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1UPM
Asym. Unit
Info
Asym.Unit (818 KB)
Biol.Unit 1 (806 KB)
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(1)
Title
:
ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT AND CA2+.
Authors
:
S. Karkehabadi, T. C. Taylor, I. Andersson
Date
:
08 Oct 03 (Deposition) - 14 Oct 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : B,C,E,F,H,I,K,L,M,O,P,R,S,T,V,W
Biol. Unit 1: B,C,E,F,H,I,K,L,M,O,P,R,S,T,V,W (1x)
Keywords
:
Lyase, Carbon-Carbon, Oxidoreductase, Photosynthesis, Carbon-Dioxide Fixation Lyase (Carbon-Carbon)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Karkehabadi, T. C. Taylor, I. Andersson
Calcium Supports Loop Closure But Not Catalysis In Rubisco
J. Mol. Biol. V. 334 65 2003
[
close entry info
]
Hetero Components
(3, 24)
Info
All Hetero Components
2a: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPa)
2b: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPb)
2c: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPc)
2d: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPd)
2e: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPe)
2f: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPf)
2g: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPg)
2h: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPh)
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
3a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
3b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
3c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
3d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
3e: LYSINE NZ-CARBOXYLIC ACID (KCXe)
3f: LYSINE NZ-CARBOXYLIC ACID (KCXf)
3g: LYSINE NZ-CARBOXYLIC ACID (KCXg)
3h: LYSINE NZ-CARBOXYLIC ACID (KCXh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
8
Ligand/Ion
CALCIUM ION
2
CAP
8
Ligand/Ion
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
3
KCX
8
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS B:177 , KCX B:201 , ASP B:203 , GLU B:204 , CAP B:477
BINDING SITE FOR RESIDUE CA B 476
02
AC2
SOFTWARE
LYS E:177 , KCX E:201 , ASP E:203 , GLU E:204 , CAP E:477
BINDING SITE FOR RESIDUE CA E 476
03
AC3
SOFTWARE
LYS H:177 , KCX H:201 , ASP H:203 , GLU H:204 , CAP H:477
BINDING SITE FOR RESIDUE CA H 476
04
AC4
SOFTWARE
LYS K:177 , KCX K:201 , ASP K:203 , GLU K:204 , CAP K:477
BINDING SITE FOR RESIDUE CA K 476
05
AC5
SOFTWARE
LYS L:177 , KCX L:201 , ASP L:203 , GLU L:204 , CAP L:477
BINDING SITE FOR RESIDUE CA L 476
06
AC6
SOFTWARE
LYS O:177 , KCX O:201 , ASP O:203 , GLU O:204 , CAP O:477
BINDING SITE FOR RESIDUE CA O 476
07
AC7
SOFTWARE
LYS R:177 , KCX R:201 , ASP R:203 , GLU R:204 , CAP R:477
BINDING SITE FOR RESIDUE CA R 476
08
AC8
SOFTWARE
LYS V:177 , KCX V:201 , ASP V:203 , GLU V:204 , CAP V:477
BINDING SITE FOR RESIDUE CA V 476
09
AC9
SOFTWARE
THR B:173 , LYS B:175 , LYS B:177 , KCX B:201 , HIS B:294 , ARG B:295 , HIS B:327 , LYS B:334 , LEU B:335 , SER B:379 , GLY B:380 , GLY B:381 , GLY B:403 , GLY B:404 , CA B:476 , HOH B:2119 , HOH B:2222 , HOH B:2259 , HOH B:2260 , HOH B:2261 , HOH B:2262 , HOH B:2263 , GLU L:60 , THR L:65 , TRP L:66 , ASN L:123
BINDING SITE FOR RESIDUE CAP B 477
10
BC1
SOFTWARE
THR E:173 , LYS E:175 , LYS E:177 , KCX E:201 , GLU E:204 , HIS E:294 , ARG E:295 , HIS E:327 , LYS E:334 , LEU E:335 , SER E:379 , GLY E:380 , GLY E:381 , GLY E:403 , GLY E:404 , CA E:476 , HOH E:2110 , HOH E:2180 , HOH E:2226 , HOH E:2228 , HOH E:2295 , HOH E:2296 , HOH E:2297 , GLU H:60 , THR H:65 , TRP H:66 , ASN H:123
BINDING SITE FOR RESIDUE CAP E 477
11
BC2
SOFTWARE
GLU E:60 , THR E:65 , TRP E:66 , ASN E:123 , HOH E:2040 , THR H:173 , LYS H:175 , LYS H:177 , KCX H:201 , GLU H:204 , HIS H:294 , ARG H:295 , HIS H:327 , LYS H:334 , LEU H:335 , SER H:379 , GLY H:380 , GLY H:381 , GLY H:403 , GLY H:404 , CA H:476 , HOH H:2112 , HOH H:2168 , HOH H:2211 , HOH H:2212 , HOH H:2221 , HOH H:2245 , HOH H:2246
BINDING SITE FOR RESIDUE CAP H 477
12
BC3
SOFTWARE
THR K:173 , LYS K:175 , LYS K:177 , KCX K:201 , HIS K:294 , ARG K:295 , HIS K:327 , LYS K:334 , LEU K:335 , SER K:379 , GLY K:380 , GLY K:381 , GLY K:403 , GLY K:404 , CA K:476 , HOH K:2112 , HOH K:2170 , HOH K:2220 , HOH K:2221 , HOH K:2276 , HOH K:2277 , HOH K:2278 , GLU O:60 , THR O:65 , TRP O:66 , ASN O:123
BINDING SITE FOR RESIDUE CAP K 477
13
BC4
SOFTWARE
GLU B:60 , THR B:65 , TRP B:66 , ASN B:123 , THR L:173 , LYS L:175 , LYS L:177 , KCX L:201 , HIS L:294 , ARG L:295 , HIS L:327 , LYS L:334 , LEU L:335 , SER L:379 , GLY L:380 , GLY L:381 , GLY L:403 , GLY L:404 , CA L:476 , HOH L:2123 , HOH L:2185 , HOH L:2188 , HOH L:2305 , HOH L:2306 , HOH L:2307 , HOH L:2308
BINDING SITE FOR RESIDUE CAP L 477
14
BC5
SOFTWARE
GLU K:60 , THR K:65 , TRP K:66 , ASN K:123 , THR O:173 , LYS O:175 , LYS O:177 , KCX O:201 , GLU O:204 , HIS O:294 , ARG O:295 , HIS O:327 , LYS O:334 , LEU O:335 , SER O:379 , GLY O:380 , GLY O:381 , GLY O:403 , GLY O:404 , CA O:476 , HOH O:2117 , HOH O:2220 , HOH O:2229 , HOH O:2258 , HOH O:2259 , HOH O:2260 , HOH O:2261
BINDING SITE FOR RESIDUE CAP O 477
15
BC6
SOFTWARE
THR R:173 , LYS R:175 , LYS R:177 , KCX R:201 , HIS R:294 , ARG R:295 , HIS R:327 , LYS R:334 , LEU R:335 , SER R:379 , GLY R:380 , GLY R:381 , GLY R:403 , GLY R:404 , CA R:476 , HOH R:2115 , HOH R:2177 , HOH R:2179 , HOH R:2227 , HOH R:2289 , HOH R:2290 , GLU V:60 , THR V:65 , TRP V:66 , ASN V:123 , HOH V:2093
BINDING SITE FOR RESIDUE CAP R 477
16
BC7
SOFTWARE
GLU R:60 , THR R:65 , TRP R:66 , ASN R:123 , HOH R:2044 , THR V:173 , LYS V:175 , LYS V:177 , KCX V:201 , HIS V:294 , ARG V:295 , HIS V:327 , LYS V:334 , LEU V:335 , SER V:379 , GLY V:380 , GLY V:381 , GLY V:403 , GLY V:404 , CA V:476 , HOH V:2121 , HOH V:2182 , HOH V:2235 , HOH V:2271 , HOH V:2272 , HOH V:2273 , HOH V:2274
BINDING SITE FOR RESIDUE CAP V 477
[
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
(1, 8)
Info
All PROSITE Patterns/Profiles
1: RUBISCO_LARGE (B:196-204,E:196-204,H:196-204,K:19...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RUBISCO_LARGE
PS00157
Ribulose bisphosphate carboxylase large chain active site.
RBL_SPIOL
196-204
8
B:196-204
E:196-204
H:196-204
K:196-204
L:196-204
O:196-204
R:196-204
V:196-204
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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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
(3, 24)
Info
All SCOP Domains
1a: SCOP_d1upmb1 (B:9-147)
1b: SCOP_d1upme1 (E:9-147)
1c: SCOP_d1upmh1 (H:9-147)
1d: SCOP_d1upmk1 (K:9-147)
1e: SCOP_d1upml1 (L:9-147)
1f: SCOP_d1upmo1 (O:9-147)
1g: SCOP_d1upmr1 (R:9-147)
1h: SCOP_d1upmv1 (V:9-147)
2a: SCOP_d1upmc_ (C:)
2b: SCOP_d1upmf_ (F:)
2c: SCOP_d1upmi_ (I:)
2d: SCOP_d1upmm_ (M:)
2e: SCOP_d1upmp_ (P:)
2f: SCOP_d1upms_ (S:)
2g: SCOP_d1upmt_ (T:)
2h: SCOP_d1upmw_ (W:)
3a: SCOP_d1upmb2 (B:148-475)
3b: SCOP_d1upme2 (E:148-475)
3c: SCOP_d1upmh2 (H:148-475)
3d: SCOP_d1upmk2 (K:148-475)
3e: SCOP_d1upml2 (L:148-475)
3f: SCOP_d1upmo2 (O:148-475)
3g: SCOP_d1upmr2 (R:148-475)
3h: SCOP_d1upmv2 (V:148-475)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
RuBisCO, large subunit, small (N-terminal) domain
(66)
Family
:
Ribulose 1,5-bisphosphate carboxylase-oxygenase
(39)
Protein domain
:
Ribulose 1,5-bisphosphate carboxylase-oxygenase
(39)
Spinach (Spinacia oleracea) [TaxId: 3562]
(10)
1a
d1upmb1
B:9-147
1b
d1upme1
E:9-147
1c
d1upmh1
H:9-147
1d
d1upmk1
K:9-147
1e
d1upml1
L:9-147
1f
d1upmo1
O:9-147
1g
d1upmr1
R:9-147
1h
d1upmv1
V:9-147
Fold
:
RuBisCO, small subunit
(44)
Superfamily
:
RuBisCO, small subunit
(44)
Family
:
RuBisCO, small subunit
(44)
Protein domain
:
Ribulose 1,5-bisphosphate carboxylase-oxygenase
(28)
Spinach (Spinacia oleracea) [TaxId: 3562]
(10)
2a
d1upmc_
C:
2b
d1upmf_
F:
2c
d1upmi_
I:
2d
d1upmm_
M:
2e
d1upmp_
P:
2f
d1upms_
S:
2g
d1upmt_
T:
2h
d1upmw_
W:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
RuBisCo, C-terminal domain
(66)
Family
:
RuBisCo, large subunit, C-terminal domain
(56)
Protein domain
:
Ribulose 1,5-bisphosphate carboxylase-oxygenase
(40)
Spinach (Spinacia oleracea) [TaxId: 3562]
(10)
3a
d1upmb2
B:148-475
3b
d1upme2
E:148-475
3c
d1upmh2
H:148-475
3d
d1upmk2
K:148-475
3e
d1upml2
L:148-475
3f
d1upmo2
O:148-475
3g
d1upmr2
R:148-475
3h
d1upmv2
V:148-475
[
close SCOP info
]
CATH Domains
(3, 24)
Info
all CATH domains
1a: CATH_1upmB01 (B:22-148)
1b: CATH_1upmE01 (E:22-148)
1c: CATH_1upmH01 (H:22-148)
1d: CATH_1upmK01 (K:22-148)
1e: CATH_1upmL01 (L:22-148)
1f: CATH_1upmO01 (O:22-148)
1g: CATH_1upmR01 (R:22-148)
1h: CATH_1upmV01 (V:22-148)
2a: CATH_1upmC00 (C:1-123)
2b: CATH_1upmF00 (F:1-123)
2c: CATH_1upmI00 (I:1-123)
2d: CATH_1upmM00 (M:1-123)
2e: CATH_1upmP00 (P:1-123)
2f: CATH_1upmS00 (S:1-123)
2g: CATH_1upmT00 (T:1-123)
2h: CATH_1upmW00 (W:1-123)
3a: CATH_1upmB02 (B:149-462)
3b: CATH_1upmE02 (E:149-462)
3c: CATH_1upmH02 (H:149-462)
3d: CATH_1upmK02 (K:149-462)
3e: CATH_1upmL02 (L:149-462)
3f: CATH_1upmO02 (O:149-462)
3g: CATH_1upmR02 (R:149-462)
3h: CATH_1upmV02 (V:149-462)
View:
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Classes
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)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.150, no name defined]
(49)
Spinach (Spinacia oleracea)
(10)
1a
1upmB01
B:22-148
1b
1upmE01
E:22-148
1c
1upmH01
H:22-148
1d
1upmK01
K:22-148
1e
1upmL01
L:22-148
1f
1upmO01
O:22-148
1g
1upmR01
R:22-148
1h
1upmV01
V:22-148
Topology
:
Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
(42)
Homologous Superfamily
:
[code=3.30.190.10, no name defined]
(35)
Spinach (Spinacia oleracea)
(10)
2a
1upmC00
C:1-123
2b
1upmF00
F:1-123
2c
1upmI00
I:1-123
2d
1upmM00
M:1-123
2e
1upmP00
P:1-123
2f
1upmS00
S:1-123
2g
1upmT00
T:1-123
2h
1upmW00
W:1-123
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Rubisco
(49)
Spinach (Spinacia oleracea)
(10)
3a
1upmB02
B:149-462
3b
1upmE02
E:149-462
3c
1upmH02
H:149-462
3d
1upmK02
K:149-462
3e
1upmL02
L:149-462
3f
1upmO02
O:149-462
3g
1upmR02
R:149-462
3h
1upmV02
V:149-462
[
close CATH info
]
Pfam Domains
(3, 24)
Info
all PFAM domains
1a: PFAM_RuBisCO_large_1upmV01 (V:154-462)
1b: PFAM_RuBisCO_large_1upmV02 (V:154-462)
1c: PFAM_RuBisCO_large_1upmV03 (V:154-462)
1d: PFAM_RuBisCO_large_1upmV04 (V:154-462)
1e: PFAM_RuBisCO_large_1upmV05 (V:154-462)
1f: PFAM_RuBisCO_large_1upmV06 (V:154-462)
1g: PFAM_RuBisCO_large_1upmV07 (V:154-462)
1h: PFAM_RuBisCO_large_1upmV08 (V:154-462)
2a: PFAM_RuBisCO_large_N_1upmV09 (V:21-146)
2b: PFAM_RuBisCO_large_N_1upmV10 (V:21-146)
2c: PFAM_RuBisCO_large_N_1upmV11 (V:21-146)
2d: PFAM_RuBisCO_large_N_1upmV12 (V:21-146)
2e: PFAM_RuBisCO_large_N_1upmV13 (V:21-146)
2f: PFAM_RuBisCO_large_N_1upmV14 (V:21-146)
2g: PFAM_RuBisCO_large_N_1upmV15 (V:21-146)
2h: PFAM_RuBisCO_large_N_1upmV16 (V:21-146)
3a: PFAM_RuBisCO_small_1upmW01 (W:11-121)
3b: PFAM_RuBisCO_small_1upmW02 (W:11-121)
3c: PFAM_RuBisCO_small_1upmW03 (W:11-121)
3d: PFAM_RuBisCO_small_1upmW04 (W:11-121)
3e: PFAM_RuBisCO_small_1upmW05 (W:11-121)
3f: PFAM_RuBisCO_small_1upmW06 (W:11-121)
3g: PFAM_RuBisCO_small_1upmW07 (W:11-121)
3h: PFAM_RuBisCO_small_1upmW08 (W:11-121)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: RuBisCO_large]
(36)
Family
:
RuBisCO_large
(36)
Spinacia oleracea (Spinach)
(6)
1a
RuBisCO_large-1upmV01
V:154-462
1b
RuBisCO_large-1upmV02
V:154-462
1c
RuBisCO_large-1upmV03
V:154-462
1d
RuBisCO_large-1upmV04
V:154-462
1e
RuBisCO_large-1upmV05
V:154-462
1f
RuBisCO_large-1upmV06
V:154-462
1g
RuBisCO_large-1upmV07
V:154-462
1h
RuBisCO_large-1upmV08
V:154-462
Clan
:
no clan defined [family: RuBisCO_large_N]
(27)
Family
:
RuBisCO_large_N
(27)
Spinacia oleracea (Spinach)
(6)
2a
RuBisCO_large_N-1upmV09
V:21-146
2b
RuBisCO_large_N-1upmV10
V:21-146
2c
RuBisCO_large_N-1upmV11
V:21-146
2d
RuBisCO_large_N-1upmV12
V:21-146
2e
RuBisCO_large_N-1upmV13
V:21-146
2f
RuBisCO_large_N-1upmV14
V:21-146
2g
RuBisCO_large_N-1upmV15
V:21-146
2h
RuBisCO_large_N-1upmV16
V:21-146
Clan
:
no clan defined [family: RuBisCO_small]
(23)
Family
:
RuBisCO_small
(23)
Spinacia oleracea (Spinach)
(6)
3a
RuBisCO_small-1upmW01
W:11-121
3b
RuBisCO_small-1upmW02
W:11-121
3c
RuBisCO_small-1upmW03
W:11-121
3d
RuBisCO_small-1upmW04
W:11-121
3e
RuBisCO_small-1upmW05
W:11-121
3f
RuBisCO_small-1upmW06
W:11-121
3g
RuBisCO_small-1upmW07
W:11-121
3h
RuBisCO_small-1upmW08
W:11-121
[
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 B
Chain C
Chain E
Chain F
Chain H
Chain I
Chain K
Chain L
Chain M
Chain O
Chain P
Chain R
Chain S
Chain T
Chain V
Chain W
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...
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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
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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") .
QuickSearch:
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Asym.Unit (818 KB)
Header - Asym.Unit
Biol.Unit 1 (806 KB)
Header - Biol.Unit 1
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