PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
1X0R
Biol. Unit 2
Info
Asym.Unit (448 KB)
Biol.Unit 1 (432 KB)
Biol.Unit 2 (93 KB)
Biol.Unit 3 (95 KB)
Biol.Unit 4 (94 KB)
Biol.Unit 5 (94 KB)
Biol.Unit 6 (94 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THIOREDOXIN PEROXIDASE FROM AEROPYRUM PERNIX K1
Authors
:
T. Nakamura, T. Yamamoto, T. Inoue, H. Matsumura, A. Kobayashi, Y. Hagi K. Uegaki, M. Ataka, Y. Kai, K. Ishikawa
Date
:
28 Mar 05 (Deposition) - 20 Dec 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J (1x)
Biol. Unit 2: G,H (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: I,J (1x)
Biol. Unit 5: C,D (1x)
Biol. Unit 6: A,B (1x)
Keywords
:
Thioredoxin Fold, Peroxiredoxin, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Nakamura, T. Yamamoto, T. Inoue, H. Matsumura, A. Kobayashi, Y. Hagihara, K. Uegaki, M. Ataka, Y. Kai, K. Ishikawa
Crystal Structure Of Thioredoxin Peroxidase From Aerobic Hyperthermophilic Archaeon Aeropyrum Pernix K1
Proteins V. 62 822 2006
[
close entry info
]
Hetero Components
(2, 26)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1aa: 1,2-ETHANEDIOL (EDOaa)
1ab: 1,2-ETHANEDIOL (EDOab)
1ac: 1,2-ETHANEDIOL (EDOac)
1ad: 1,2-ETHANEDIOL (EDOad)
1ae: 1,2-ETHANEDIOL (EDOae)
1af: 1,2-ETHANEDIOL (EDOaf)
1ag: 1,2-ETHANEDIOL (EDOag)
1ah: 1,2-ETHANEDIOL (EDOah)
1ai: 1,2-ETHANEDIOL (EDOai)
1aj: 1,2-ETHANEDIOL (EDOaj)
1ak: 1,2-ETHANEDIOL (EDOak)
1al: 1,2-ETHANEDIOL (EDOal)
1am: 1,2-ETHANEDIOL (EDOam)
1an: 1,2-ETHANEDIOL (EDOan)
1ao: 1,2-ETHANEDIOL (EDOao)
1ap: 1,2-ETHANEDIOL (EDOap)
1aq: 1,2-ETHANEDIOL (EDOaq)
1ar: 1,2-ETHANEDIOL (EDOar)
1as: 1,2-ETHANEDIOL (EDOas)
1at: 1,2-ETHANEDIOL (EDOat)
1au: 1,2-ETHANEDIOL (EDOau)
1av: 1,2-ETHANEDIOL (EDOav)
1aw: 1,2-ETHANEDIOL (EDOaw)
1ax: 1,2-ETHANEDIOL (EDOax)
1ay: 1,2-ETHANEDIOL (EDOay)
1az: 1,2-ETHANEDIOL (EDOaz)
1b: 1,2-ETHANEDIOL (EDOb)
1ba: 1,2-ETHANEDIOL (EDOba)
1bb: 1,2-ETHANEDIOL (EDObb)
1bc: 1,2-ETHANEDIOL (EDObc)
1bd: 1,2-ETHANEDIOL (EDObd)
1be: 1,2-ETHANEDIOL (EDObe)
1bf: 1,2-ETHANEDIOL (EDObf)
1bg: 1,2-ETHANEDIOL (EDObg)
1bh: 1,2-ETHANEDIOL (EDObh)
1bi: 1,2-ETHANEDIOL (EDObi)
1bj: 1,2-ETHANEDIOL (EDObj)
1bk: 1,2-ETHANEDIOL (EDObk)
1bl: 1,2-ETHANEDIOL (EDObl)
1bm: 1,2-ETHANEDIOL (EDObm)
1bn: 1,2-ETHANEDIOL (EDObn)
1bo: 1,2-ETHANEDIOL (EDObo)
1bp: 1,2-ETHANEDIOL (EDObp)
1bq: 1,2-ETHANEDIOL (EDObq)
1br: 1,2-ETHANEDIOL (EDObr)
1bs: 1,2-ETHANEDIOL (EDObs)
1bt: 1,2-ETHANEDIOL (EDObt)
1bu: 1,2-ETHANEDIOL (EDObu)
1bv: 1,2-ETHANEDIOL (EDObv)
1bw: 1,2-ETHANEDIOL (EDObw)
1bx: 1,2-ETHANEDIOL (EDObx)
1by: 1,2-ETHANEDIOL (EDOby)
1bz: 1,2-ETHANEDIOL (EDObz)
1c: 1,2-ETHANEDIOL (EDOc)
1ca: 1,2-ETHANEDIOL (EDOca)
1cb: 1,2-ETHANEDIOL (EDOcb)
1cc: 1,2-ETHANEDIOL (EDOcc)
1cd: 1,2-ETHANEDIOL (EDOcd)
1ce: 1,2-ETHANEDIOL (EDOce)
1cf: 1,2-ETHANEDIOL (EDOcf)
1cg: 1,2-ETHANEDIOL (EDOcg)
1ch: 1,2-ETHANEDIOL (EDOch)
1ci: 1,2-ETHANEDIOL (EDOci)
1cj: 1,2-ETHANEDIOL (EDOcj)
1ck: 1,2-ETHANEDIOL (EDOck)
1cl: 1,2-ETHANEDIOL (EDOcl)
1cm: 1,2-ETHANEDIOL (EDOcm)
1cn: 1,2-ETHANEDIOL (EDOcn)
1co: 1,2-ETHANEDIOL (EDOco)
1cp: 1,2-ETHANEDIOL (EDOcp)
1cq: 1,2-ETHANEDIOL (EDOcq)
1cr: 1,2-ETHANEDIOL (EDOcr)
1cs: 1,2-ETHANEDIOL (EDOcs)
1ct: 1,2-ETHANEDIOL (EDOct)
1cu: 1,2-ETHANEDIOL (EDOcu)
1cv: 1,2-ETHANEDIOL (EDOcv)
1cw: 1,2-ETHANEDIOL (EDOcw)
1cx: 1,2-ETHANEDIOL (EDOcx)
1cy: 1,2-ETHANEDIOL (EDOcy)
1cz: 1,2-ETHANEDIOL (EDOcz)
1d: 1,2-ETHANEDIOL (EDOd)
1da: 1,2-ETHANEDIOL (EDOda)
1db: 1,2-ETHANEDIOL (EDOdb)
1dc: 1,2-ETHANEDIOL (EDOdc)
1dd: 1,2-ETHANEDIOL (EDOdd)
1de: 1,2-ETHANEDIOL (EDOde)
1df: 1,2-ETHANEDIOL (EDOdf)
1dg: 1,2-ETHANEDIOL (EDOdg)
1dh: 1,2-ETHANEDIOL (EDOdh)
1di: 1,2-ETHANEDIOL (EDOdi)
1dj: 1,2-ETHANEDIOL (EDOdj)
1dk: 1,2-ETHANEDIOL (EDOdk)
1dl: 1,2-ETHANEDIOL (EDOdl)
1dm: 1,2-ETHANEDIOL (EDOdm)
1dn: 1,2-ETHANEDIOL (EDOdn)
1do: 1,2-ETHANEDIOL (EDOdo)
1dp: 1,2-ETHANEDIOL (EDOdp)
1dq: 1,2-ETHANEDIOL (EDOdq)
1dr: 1,2-ETHANEDIOL (EDOdr)
1ds: 1,2-ETHANEDIOL (EDOds)
1dt: 1,2-ETHANEDIOL (EDOdt)
1du: 1,2-ETHANEDIOL (EDOdu)
1dv: 1,2-ETHANEDIOL (EDOdv)
1dw: 1,2-ETHANEDIOL (EDOdw)
1dx: 1,2-ETHANEDIOL (EDOdx)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
1n: 1,2-ETHANEDIOL (EDOn)
1o: 1,2-ETHANEDIOL (EDOo)
1p: 1,2-ETHANEDIOL (EDOp)
1q: 1,2-ETHANEDIOL (EDOq)
1r: 1,2-ETHANEDIOL (EDOr)
1s: 1,2-ETHANEDIOL (EDOs)
1t: 1,2-ETHANEDIOL (EDOt)
1u: 1,2-ETHANEDIOL (EDOu)
1v: 1,2-ETHANEDIOL (EDOv)
1w: 1,2-ETHANEDIOL (EDOw)
1x: 1,2-ETHANEDIOL (EDOx)
1y: 1,2-ETHANEDIOL (EDOy)
1z: 1,2-ETHANEDIOL (EDOz)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2ae: SELENOMETHIONINE (MSEae)
2af: SELENOMETHIONINE (MSEaf)
2ag: SELENOMETHIONINE (MSEag)
2ah: SELENOMETHIONINE (MSEah)
2ai: SELENOMETHIONINE (MSEai)
2aj: SELENOMETHIONINE (MSEaj)
2ak: SELENOMETHIONINE (MSEak)
2al: SELENOMETHIONINE (MSEal)
2am: SELENOMETHIONINE (MSEam)
2an: SELENOMETHIONINE (MSEan)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
18
Ligand/Ion
1,2-ETHANEDIOL
2
MSE
8
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(26, 26)
Info
All Sites
01: AC9 (SOFTWARE)
02: BC1 (SOFTWARE)
03: DC9 (SOFTWARE)
04: EC1 (SOFTWARE)
05: EC2 (SOFTWARE)
06: EC8 (SOFTWARE)
07: FC2 (SOFTWARE)
08: FC5 (SOFTWARE)
09: FC9 (SOFTWARE)
10: GC2 (SOFTWARE)
11: GC3 (SOFTWARE)
12: GC4 (SOFTWARE)
13: GC5 (SOFTWARE)
14: GC6 (SOFTWARE)
15: JC2 (SOFTWARE)
16: JC3 (SOFTWARE)
17: KC2 (SOFTWARE)
18: KC3 (SOFTWARE)
19: KC9 (SOFTWARE)
20: LC2 (SOFTWARE)
21: LC3 (SOFTWARE)
22: LC9 (SOFTWARE)
23: MC3 (SOFTWARE)
24: MC4 (SOFTWARE)
25: MC5 (SOFTWARE)
26: MC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC9
SOFTWARE
ARG G:232 , GLU G:235 , HOH G:1164 , GLU H:179
BINDING SITE FOR RESIDUE EDO G 2009
02
BC1
SOFTWARE
GLU G:179 , ARG H:232 , GLU H:235 , HOH H:1165
BINDING SITE FOR RESIDUE EDO H 2010
03
DC9
SOFTWARE
LEU C:163 , LEU C:167 , ALA C:218 , SER C:219 , ASP C:222 , HOH C:2257 , SER H:166
BINDING SITE FOR RESIDUE EDO C 2036
04
EC1
SOFTWARE
THR E:191 , THR F:122 , HIS F:123 , EDO F:2086 , PHE G:80
BINDING SITE FOR RESIDUE EDO F 2037
05
EC2
SOFTWARE
THR F:18 , VAL F:79 , PHE F:80 , HOH F:466 , HIS G:123 , THR H:191
BINDING SITE FOR RESIDUE EDO F 2038
06
EC8
SOFTWARE
VAL H:17 , THR H:18 , ILE H:102 , ALA H:103
BINDING SITE FOR RESIDUE EDO H 2044
07
FC2
SOFTWARE
ARG G:199 , MSE G:200 , SER G:202 , GLY G:203 , GLN G:204 , TYR G:205
BINDING SITE FOR RESIDUE EDO G 2047
08
FC5
SOFTWARE
ALA G:196 , ARG G:197 , MSE G:200 , TRP G:210 , GLU I:87
BINDING SITE FOR RESIDUE EDO G 2050
09
FC9
SOFTWARE
ILE H:83 , GLU H:87 , HOH H:1173 , GLU J:193 , ALA J:196 , ARG J:197
BINDING SITE FOR RESIDUE EDO H 2054
10
GC2
SOFTWARE
THR G:47 , PRO G:48 , VAL G:49 , CYS G:50 , ARG G:126 , MSE G:145 , HOH G:1153
BINDING SITE FOR RESIDUE EDO G 2056
11
GC3
SOFTWARE
ILE G:181 , GLY G:182 , GLU G:183 , LEU H:240
BINDING SITE FOR RESIDUE EDO G 2057
12
GC4
SOFTWARE
LEU G:240 , ILE H:181 , GLY H:182 , GLU H:183
BINDING SITE FOR RESIDUE EDO H 2058
13
GC5
SOFTWARE
VAL H:95 , ARG H:96 , HOH H:1074
BINDING SITE FOR RESIDUE EDO H 2059
14
GC6
SOFTWARE
ARG H:199 , MSE H:200 , SER H:202 , GLY H:203 , GLN H:204 , TYR H:205 , SER H:207 , CYS H:213
BINDING SITE FOR RESIDUE EDO H 2060
15
JC2
SOFTWARE
GLN C:65 , GLY C:68 , EDO C:2084 , GLY H:34 , TRP H:36 , ALA H:133
BINDING SITE FOR RESIDUE EDO C 2083
16
JC3
SOFTWARE
GLN C:33 , GLY C:34 , LYS C:35 , EDO C:2083 , GLY H:34 , GLY H:68 , LYS H:162
BINDING SITE FOR RESIDUE EDO C 2084
17
KC2
SOFTWARE
ALA E:196 , ARG E:197 , TRP E:210 , GLU G:87
BINDING SITE FOR RESIDUE EDO E 2092
18
KC3
SOFTWARE
HIS G:21 , HIS G:29 , TYR G:30
BINDING SITE FOR RESIDUE EDO G 2093
19
KC9
SOFTWARE
THR H:18 , HIS I:123 , HOH I:2135 , THR J:191
BINDING SITE FOR RESIDUE EDO I 2099
20
LC2
SOFTWARE
THR G:191 , HOH G:616 , HIS H:123 , THR I:18
BINDING SITE FOR RESIDUE EDO G 2101
21
LC3
SOFTWARE
GLN G:195 , ARG G:199
BINDING SITE FOR RESIDUE EDO G 2102
22
LC9
SOFTWARE
PRO G:217 , ALA G:218 , SER G:219 , HOH G:800 , ASP J:28 , VAL J:31 , SER J:32 , HOH J:2139 , HOH J:2191
BINDING SITE FOR RESIDUE EDO J 2108
23
MC3
SOFTWARE
GLU G:146 , GLY H:164 , ARG H:169 , HOH H:787
BINDING SITE FOR RESIDUE EDO H 2111
24
MC4
SOFTWARE
GLY G:164 , ASP G:165 , ARG G:169 , HOH G:789
BINDING SITE FOR RESIDUE EDO G 2112
25
MC5
SOFTWARE
HOH C:2229 , TYR H:30 , TYR H:61 , GLN H:65 , ASP H:70 , LEU H:71 , PHE H:99 , PRO H:100
BINDING SITE FOR RESIDUE EDO H 2113
26
MC6
SOFTWARE
SER C:166 , HOH C:2190 , LEU H:163 , PRO H:217 , ALA H:218 , SER H:219 , ASP H:222
BINDING SITE FOR RESIDUE EDO H 2114
[
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: THIOREDOXIN_2 (G:6-163,H:6-163)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THIOREDOXIN_2
PS51352
Thioredoxin domain profile.
TDXH_AERPE
6-163
2
-
-
-
-
-
-
G:6-163
H:6-163
-
-
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 10)
Info
All SCOP Domains
1a: SCOP_d1x0ra1 (A:2-242)
1b: SCOP_d1x0rb_ (B:)
1c: SCOP_d1x0rc_ (C:)
1d: SCOP_d1x0rd_ (D:)
1e: SCOP_d1x0re_ (E:)
1f: SCOP_d1x0rf_ (F:)
1g: SCOP_d1x0rg_ (G:)
1h: SCOP_d1x0rh_ (H:)
1i: SCOP_d1x0ri_ (I:)
1j: SCOP_d1x0rj_ (J:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Thioredoxin fold
(994)
Superfamily
:
Thioredoxin-like
(992)
Family
:
Glutathione peroxidase-like
(136)
Protein domain
:
Peroxiredoxin
(2)
Aeropyrum pernix [TaxId: 56636]
(2)
1a
d1x0ra1
A:2-242
1b
d1x0rb_
B:
1c
d1x0rc_
C:
1d
d1x0rd_
D:
1e
d1x0re_
E:
1f
d1x0rf_
F:
1g
d1x0rg_
G:
1h
d1x0rh_
H:
1i
d1x0ri_
I:
1j
d1x0rj_
J:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 20)
Info
all PFAM domains
1a: PFAM_AhpC_TSA_1x0rJ01 (J:8-140)
1b: PFAM_AhpC_TSA_1x0rJ02 (J:8-140)
1c: PFAM_AhpC_TSA_1x0rJ03 (J:8-140)
1d: PFAM_AhpC_TSA_1x0rJ04 (J:8-140)
1e: PFAM_AhpC_TSA_1x0rJ05 (J:8-140)
1f: PFAM_AhpC_TSA_1x0rJ06 (J:8-140)
1g: PFAM_AhpC_TSA_1x0rJ07 (J:8-140)
1h: PFAM_AhpC_TSA_1x0rJ08 (J:8-140)
1i: PFAM_AhpC_TSA_1x0rJ09 (J:8-140)
1j: PFAM_AhpC_TSA_1x0rJ10 (J:8-140)
2a: PFAM_1_cysPrx_C_1x0rJ11 (J:160-203)
2b: PFAM_1_cysPrx_C_1x0rJ12 (J:160-203)
2c: PFAM_1_cysPrx_C_1x0rJ13 (J:160-203)
2d: PFAM_1_cysPrx_C_1x0rJ14 (J:160-203)
2e: PFAM_1_cysPrx_C_1x0rJ15 (J:160-203)
2f: PFAM_1_cysPrx_C_1x0rJ16 (J:160-203)
2g: PFAM_1_cysPrx_C_1x0rJ17 (J:160-203)
2h: PFAM_1_cysPrx_C_1x0rJ18 (J:160-203)
2i: PFAM_1_cysPrx_C_1x0rJ19 (J:160-203)
2j: PFAM_1_cysPrx_C_1x0rJ20 (J:160-203)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Thioredoxin
(367)
Family
:
AhpC-TSA
(28)
Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
(3)
1a
AhpC-TSA-1x0rJ01
J:8-140
1b
AhpC-TSA-1x0rJ02
J:8-140
1c
AhpC-TSA-1x0rJ03
J:8-140
1d
AhpC-TSA-1x0rJ04
J:8-140
1e
AhpC-TSA-1x0rJ05
J:8-140
1f
AhpC-TSA-1x0rJ06
J:8-140
1g
AhpC-TSA-1x0rJ07
J:8-140
1h
AhpC-TSA-1x0rJ08
J:8-140
1i
AhpC-TSA-1x0rJ09
J:8-140
1j
AhpC-TSA-1x0rJ10
J:8-140
Clan
:
no clan defined [family: 1-cysPrx_C]
(19)
Family
:
1-cysPrx_C
(19)
Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
(3)
2a
1-cysPrx_C-1x0rJ11
J:160-203
2b
1-cysPrx_C-1x0rJ12
J:160-203
2c
1-cysPrx_C-1x0rJ13
J:160-203
2d
1-cysPrx_C-1x0rJ14
J:160-203
2e
1-cysPrx_C-1x0rJ15
J:160-203
2f
1-cysPrx_C-1x0rJ16
J:160-203
2g
1-cysPrx_C-1x0rJ17
J:160-203
2h
1-cysPrx_C-1x0rJ18
J:160-203
2i
1-cysPrx_C-1x0rJ19
J:160-203
2j
1-cysPrx_C-1x0rJ20
J:160-203
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain G
Chain H
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(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)
[
close Script example commands
]
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") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (448 KB)
Header - Asym.Unit
Biol.Unit 1 (432 KB)
Header - Biol.Unit 1
Biol.Unit 2 (93 KB)
Header - Biol.Unit 2
Biol.Unit 3 (95 KB)
Header - Biol.Unit 3
Biol.Unit 4 (94 KB)
Header - Biol.Unit 4
Biol.Unit 5 (94 KB)
Header - Biol.Unit 5
Biol.Unit 6 (94 KB)
Header - Biol.Unit 6
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1X0R
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help