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1WPG
Asym. Unit
Info
Asym.Unit (651 KB)
Biol.Unit 1 (642 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE SR CA2+-ATPASE WITH MGF4
Authors
:
C. Toyoshima, H. Nomura, T. Tsuda
Date
:
02 Sep 04 (Deposition) - 05 Oct 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Membrane Protein, P-Type Atpase, Had Fold, Hydrolase, Hydrolase- Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Toyoshima, H. Nomura, T. Tsuda
Lumenal Gating Mechanism Revealed In Calcium Pump Crystal Structures With Phosphate Analogues
Nature V. 432 361 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 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)
2a: TETRAFLUOROMAGNESATE(2-) (MF4a)
2b: TETRAFLUOROMAGNESATE(2-) (MF4b)
2c: TETRAFLUOROMAGNESATE(2-) (MF4c)
2d: TETRAFLUOROMAGNESATE(2-) (MF4d)
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)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
5a: OCTANOIC ACID [3S-[3ALPHA, 3ABETA,... (TG1a)
5b: OCTANOIC ACID [3S-[3ALPHA, 3ABETA,... (TG1b)
5c: OCTANOIC ACID [3S-[3ALPHA, 3ABETA,... (TG1c)
5d: OCTANOIC ACID [3S-[3ALPHA, 3ABETA,... (TG1d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
4
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
MF4
4
Ligand/Ion
TETRAFLUOROMAGNESATE(2-)
3
MG
8
Ligand/Ion
MAGNESIUM ION
4
NA
4
Ligand/Ion
SODIUM ION
5
TG1
4
Ligand/Ion
OCTANOIC ACID [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA,6ABETA, 7BETA, 8ALPHA(Z), 9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OXY]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER
[
close Hetero Component info
]
Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:351 , THR A:353 , ASP A:703 , MF4 A:998 , HOH A:2100 , HOH A:2105
BINDING SITE FOR RESIDUE MG A 997
02
AC2
SOFTWARE
ASP B:351 , THR B:353 , ASP B:703 , MF4 B:1098 , HOH B:3100 , HOH B:3105
BINDING SITE FOR RESIDUE MG B 997
03
AC3
SOFTWARE
ASP C:351 , THR C:353 , ASP C:703 , MF4 C:1198 , HOH C:4100 , HOH C:4105
BINDING SITE FOR RESIDUE MG C 997
04
AC4
SOFTWARE
ASP D:351 , THR D:353 , ASP D:703 , MF4 D:1298 , HOH D:5100 , HOH D:5105
BINDING SITE FOR RESIDUE MG D 997
05
AC5
SOFTWARE
LYS A:205 , ADP A:1002
BINDING SITE FOR RESIDUE MG A 1001
06
AC6
SOFTWARE
ADP B:1102
BINDING SITE FOR RESIDUE MG B 1101
07
AC7
SOFTWARE
ADP C:1202
BINDING SITE FOR RESIDUE MG C 1201
08
AC8
SOFTWARE
LYS D:205 , ADP D:1302
BINDING SITE FOR RESIDUE MG D 1301
09
AC9
SOFTWARE
LEU A:711 , LYS A:712 , ALA A:714 , GLU A:732 , HOH A:2127
BINDING SITE FOR RESIDUE NA A 1000
10
BC1
SOFTWARE
GLN B:244 , LEU B:711 , LYS B:712 , ALA B:714 , GLU B:732 , HOH B:3127
BINDING SITE FOR RESIDUE NA B 1100
11
BC2
SOFTWARE
GLN C:244 , LEU C:711 , LYS C:712 , ALA C:714 , GLU C:732 , HOH C:4127
BINDING SITE FOR RESIDUE NA C 1200
12
BC3
SOFTWARE
LEU D:711 , LYS D:712 , ALA D:714 , GLU D:732 , HOH D:5127
BINDING SITE FOR RESIDUE NA D 1300
13
BC4
SOFTWARE
THR A:181 , GLY A:182 , GLU A:183 , ASP A:351 , LYS A:352 , THR A:353 , THR A:625 , GLY A:626 , ASP A:627 , LYS A:684 , ASN A:706 , MG A:997 , HOH A:2100 , HOH A:2105
BINDING SITE FOR RESIDUE MF4 A 998
14
BC5
SOFTWARE
ILE A:188 , LYS A:205 , PHE A:487 , MET A:494 , LYS A:515 , GLY A:516 , ARG A:560 , LEU A:562 , MG A:1001 , HOH A:2030 , HOH A:2046 , HOH A:2053
BINDING SITE FOR RESIDUE ADP A 1002
15
BC6
SOFTWARE
GLU A:255 , GLN A:259 , LEU A:260 , VAL A:263 , ALA A:306 , ILE A:765 , ASN A:768 , LEU A:828 , ILE A:829 , PHE A:834 , TYR A:837 , MET A:838
BINDING SITE FOR RESIDUE TG1 A 1003
16
BC7
SOFTWARE
THR B:181 , GLY B:182 , GLU B:183 , ASP B:351 , LYS B:352 , THR B:353 , THR B:625 , GLY B:626 , ASP B:627 , LYS B:684 , ASN B:706 , MG B:997 , HOH B:3100 , HOH B:3105
BINDING SITE FOR RESIDUE MF4 B 1098
17
BC8
SOFTWARE
LYS B:205 , PHE B:487 , MET B:494 , LYS B:515 , LEU B:562 , MG B:1101 , HOH B:3030 , HOH B:3046 , HOH B:3053
BINDING SITE FOR RESIDUE ADP B 1102
18
BC9
SOFTWARE
GLU B:255 , PHE B:256 , GLN B:259 , LEU B:260 , VAL B:263 , ALA B:306 , ASN B:768 , VAL B:769 , LEU B:828 , ILE B:829 , PHE B:834 , TYR B:837 , MET B:838
BINDING SITE FOR RESIDUE TG1 B 1103
19
CC1
SOFTWARE
THR C:181 , GLY C:182 , GLU C:183 , ASP C:351 , LYS C:352 , THR C:353 , THR C:625 , GLY C:626 , ASP C:627 , LYS C:684 , ASN C:706 , MG C:997 , HOH C:4100 , HOH C:4105
BINDING SITE FOR RESIDUE MF4 C 1198
20
CC2
SOFTWARE
LYS C:205 , PHE C:487 , MET C:494 , LYS C:515 , GLY C:516 , LEU C:562 , MG C:1201 , HOH C:4030 , HOH C:4046 , HOH C:4053
BINDING SITE FOR RESIDUE ADP C 1202
21
CC3
SOFTWARE
GLU C:255 , PHE C:256 , GLN C:259 , LEU C:260 , VAL C:263 , ALA C:306 , ASN C:768 , VAL C:769 , LEU C:828 , ILE C:829 , PHE C:834 , TYR C:837 , MET C:838
BINDING SITE FOR RESIDUE TG1 C 1203
22
CC4
SOFTWARE
THR D:181 , GLY D:182 , GLU D:183 , ASP D:351 , LYS D:352 , THR D:353 , THR D:625 , GLY D:626 , ASP D:627 , LYS D:684 , ASN D:706 , MG D:997 , HOH D:5100 , HOH D:5105
BINDING SITE FOR RESIDUE MF4 D 1298
23
CC5
SOFTWARE
ILE D:188 , LYS D:205 , PHE D:487 , MET D:494 , LYS D:515 , GLY D:516 , ARG D:560 , LEU D:562 , MG D:1301 , HOH D:5030 , HOH D:5046 , HOH D:5047 , HOH D:5053
BINDING SITE FOR RESIDUE ADP D 1302
24
CC6
SOFTWARE
GLU D:255 , GLN D:259 , LEU D:260 , VAL D:263 , ALA D:306 , ILE D:765 , ASN D:768 , LEU D:828 , ILE D:829 , PHE D:834 , TYR D:837 , MET D:838
BINDING SITE FOR RESIDUE TG1 D 1303
[
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
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ATPASE_E1_E2 (A:351-357,B:351-357,C:351-357,D:35...)
;
View:
Select:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ATPASE_E1_E2
PS00154
E1-E2 ATPases phosphorylation site.
AT2A1_RABIT
351-357
4
A:351-357
B:351-357
C:351-357
D:351-357
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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
(4, 16)
Info
All SCOP Domains
1a: SCOP_d1wpga1 (A:125-239)
1b: SCOP_d1wpgb1 (B:125-239)
1c: SCOP_d1wpgc1 (C:125-239)
1d: SCOP_d1wpgd1 (D:125-239)
2a: SCOP_d1wpga3 (A:361-599)
2b: SCOP_d1wpgb3 (B:361-599)
2c: SCOP_d1wpgc3 (C:361-599)
2d: SCOP_d1wpgd3 (D:361-599)
3a: SCOP_d1wpga2 (A:344-360,A:600-750)
3b: SCOP_d1wpgb2 (B:344-360,B:600-750)
3c: SCOP_d1wpgc2 (C:344-360,C:600-750)
3d: SCOP_d1wpgd2 (D:344-360,D:600-750)
4a: SCOP_d1wpga4 (A:1-124,A:240-343,A:751-994)
4b: SCOP_d1wpgb4 (B:1-124,B:240-343,B:751-994)
4c: SCOP_d1wpgc4 (C:1-124,C:240-343,C:751-994)
4d: SCOP_d1wpgd4 (D:1-124,D:240-343,D:751-994)
View:
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Classes
(
)
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)
Folds
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Superfamilies
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)
(
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Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double-stranded beta-helix
(580)
Superfamily
:
Calcium ATPase, transduction domain A
(37)
Family
:
Calcium ATPase, transduction domain A
(37)
Protein domain
:
Calcium ATPase, transduction domain A
(37)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(37)
1a
d1wpga1
A:125-239
1b
d1wpgb1
B:125-239
1c
d1wpgc1
C:125-239
1d
d1wpgd1
D:125-239
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Metal cation-transporting ATPase, ATP-binding domain N
(45)
Superfamily
:
Metal cation-transporting ATPase, ATP-binding domain N
(45)
Family
:
Metal cation-transporting ATPase, ATP-binding domain N
(45)
Protein domain
:
Calcium ATPase
(37)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(37)
2a
d1wpga3
A:361-599
2b
d1wpgb3
B:361-599
2c
d1wpgc3
C:361-599
2d
d1wpgd3
D:361-599
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
HAD-like
(349)
Superfamily
:
HAD-like
(349)
Family
:
Meta-cation ATPase, catalytic domain P
(38)
Protein domain
:
Calcium ATPase, catalytic domain P
(37)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(37)
3a
d1wpga2
A:344-360,A:600-750
3b
d1wpgb2
B:344-360,B:600-750
3c
d1wpgc2
C:344-360,C:600-750
3d
d1wpgd2
D:344-360,D:600-750
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Calcium ATPase, transmembrane domain M
(37)
Superfamily
:
Calcium ATPase, transmembrane domain M
(37)
Family
:
Calcium ATPase, transmembrane domain M
(37)
Protein domain
:
Calcium ATPase, transmembrane domain M
(37)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(37)
4a
d1wpga4
A:1-124,A:240-343,A:751-994
4b
d1wpgb4
B:1-124,B:240-343,B:751-994
4c
d1wpgc4
C:1-124,C:240-343,C:751-994
4d
d1wpgd4
D:1-124,D:240-343,D:751-994
[
close SCOP info
]
CATH Domains
(4, 16)
Info
all CATH domains
1a: CATH_1wpgA03 (A:359-602)
1b: CATH_1wpgB03 (B:359-602)
1c: CATH_1wpgC03 (C:359-602)
1d: CATH_1wpgD03 (D:359-602)
2a: CATH_1wpgA04 (A:346-358,A:603-745)
2b: CATH_1wpgB04 (B:346-358,B:603-745)
2c: CATH_1wpgC04 (C:346-358,C:603-745)
2d: CATH_1wpgD04 (D:346-358,D:603-745)
3a: CATH_1wpgB02 (B:56-112,B:241-345,B:746-994)
3b: CATH_1wpgC02 (C:56-112,C:241-345,C:746-994)
3c: CATH_1wpgA02 (A:52-110,A:221-345,A:746-994)
3d: CATH_1wpgD02 (D:52-110,D:221-345,D:746-994)
4a: CATH_1wpgB01 (B:12-55,B:113-240)
4b: CATH_1wpgC01 (C:12-55,C:113-240)
4c: CATH_1wpgA01 (A:9-51,A:111-220)
4d: CATH_1wpgD01 (D:9-51,D:111-220)
View:
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Classes
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)
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Architectures
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Calcium-transporting ATPase, cytoplasmic domain N
(43)
Homologous Superfamily
:
Calcium-transporting ATPase, cytoplasmic domain N
(43)
Rabbit (Oryctolagus cuniculus)
(31)
1a
1wpgA03
A:359-602
1b
1wpgB03
B:359-602
1c
1wpgC03
C:359-602
1d
1wpgD03
D:359-602
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1000, no name defined]
(211)
Rabbit (Oryctolagus cuniculus)
(31)
2a
1wpgA04
A:346-358,A:603-745
2b
1wpgB04
B:346-358,B:603-745
2c
1wpgC04
C:346-358,C:603-745
2d
1wpgD04
D:346-358,D:603-745
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Calcium-transporting ATPase, transmembrane domain
(36)
Homologous Superfamily
:
Calcium-transporting ATPase, transmembrane domain
(36)
Rabbit (Oryctolagus cuniculus)
(31)
3a
1wpgB02
B:56-112,B:241-345,B:746-994
3b
1wpgC02
C:56-112,C:241-345,C:746-994
3c
1wpgA02
A:52-110,A:221-345,A:746-994
3d
1wpgD02
D:52-110,D:221-345,D:746-994
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Calcium-transporting ATPase, cytoplasmic transduction domain A
(35)
Homologous Superfamily
:
Calcium-transporting ATPase, cytoplasmic transduction domain A
(35)
Rabbit (Oryctolagus cuniculus)
(31)
4a
1wpgB01
B:12-55,B:113-240
4b
1wpgC01
C:12-55,C:113-240
4c
1wpgA01
A:9-51,A:111-220
4d
1wpgD01
D:9-51,D:111-220
[
close CATH info
]
Pfam Domains
(4, 16)
Info
all PFAM domains
1a: PFAM_Hydrolase_1wpgD01 (D:345-715)
1b: PFAM_Hydrolase_1wpgD02 (D:345-715)
1c: PFAM_Hydrolase_1wpgD03 (D:345-715)
1d: PFAM_Hydrolase_1wpgD04 (D:345-715)
2a: PFAM_Cation_ATPase_C_1wpgD05 (D:784-987)
2b: PFAM_Cation_ATPase_C_1wpgD06 (D:784-987)
2c: PFAM_Cation_ATPase_C_1wpgD07 (D:784-987)
2d: PFAM_Cation_ATPase_C_1wpgD08 (D:784-987)
3a: PFAM_Cation_ATPase_N_1wpgD09 (D:4-72)
3b: PFAM_Cation_ATPase_N_1wpgD10 (D:4-72)
3c: PFAM_Cation_ATPase_N_1wpgD11 (D:4-72)
3d: PFAM_Cation_ATPase_N_1wpgD12 (D:4-72)
4a: PFAM_E1_E2_ATPase_1wpgD13 (D:93-341)
4b: PFAM_E1_E2_ATPase_1wpgD14 (D:93-341)
4c: PFAM_E1_E2_ATPase_1wpgD15 (D:93-341)
4d: PFAM_E1_E2_ATPase_1wpgD16 (D:93-341)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HAD
(186)
Family
:
Hydrolase
(64)
Oryctolagus cuniculus (Rabbit)
(16)
1a
Hydrolase-1wpgD01
D:345-715
1b
Hydrolase-1wpgD02
D:345-715
1c
Hydrolase-1wpgD03
D:345-715
1d
Hydrolase-1wpgD04
D:345-715
Clan
:
no clan defined [family: Cation_ATPase_C]
(21)
Family
:
Cation_ATPase_C
(21)
Oryctolagus cuniculus (Rabbit)
(17)
2a
Cation_ATPase_C-1wpgD05
D:784-987
2b
Cation_ATPase_C-1wpgD06
D:784-987
2c
Cation_ATPase_C-1wpgD07
D:784-987
2d
Cation_ATPase_C-1wpgD08
D:784-987
Clan
:
no clan defined [family: Cation_ATPase_N]
(22)
Family
:
Cation_ATPase_N
(22)
Oryctolagus cuniculus (Rabbit)
(17)
3a
Cation_ATPase_N-1wpgD09
D:4-72
3b
Cation_ATPase_N-1wpgD10
D:4-72
3c
Cation_ATPase_N-1wpgD11
D:4-72
3d
Cation_ATPase_N-1wpgD12
D:4-72
Clan
:
no clan defined [family: E1-E2_ATPase]
(23)
Family
:
E1-E2_ATPase
(23)
Oryctolagus cuniculus (Rabbit)
(17)
4a
E1-E2_ATPase-1wpgD13
D:93-341
4b
E1-E2_ATPase-1wpgD14
D:93-341
4c
E1-E2_ATPase-1wpgD15
D:93-341
4d
E1-E2_ATPase-1wpgD16
D:93-341
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
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Protein
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Backbone
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Protein & NOT Site
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Chain C
Chain D
Asymmetric Unit 1
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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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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 (651 KB)
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Biol.Unit 1 (642 KB)
Header - Biol.Unit 1
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