697 , ASN E:699 , GLY E:701 , ARG E:702 , ASN E:703 , ASN E:704 , VAL E:706 , TRP E:707 , GLN E:708 , LYS E:798 , MGD E:5201 , O E:5203 , 4MO E:5204 , HOH E:7029 , HOH E:7047 , HOH E:7095
BINDING SITE FOR RESIDUE MGD E 5202
13
DC8
SOFTWARE
ASN E:196 , LYS E:385 , MGD E:5201 , MGD E:5202 , 4MO E:5204 , HOH E:7162
BINDING SITE FOR RESIDUE O E 5203
14
DC9
SOFTWARE
ARG E:702 , MGD E:5201 , MGD E:5202 , O E:5203
BINDING SITE FOR RESIDUE 4MO E 5204
15
EC1
SOFTWARE
CYS E:21 , CYS E:24 , GLY E:27 , CYS E:28 , TYR E:30 , SER E:99 , ARG E:101 , ASN E:241
BINDING SITE FOR RESIDUE F3S E 5205
16
EC2
SOFTWARE
CYS F:60 , HIS F:62 , MET F:63 , CYS F:78 , HIS F:81 , THR F:83
BINDING SITE FOR RESIDUE FES F 5206
17
EC3
SOFTWARE
GLY G:170 , HIS G:195 , ASN G:196 , LYS G:385 , TRP G:389 , HIS G:423 , GLY G:456 , CYS G:457 , ASN G:458 , ASN G:459 , THR G:462 , ILE G:513 , ASN G:514 , LEU G:515 , THR G:518 , ALA G:530 , ALA G:531 , ASP G:563 , ASN G:700 , ARG G:702 , GLN G:708 , THR G:709 , TYR G:711 , PHE G:774 , GLN G:781 , TYR G:797 , LYS G:798 , MGD G:5302 , O G:5303 , 4MO G:5304 , HOH G:7023 , HOH G:7030 , HOH G:7037 , HOH G:7053 , HOH G:7110 , HOH G:7120
BINDING SITE FOR RESIDUE MGD G 5301
18
EC4
SOFTWARE
ARG G:101 , GLY G:232 , ASN G:233 , ASN G:234 , GLU G:237 , SER G:238 , GLN G:239 , VAL G:276 , ASP G:277 , PRO G:278 , ARG G:279 , THR G:281 , GLY G:304 , ASP G:306 , GLU G:384 , LYS G:385 , GLY G:386 , GLY G:422 , HIS G:423 , TRP G:697 , ASN G:699 , GLY G:701 , ARG G:702 , ASN G:703 , ASN G:704 , VAL G:706 , TRP G:707 , GLN G:708 , LYS G:798 , MGD G:5301 , O G:5303 , 4MO G:5304 , HOH G:7014 , HOH G:7084 , HOH G:7088
BINDING SITE FOR RESIDUE MGD G 5302
19
EC5
SOFTWARE
ASN G:196 , LYS G:385 , MGD G:5301 , MGD G:5302 , 4MO G:5304 , HOH G:7217
BINDING SITE FOR RESIDUE O G 5303
20
EC6
SOFTWARE
ARG G:702 , MGD G:5301 , MGD G:5302 , O G:5303
BINDING SITE FOR RESIDUE 4MO G 5304
21
EC7
SOFTWARE
CYS G:21 , CYS G:24 , GLY G:27 , CYS G:28 , TYR G:30 , SER G:99 , ARG G:101 , ASN G:241
BINDING SITE FOR RESIDUE F3S G 5305
22
EC8
SOFTWARE
CYS H:60 , HIS H:62 , MET H:63 , CYS H:78 , HIS H:81 , THR H:83
BINDING SITE FOR RESIDUE FES H 5306
23
EC9
SOFTWARE
VAL A:92 , VAL A:93 , TYR A:219 , GLU A:220 , HIS A:246 , GLU A:544 , ARG A:546 , HOH A:7052 , ALA F:112
BINDING SITE FOR RESIDUE EDO A 7001
24
FC1
SOFTWARE
VAL C:92 , VAL C:93 , TYR C:219 , GLU C:220 , HIS C:246 , GLU C:544 , ARG C:546 , HOH C:7090 , ALA H:112
BINDING SITE FOR RESIDUE EDO C 7002
25
FC2
SOFTWARE
ALA B:112 , VAL E:92 , VAL E:93 , TYR E:219 , GLU E:220 , HIS E:246 , GLU E:544 , HOH E:7051
BINDING SITE FOR RESIDUE EDO E 7003
26
FC3
SOFTWARE
ALA D:112 , VAL G:92 , VAL G:93 , TYR G:219 , GLU G:220 , HIS G:246 , GLU G:544 , HOH G:7031
BINDING SITE FOR RESIDUE EDO G 7004
27
FC6
SOFTWARE
ASP E:88 , SER E:636 , GLY E:637 , ASN E:638 , ASN E:639 , HOH E:7189 , HOH E:7248
BINDING SITE FOR RESIDUE EDO E 7007
28
FC7
SOFTWARE
ASP G:88 , SER G:636 , GLY G:637 , ASN G:638 , ASN G:639 , HOH G:7172 , HOH G:7240
BINDING SITE FOR RESIDUE EDO G 7008
29
FC8
SOFTWARE
ARG C:450 , GLN C:504 , ASP E:392 , VAL E:395 , ASP E:790 , ARG E:791 , HOH E:7494
BINDING SITE FOR RESIDUE EDO E 7009
[
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
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: RIESKE (F:20-116,H:20-116)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
AIOB_ALCFA
62-158
2
-
-
F:20-116
H:20-116
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 12)
Info
All SCOP Domains
1a: SCOP_d1g8ka1 (A:683-825)
1b: SCOP_d1g8kc1 (C:683-825)
1c: SCOP_d1g8ke1 (E:683-825)
1d: SCOP_d1g8kg1 (G:683-825)
2a: SCOP_d1g8kb_ (B:)
2b: SCOP_d1g8kd_ (D:)
2c: SCOP_d1g8kf_ (F:)
2d: SCOP_d1g8kh_ (H:)
3a: SCOP_d1g8ka2 (A:4-682)
3b: SCOP_d1g8kc2 (C:4-682)
3c: SCOP_d1g8ke2 (E:4-682)
3d: SCOP_d1g8kg2 (G:4-682)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double psi beta-barrel
(111)
Superfamily
:
ADC-like
(88)
Family
:
Formate dehydrogenase/DMSO reductase, C-terminal domain
(41)
Protein domain
:
Arsenite oxidase large subunit
(2)
Alcaligenes faecalis [TaxId: 511]
(2)
1a
d1g8ka1
A:683-825
1b
d1g8kc1
C:683-825
1c
d1g8ke1
E:683-825
1d
d1g8kg1
G:683-825
Fold
:
ISP domain
(115)
Superfamily
:
ISP domain
(115)
Family
:
Rieske iron-sulfur protein (ISP)
(50)
Protein domain
:
Arsenite oxidase Rieske subunit
(2)
Alcaligenes faecalis [TaxId: 511]
(2)
2a
d1g8kb_
B:
2b
d1g8kd_
D:
2c
d1g8kf_
F:
2d
d1g8kh_
H:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Superfamily
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Family
:
Formate dehydrogenase/DMSO reductase, domains 1-3
(53)
Protein domain
:
Arsenite oxidase large subunit
(2)
Alcaligenes faecalis [TaxId: 511]
(2)
3a
d1g8ka2
A:4-682
3b
d1g8kc2
C:4-682
3c
d1g8ke2
E:4-682
3d
d1g8kg2
G:4-682
[
close SCOP info
]
CATH Domains
(4, 16)
Info
all CATH domains
1a: CATH_1g8kA03 (A:202-423,A:658-682)
1b: CATH_1g8kC03 (C:202-423,C:658-682)
1c: CATH_1g8kE03 (E:202-423,E:658-682)
1d: CATH_1g8kG03 (G:202-423,G:658-682)
2a: CATH_1g8kA02 (A:120-201,A:424-531,A:559-621)
2b: CATH_1g8kE02 (E:120-201,E:424-531,E:559-621)
2c: CATH_1g8kG02 (G:120-201,G:424-531,G:559-621)
2d: CATH_1g8kC02 (C:120-201,C:424-657)
3a: CATH_1g8kB00 (B:1-133)
3b: CATH_1g8kD00 (D:1-133)
3c: CATH_1g8kF00 (F:1-133)
3d: CATH_1g8kH00 (H:1-133)
4a: CATH_1g8kA04 (A:683-817)
4b: CATH_1g8kE04 (E:683-817)
4c: CATH_1g8kG04 (G:683-817)
4d: CATH_1g8kC04 (C:683-825)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Dimethylsulfoxide Reductase; domain 2
(37)
Homologous Superfamily
:
Dimethylsulfoxide Reductase, domain 2
(37)
Alcaligenes faecalis. Organism_taxid: 511. Strain: ncib 8687.
(2)
1a
1g8kA03
A:202-423,A:658-682
1b
1g8kC03
C:202-423,C:658-682
1c
1g8kE03
E:202-423,E:658-682
1d
1g8kG03
G:202-423,G:658-682
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.740, no name defined]
(37)
Alcaligenes faecalis. Organism_taxid: 511. Strain: ncib 8687.
(2)
2a
1g8kA02
A:120-201,A:424-531,A:559-621
2b
1g8kE02
E:120-201,E:424-531,E:559-621
2c
1g8kG02
G:120-201,G:424-531,G:559-621
2d
1g8kC02
C:120-201,C:424-657
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Alcaligenes faecalis. Organism_taxid: 511. Strain: ncib 8687.
(2)
3a
1g8kB00
B:1-133
3b
1g8kD00
D:1-133
3c
1g8kF00
F:1-133
3d
1g8kH00
H:1-133
Architecture
:
Beta Barrel
(4804)
Topology
:
Barwin-like endoglucanases
(75)
Homologous Superfamily
:
[code=2.40.40.20, no name defined]
(63)
Alcaligenes faecalis. Organism_taxid: 511. Strain: ncib 8687.
(2)
4a
1g8kA04
A:683-817
4b
1g8kE04
E:683-817
4c
1g8kG04
G:683-817
4d
1g8kC04
C:683-825
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Atom Selection
(currently selected atoms:
all
)
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Protein & NOT PROSITE
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Chain G
Chain H
Asymmetric Unit 1
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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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View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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