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2WQY
Biol. Unit 1
Info
Asym.Unit (407 KB)
Biol.Unit 1 (202 KB)
Biol.Unit 2 (202 KB)
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(1)
Title
:
REMODELLING OF CARBOXIN BINDING TO THE Q-SITE OF AVIAN RESPIRATORY COMPLEX II
Authors
:
J. Ruprecht, S. Iwata, G. Cecchini
Date
:
27 Aug 09 (Deposition) - 25 Aug 10 (Release) - 20 May 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,N,O,P,Q
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: N,O,P,Q (1x)
Keywords
:
Oxaloacetate Nitropropionate Ubiquinone, Respiratory Chain, Complex Ii, Cytocrome B, Redox Enzyme, Heme Protein, Flavoprotein, Oxidoreductase, Metal-Binding, Mitochondrion Inner Membrane, Iron Sulfur Protein, Tricarboxylic Acid Cycle
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Ruprecht, S. Iwata, G. Cecchini
Remodelling Of Carboxin Binding To The Q-Site Of Avian Respiratory Complex Ii
To Be Published
[
close entry info
]
Hetero Components
(12, 67)
Info
All Hetero Components
01a: AZIDE ION (AZIa)
02a: 2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHY... (BHGa)
02b: 2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHY... (BHGb)
03a: 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-... (CBEa)
03b: 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-... (CBEb)
04a: FE3-S4 CLUSTER (F3Sa)
04b: FE3-S4 CLUSTER (F3Sb)
05a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
05b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
06a: FE2/S2 (INORGANIC) CLUSTER (FESa)
06b: FE2/S2 (INORGANIC) CLUSTER (FESb)
07a: GLYCEROL (GOLa)
07b: GLYCEROL (GOLb)
07c: GLYCEROL (GOLc)
07d: GLYCEROL (GOLd)
08a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
08b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
09a: POTASSIUM ION (Ka)
09b: POTASSIUM ION (Kb)
09c: POTASSIUM ION (Kc)
09d: POTASSIUM ION (Kd)
10a: OXALOACETATE ION (OAAa)
10b: OXALOACETATE ION (OAAb)
11a: PHOSPHATIDYLETHANOLAMINE1,2-DIOLEO... (PEEa)
11b: PHOSPHATIDYLETHANOLAMINE1,2-DIOLEO... (PEEb)
12a: IRON/SULFUR CLUSTER (SF4a)
12b: IRON/SULFUR CLUSTER (SF4b)
13a: UNKNOWN LIGAND (UNLa)
13aa: UNKNOWN LIGAND (UNLaa)
13ab: UNKNOWN LIGAND (UNLab)
13ac: UNKNOWN LIGAND (UNLac)
13ad: UNKNOWN LIGAND (UNLad)
13ae: UNKNOWN LIGAND (UNLae)
13af: UNKNOWN LIGAND (UNLaf)
13ag: UNKNOWN LIGAND (UNLag)
13ah: UNKNOWN LIGAND (UNLah)
13ai: UNKNOWN LIGAND (UNLai)
13aj: UNKNOWN LIGAND (UNLaj)
13ak: UNKNOWN LIGAND (UNLak)
13al: UNKNOWN LIGAND (UNLal)
13am: UNKNOWN LIGAND (UNLam)
13an: UNKNOWN LIGAND (UNLan)
13ao: UNKNOWN LIGAND (UNLao)
13ap: UNKNOWN LIGAND (UNLap)
13aq: UNKNOWN LIGAND (UNLaq)
13ar: UNKNOWN LIGAND (UNLar)
13as: UNKNOWN LIGAND (UNLas)
13at: UNKNOWN LIGAND (UNLat)
13au: UNKNOWN LIGAND (UNLau)
13av: UNKNOWN LIGAND (UNLav)
13aw: UNKNOWN LIGAND (UNLaw)
13ax: UNKNOWN LIGAND (UNLax)
13ay: UNKNOWN LIGAND (UNLay)
13az: UNKNOWN LIGAND (UNLaz)
13b: UNKNOWN LIGAND (UNLb)
13ba: UNKNOWN LIGAND (UNLba)
13bb: UNKNOWN LIGAND (UNLbb)
13bc: UNKNOWN LIGAND (UNLbc)
13bd: UNKNOWN LIGAND (UNLbd)
13be: UNKNOWN LIGAND (UNLbe)
13bf: UNKNOWN LIGAND (UNLbf)
13bg: UNKNOWN LIGAND (UNLbg)
13bh: UNKNOWN LIGAND (UNLbh)
13bi: UNKNOWN LIGAND (UNLbi)
13bj: UNKNOWN LIGAND (UNLbj)
13bk: UNKNOWN LIGAND (UNLbk)
13bl: UNKNOWN LIGAND (UNLbl)
13bm: UNKNOWN LIGAND (UNLbm)
13bn: UNKNOWN LIGAND (UNLbn)
13bo: UNKNOWN LIGAND (UNLbo)
13bp: UNKNOWN LIGAND (UNLbp)
13bq: UNKNOWN LIGAND (UNLbq)
13br: UNKNOWN LIGAND (UNLbr)
13bs: UNKNOWN LIGAND (UNLbs)
13bt: UNKNOWN LIGAND (UNLbt)
13bu: UNKNOWN LIGAND (UNLbu)
13bv: UNKNOWN LIGAND (UNLbv)
13bw: UNKNOWN LIGAND (UNLbw)
13bx: UNKNOWN LIGAND (UNLbx)
13by: UNKNOWN LIGAND (UNLby)
13bz: UNKNOWN LIGAND (UNLbz)
13c: UNKNOWN LIGAND (UNLc)
13ca: UNKNOWN LIGAND (UNLca)
13cb: UNKNOWN LIGAND (UNLcb)
13cc: UNKNOWN LIGAND (UNLcc)
13cd: UNKNOWN LIGAND (UNLcd)
13ce: UNKNOWN LIGAND (UNLce)
13cf: UNKNOWN LIGAND (UNLcf)
13cg: UNKNOWN LIGAND (UNLcg)
13ch: UNKNOWN LIGAND (UNLch)
13ci: UNKNOWN LIGAND (UNLci)
13cj: UNKNOWN LIGAND (UNLcj)
13ck: UNKNOWN LIGAND (UNLck)
13cl: UNKNOWN LIGAND (UNLcl)
13cm: UNKNOWN LIGAND (UNLcm)
13cn: UNKNOWN LIGAND (UNLcn)
13co: UNKNOWN LIGAND (UNLco)
13cp: UNKNOWN LIGAND (UNLcp)
13cq: UNKNOWN LIGAND (UNLcq)
13d: UNKNOWN LIGAND (UNLd)
13e: UNKNOWN LIGAND (UNLe)
13f: UNKNOWN LIGAND (UNLf)
13g: UNKNOWN LIGAND (UNLg)
13h: UNKNOWN LIGAND (UNLh)
13i: UNKNOWN LIGAND (UNLi)
13j: UNKNOWN LIGAND (UNLj)
13k: UNKNOWN LIGAND (UNLk)
13l: UNKNOWN LIGAND (UNLl)
13m: UNKNOWN LIGAND (UNLm)
13n: UNKNOWN LIGAND (UNLn)
13o: UNKNOWN LIGAND (UNLo)
13p: UNKNOWN LIGAND (UNLp)
13q: UNKNOWN LIGAND (UNLq)
13r: UNKNOWN LIGAND (UNLr)
13s: UNKNOWN LIGAND (UNLs)
13t: UNKNOWN LIGAND (UNLt)
13u: UNKNOWN LIGAND (UNLu)
13v: UNKNOWN LIGAND (UNLv)
13w: UNKNOWN LIGAND (UNLw)
13x: UNKNOWN LIGAND (UNLx)
13y: UNKNOWN LIGAND (UNLy)
13z: UNKNOWN LIGAND (UNLz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AZI
1
Ligand/Ion
AZIDE ION
2
BHG
1
Ligand/Ion
2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL
3
CBE
1
Ligand/Ion
2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE
4
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
5
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
6
FES
1
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
7
GOL
2
Ligand/Ion
GLYCEROL
8
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
9
K
-1
Ligand/Ion
POTASSIUM ION
10
OAA
1
Ligand/Ion
OXALOACETATE ION
11
PEE
1
Ligand/Ion
PHOSPHATIDYLETHANOLAMINE1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
12
SF4
1
Ligand/Ion
IRON/SULFUR CLUSTER
13
UNL
55
Ligand/Ion
UNKNOWN LIGAND
[
close Hetero Component info
]
Sites
(15, 15)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC2 (SOFTWARE)
10: BC7 (SOFTWARE)
11: BC8 (SOFTWARE)
12: BC9 (SOFTWARE)
13: CC1 (SOFTWARE)
14: CC6 (SOFTWARE)
15: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS C:31 , TRP C:32 , LEU C:34 , PRO C:35 , GLU C:120 , HOH C:2046 , HOH C:2095 , TYR P:85
BINDING SITE FOR RESIDUE BHG C 142
02
AC2
SOFTWARE
ALA C:139 , TRP P:32 , LEU P:34 , PRO P:35 , GLU P:120 , HOH P:2039 , HOH P:2079 , HOH P:2080
BINDING SITE FOR RESIDUE BHG P 204
03
AC3
SOFTWARE
TYR A:365 , ASN A:366 , MET A:367 , GLY A:368 , GLU A:397 , ALA A:399
BINDING SITE FOR RESIDUE K A 622
04
AC4
SOFTWARE
MET B:191 , ASP B:193 , ASP B:196 , THR B:199 , HOH B:2241
BINDING SITE FOR RESIDUE K B 253
05
AC7
SOFTWARE
TYR A:172 , VAL A:174 , HOH A:2540
BINDING SITE FOR RESIDUE AZI A 623
06
AC8
SOFTWARE
VAL A:24 , GLY A:25 , ALA A:26 , GLY A:27 , GLY A:28 , ALA A:29 , THR A:48 , LYS A:49 , LEU A:50 , SER A:55 , HIS A:56 , THR A:57 , ALA A:59 , ALA A:60 , GLN A:61 , GLY A:62 , GLY A:63 , TYR A:176 , PHE A:177 , ALA A:178 , ALA A:212 , THR A:213 , THR A:224 , ASP A:232 , LEU A:263 , HIS A:364 , TYR A:365 , GLY A:396 , GLU A:397 , ARG A:408 , ALA A:411 , ASN A:412 , SER A:413 , LEU A:414 , LEU A:417 , OAA A:1002 , HOH A:2256 , HOH A:2368 , HOH A:2370 , HOH A:2542
BINDING SITE FOR RESIDUE FAD A1001
07
AC9
SOFTWARE
SER B:64 , CYS B:65 , ARG B:66 , GLY B:68 , CYS B:70 , GLY B:71 , CYS B:73 , CYS B:85
BINDING SITE FOR RESIDUE FES B1002
08
BC1
SOFTWARE
CYS B:158 , ILE B:159 , CYS B:161 , ALA B:162 , CYS B:164 , CYS B:225 , PRO B:226 , LYS B:227
BINDING SITE FOR RESIDUE SF4 B1003
09
BC2
SOFTWARE
CYS B:168 , TYR B:178 , CYS B:215 , HIS B:216 , THR B:217 , ILE B:218 , MET B:219 , ASN B:220 , CYS B:221 , ILE B:235
BINDING SITE FOR RESIDUE F3S B1004
10
BC7
SOFTWARE
HIS C:42 , ARG C:43 , GLY C:46 , LEU C:49 , SER C:50 , HIS C:98 , GLY C:102 , HIS C:105 , HOH C:2096 , HOH C:2097 , HOH C:2098 , ARG D:14 , LEU D:20 , LEU D:43 , HIS D:46 , GLY D:50
BINDING SITE FOR RESIDUE HEM C 143
11
BC8
SOFTWARE
SER B:170 , TRP B:173 , HIS B:216 , MET C:36 , SER C:39 , ILE C:40 , ARG C:43 , HOH C:2102 , ASP D:57 , TYR D:58
BINDING SITE FOR RESIDUE CBE C 144
12
BC9
SOFTWARE
GLY A:62 , HIS A:253 , LEU A:263 , THR A:265 , GLU A:266 , ARG A:297 , HIS A:364 , ARG A:408 , GLY A:410 , ALA A:411 , FAD A:1001
BINDING SITE FOR RESIDUE OAA A1002
13
CC1
SOFTWARE
GOL C:294 , ALA D:27 , TYR D:28 , TRP D:101
BINDING SITE FOR RESIDUE PEE D 109
14
CC6
SOFTWARE
PHE C:56 , ILE D:93 , PEE D:109
BINDING SITE FOR RESIDUE GOL C 294
15
CC7
SOFTWARE
HIS B:104 , MET B:105 , TYR B:171 , HOH B:2155 , HOH B:2225 , HOH B:2226 , HOH B:2296 , HOH B:2297 , TRP C:13
BINDING SITE FOR RESIDUE GOL B1010
[
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
(5, 5)
Info
All PROSITE Patterns/Profiles
1: 2FE2S_FER_2 (B:12-105)
2: FRD_SDH_FAD_BINDING (A:54-63)
3: 2FE2S_FER_1 (B:65-73)
4: 4FE4S_FER_2 (B:148-178)
5: 4FE4S_FER_1 (B:158-169)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
2FE2S_FER_2
PS51085
2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
SDHB_CHICK
50-143
1
B:12-105
-
2
FRD_SDH_FAD_BINDING
PS00504
Fumarate reductase / succinate dehydrogenase FAD-binding site.
SDHA_CHICK
98-107
1
A:54-63
-
3
2FE2S_FER_1
PS00197
2Fe-2S ferredoxin-type iron-sulfur binding region signature.
SDHB_CHICK
103-111
1
B:65-73
-
4
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
SDHB_CHICK
186-216
1
B:148-178
-
5
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
SDHB_CHICK
196-207
1
B:158-169
-
[
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]
Exons
(0, 0)
Info
All Exons
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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, 8)
Info
All SCOP Domains
1a: SCOP_d2wqyb2 (B:115-246)
1b: SCOP_d2wqyo2 (O:115-246)
2a: SCOP_d2wqyb1 (B:8-114)
2b: SCOP_d2wqyo1 (O:8-114)
3a: SCOP_d2wqyc_ (C:)
3b: SCOP_d2wqyd_ (D:)
3c: SCOP_d2wqyp_ (P:)
3d: SCOP_d2wqyq_ (Q:)
View:
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Folds
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Superfamilies
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Families
(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Globin-like
(1351)
Superfamily
:
alpha-helical ferredoxin
(43)
Family
:
Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain
(35)
Protein domain
:
Succinate dehydogenase
(16)
Chicken (Gallus gallus) [TaxId: 9031]
(6)
1a
d2wqyb2
B:115-246
1b
d2wqyo2
O:115-246
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
2Fe-2S ferredoxin-like
(174)
Family
:
2Fe-2S ferredoxin domains from multidomain proteins
(82)
Protein domain
:
Succinate dehydogenase iron-sulfur protein, N-terminal domain
(16)
Chicken (Gallus gallus) [TaxId: 9031]
(6)
2a
d2wqyb1
B:8-114
2b
d2wqyo1
O:8-114
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Heme-binding four-helical bundle
(113)
Superfamily
:
Fumarate reductase respiratory complex transmembrane subunits
(55)
Family
:
Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD)
(48)
Protein domain
:
automated matches
(11)
Chicken (Gallus gallus) [TaxId: 9031]
(6)
3a
d2wqyc_
C:
3b
d2wqyd_
D:
3c
d2wqyp_
P:
3d
d2wqyq_
Q:
[
close SCOP info
]
CATH Domains
(7, 16)
Info
all CATH domains
1a: CATH_2wqyN01 (N:10-256,N:361-439)
1b: CATH_2wqyA01 (A:9-256,A:361-439)
2a: CATH_2wqyB01 (B:8-114)
2b: CATH_2wqyO01 (O:8-114)
3a: CATH_2wqyA04 (A:557-621)
3b: CATH_2wqyN04 (N:557-621)
4a: CATH_2wqyB02 (B:115-246)
4b: CATH_2wqyO02 (O:115-246)
5a: CATH_2wqyC02 (C:33-141)
5b: CATH_2wqyD00 (D:3-103)
5c: CATH_2wqyQ00 (Q:3-103)
5d: CATH_2wqyP02 (P:33-141)
6a: CATH_2wqyA03 (A:440-556)
6b: CATH_2wqyN03 (N:440-556)
7a: CATH_2wqyC01 (C:2-32)
7b: CATH_2wqyP01 (P:2-32)
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Topologies
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
FAD/NAD(P)-binding domain
(373)
Homologous Superfamily
:
[code=3.50.50.60, no name defined]
(373)
Chicken (Gallus gallus)
(6)
1a
2wqyN01
N:10-256,N:361-439
1b
2wqyA01
A:9-256,A:361-439
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
[code=3.10.20.30, no name defined]
(153)
Chicken (Gallus gallus)
(6)
2a
2wqyB01
B:8-114
2b
2wqyO01
O:8-114
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Rhinovirus 14, subunit 4
(101)
Homologous Superfamily
:
succinate dehydrogenase protein domain
(23)
Chicken (Gallus gallus)
(6)
3a
2wqyA04
A:557-621
3b
2wqyN04
N:557-621
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2
(33)
Homologous Superfamily
:
Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2
(33)
Chicken (Gallus gallus)
(6)
4a
2wqyB02
B:115-246
4b
2wqyO02
O:115-246
Architecture
:
Up-down Bundle
(3216)
Topology
:
3 helical TM bundles of succinate and fumarate reductases
(23)
Homologous Superfamily
:
Fumarate reductase respiratory complex transmembrane subunits
(23)
Chicken (Gallus gallus)
(6)
5a
2wqyC02
C:33-141
5b
2wqyD00
D:3-103
5c
2wqyQ00
Q:3-103
5d
2wqyP02
P:33-141
Topology
:
Methane Monooxygenase Hydroxylase; Chain G, domain 1
(192)
Homologous Superfamily
:
[code=1.20.58.100, no name defined]
(37)
Chicken (Gallus gallus)
(6)
6a
2wqyA03
A:440-556
6b
2wqyN03
N:440-556
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
Single helix bin
(17)
Chicken (Gallus gallus)
(8)
7a
2wqyC01
C:2-32
7b
2wqyP01
P:2-32
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
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View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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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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