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3G7F
Asym. Unit
Info
Asym.Unit (236 KB)
Biol.Unit 1 (223 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BLASTOCHLORIS VIRIDIS HETERODIMER MUTANT REACTION CENTER
Authors
:
N. S. Ponomarenko, L. Li, V. Tereshko, R. F. Ismagilov, J. R. Norris Jr.
Date
:
09 Feb 09 (Deposition) - 22 Sep 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : C,H,L,M
Biol. Unit 1: C,H,L,M (1x)
Keywords
:
Heterodimer Mutant, Blastochloris Viridis, Photosynthetic Reaction Center, Membrane Protein Structure, Microfluidics, Plugs, Cell Membrane, Electron Transport, Heme, Iron, Lipoprotein, Membrane, Metal-Binding, Photosynthesis, Reaction Center, Transport, Bacteriochlorophyll, Chlorophyll, Chromophore, Formylation, Transmembrane, Magnesium
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. S. Ponomarenko, L. Li, A. R. Marino, V. Tereshko, A. Ostafin, J. A. Popova, E. J. Bylina, R. F. Ismagilov, J. R. Norris
Structural And Spectropotentiometric Analysis Of Blastochloris Viridis Heterodimer Mutant Reaction Center
Biochim. Biophys. Acta V. 1788 1822 2009
[
close entry info
]
Hetero Components
(11, 44)
Info
All Hetero Components
01a: BACTERIOCHLOROPHYLL B (BCBa)
01b: BACTERIOCHLOROPHYLL B (BCBb)
01c: BACTERIOCHLOROPHYLL B (BCBc)
02a: BACTERIOPHEOPHYTIN B (BPBa)
02b: BACTERIOPHEOPHYTIN B (BPBb)
02c: BACTERIOPHEOPHYTIN B (BPBc)
03a: FE (II) ION (FE2a)
04a: N-FORMYLMETHIONINE (FMEa)
05a: HEME C (HECa)
05b: HEME C (HECb)
05c: HEME C (HECc)
05d: HEME C (HECd)
06a: HEPTANE-1,2,3-TRIOL (HTOa)
06b: HEPTANE-1,2,3-TRIOL (HTOb)
06c: HEPTANE-1,2,3-TRIOL (HTOc)
06d: HEPTANE-1,2,3-TRIOL (HTOd)
06e: HEPTANE-1,2,3-TRIOL (HTOe)
07a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
07b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
07c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
07d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
08a: MENAQUINONE-9 (MQ9a)
09a: 15-CIS-1,2-DIHYDRONEUROSPORENE (NS5a)
10a: SULFATE ION (SO4a)
10b: SULFATE ION (SO4b)
10c: SULFATE ION (SO4c)
10d: SULFATE ION (SO4d)
10e: SULFATE ION (SO4e)
10f: SULFATE ION (SO4f)
10g: SULFATE ION (SO4g)
10h: SULFATE ION (SO4h)
10i: SULFATE ION (SO4i)
10j: SULFATE ION (SO4j)
10k: SULFATE ION (SO4k)
10l: SULFATE ION (SO4l)
10m: SULFATE ION (SO4m)
10n: SULFATE ION (SO4n)
10o: SULFATE ION (SO4o)
10p: SULFATE ION (SO4p)
10q: SULFATE ION (SO4q)
10r: SULFATE ION (SO4r)
10s: SULFATE ION (SO4s)
11a: UBIQUINONE-1 (UQ1a)
11b: UBIQUINONE-1 (UQ1b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCB
3
Ligand/Ion
BACTERIOCHLOROPHYLL B
2
BPB
3
Ligand/Ion
BACTERIOPHEOPHYTIN B
3
FE2
1
Ligand/Ion
FE (II) ION
4
FME
1
Mod. Amino Acid
N-FORMYLMETHIONINE
5
HEC
4
Ligand/Ion
HEME C
6
HTO
5
Ligand/Ion
HEPTANE-1,2,3-TRIOL
7
LDA
4
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
8
MQ9
1
Ligand/Ion
MENAQUINONE-9
9
NS5
1
Ligand/Ion
15-CIS-1,2-DIHYDRONEUROSPORENE
10
SO4
19
Ligand/Ion
SULFATE ION
11
UQ1
2
Ligand/Ion
UBIQUINONE-1
[
close Hetero Component info
]
Sites
(43, 43)
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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR C:56 , LYS C:57 , ASN C:58 , VAL C:59 , LYS C:60 , VAL C:61 , LEU C:62 , PHE C:70 , MET C:74 , ILE C:77 , THR C:78 , SER C:82 , CYS C:87 , CYS C:90 , HIS C:91 , LEU C:96 , ALA C:97 , TYR C:104 , ALA C:107 , ARG C:108 , VAL C:212
BINDING SITE FOR RESIDUE HEC C 401
02
AC2
SOFTWARE
TYR C:89 , TYR C:102 , PRO C:103 , VAL C:106 , MET C:110 , MET C:113 , THR C:114 , THR C:131 , CYS C:132 , CYS C:135 , HIS C:136 , PRO C:140 , LEU C:141 , PRO C:142 , ARG C:293
BINDING SITE FOR RESIDUE HEC C 402
03
AC3
SOFTWARE
ARG C:202 , VAL C:203 , VAL C:204 , MET C:233 , ILE C:236 , SER C:237 , ASN C:243 , CYS C:244 , CYS C:247 , HIS C:248 , PHE C:253 , GLU C:254 , ARG C:264 , ALA C:267 , TRP C:268 , ARG C:272 , HOH C:547 , HOH C:548 , HOH C:596 , HOH C:615 , ILE M:189
BINDING SITE FOR RESIDUE HEC C 403
04
AC4
SOFTWARE
HIS C:124 , VAL C:125 , THR C:128 , GLY C:129 , LEU C:240 , GLN C:263 , ILE C:266 , ILE C:271 , MET C:273 , VAL C:274 , ASP C:304 , CYS C:305 , CYS C:308 , HIS C:309 , THR C:313 , LYS C:314 , PRO C:315 , HOH C:551 , HOH C:695 , HOH C:715 , HOH C:788
BINDING SITE FOR RESIDUE HEC C 404
05
AC5
SOFTWARE
ALA C:319 , SER C:320 , ARG C:321 , HOH C:577 , HOH C:796
BINDING SITE FOR RESIDUE SO4 C 808
06
AC6
SOFTWARE
ARG C:115 , HOH C:641
BINDING SITE FOR RESIDUE SO4 C 809
07
AC7
SOFTWARE
LYS C:198 , ARG C:199 , HOH C:759
BINDING SITE FOR RESIDUE SO4 C 810
08
AC8
SOFTWARE
HIS C:162 , ARG C:165
BINDING SITE FOR RESIDUE SO4 C 811
09
AC9
SOFTWARE
THR C:161 , HIS C:162 , HOH C:633 , SER L:273
BINDING SITE FOR RESIDUE SO4 C 813
10
BC1
SOFTWARE
THR C:168 , ARG C:169 , SER C:170 , HIS M:78
BINDING SITE FOR RESIDUE SO4 C 815
11
BC2
SOFTWARE
PRO C:4 , HIS C:24 , ALA C:26 , HOH C:535
BINDING SITE FOR RESIDUE SO4 C 817
12
BC3
SOFTWARE
PRO C:205 , GLN C:206 , THR C:207 , LEU C:209 , PRO C:210 , LEU C:211 , ASP M:290
BINDING SITE FOR RESIDUE HTO C 706
13
BC4
SOFTWARE
GLU C:21 , LEU C:23 , LEU C:240 , GLY C:241 , GLY C:311 , VAL C:312 , THR C:313 , HOH C:610 , HOH C:764
BINDING SITE FOR RESIDUE HTO C 707
14
BC5
SOFTWARE
ARG H:253 , HOH H:561 , HOH H:634
BINDING SITE FOR RESIDUE SO4 H 803
15
BC6
SOFTWARE
ARG H:37 , TYR H:41 , LEU H:43 , GLU H:61 , HOH H:542 , HOH H:558 , HOH H:609 , ARG M:251
BINDING SITE FOR RESIDUE SO4 H 806
16
BC7
SOFTWARE
TYR H:117 , GLU H:119 , ARG H:233 , LYS H:237
BINDING SITE FOR RESIDUE SO4 H 807
17
BC8
SOFTWARE
HIS H:72 , GLY H:130
BINDING SITE FOR RESIDUE SO4 H 812
18
BC9
SOFTWARE
ARG H:33 , ASP H:56
BINDING SITE FOR RESIDUE LDA H 701
19
CC1
SOFTWARE
VAL H:59 , TYR H:60 , LEU H:62 , TYR H:64 , PRO H:65 , HOH H:574
BINDING SITE FOR RESIDUE LDA H 703
20
CC2
SOFTWARE
VAL H:123 , VAL H:124 , ASP H:125 , ALA H:126 , HOH H:509 , HOH H:629 , HOH H:652 , THR M:237
BINDING SITE FOR RESIDUE HTO H 705
21
CC3
SOFTWARE
PHE L:97 , PRO L:124 , MET L:127 , PHE L:128 , VAL L:157 , ASN L:158 , PHE L:160 , GLY L:161 , TYR L:162 , TRP L:167 , HIS L:168 , HIS L:173 , SER L:176 , VAL L:177 , ILE L:240 , PHE L:241 , GLY L:244 , THR L:248 , BCB L:401 , BPB L:402 , TYR M:195 , TYR M:208 , BPB M:401 , MQ9 M:501
BINDING SITE FOR RESIDUE BCB L 400
22
CC4
SOFTWARE
PHE L:128 , PHE L:146 , ILE L:150 , HIS L:153 , LEU L:154 , VAL L:157 , BCB L:400 , BPB L:402 , TYR M:195 , LEU M:200 , GLY M:201 , ILE M:204 , GLY M:205 , TYR M:208 , GLY M:209 , BPB M:401
BINDING SITE FOR RESIDUE BCB L 401
23
CC5
SOFTWARE
PHE L:41 , ILE L:42 , ILE L:49 , PHE L:97 , TRP L:100 , GLU L:104 , VAL L:117 , PHE L:121 , PRO L:124 , TYR L:148 , GLY L:149 , ILE L:150 , HIS L:153 , ALA L:237 , PHE L:241 , BCB L:400 , BCB L:401 , TYR M:208 , LEU M:212 , TRP M:250 , ILE M:254 , MQ9 M:501
BINDING SITE FOR RESIDUE BPB L 402
24
CC6
SOFTWARE
LEU L:189 , HIS L:190 , LEU L:193 , ASN L:213 , PHE L:216 , SER L:223 , ILE L:224 , GLY L:225 , ILE L:229
BINDING SITE FOR RESIDUE UQ1 L 502
25
CC7
SOFTWARE
ASP L:204 , LYS L:205 , LYS L:207 , HOH L:702
BINDING SITE FOR RESIDUE SO4 L 814
26
CC8
SOFTWARE
TYR L:29 , ILE M:254 , MQ9 M:501
BINDING SITE FOR RESIDUE HTO L 708
27
CC9
SOFTWARE
GLY L:114 , TRP L:115 , HOH L:755 , SO4 M:804
BINDING SITE FOR RESIDUE HTO L 709
28
DC1
SOFTWARE
HIS L:190 , HIS L:230 , HIS M:217 , GLU M:232 , HIS M:264
BINDING SITE FOR RESIDUE FE2 M 500
29
DC2
SOFTWARE
TYR L:29 , ILE L:39 , PHE L:43 , ARG L:103 , BCB L:400 , BPB L:402 , HTO L:708 , HIS M:217 , THR M:220 , ALA M:246 , TRP M:250 , ASN M:257 , ALA M:258 , THR M:259 , VAL M:263
BINDING SITE FOR RESIDUE MQ9 M 501
30
DC3
SOFTWARE
TRP L:266 , PHE M:85 , PHE M:89 , HOH M:738
BINDING SITE FOR RESIDUE UQ1 M 503
31
DC4
SOFTWARE
MET L:174 , VAL L:177 , SER L:178 , PHE L:181 , VAL L:182 , MET L:185 , PHE M:154 , VAL M:155 , ILE M:177 , TRP M:178 , HIS M:180 , ILE M:181 , LEU M:184 , BPB M:401 , BPB M:402 , NS5 M:600 , HOH M:606
BINDING SITE FOR RESIDUE BCB M 400
32
DC5
SOFTWARE
TYR L:162 , PHE L:181 , BCB L:400 , BCB L:401 , PHE M:148 , VAL M:155 , LEU M:184 , PHE M:187 , SER M:188 , PHE M:194 , TYR M:195 , LEU M:200 , SER M:203 , ILE M:204 , TYR M:208 , MET M:275 , ALA M:278 , ILE M:282 , BCB M:400 , BPB M:402
BINDING SITE FOR RESIDUE BPB M 401
33
DC6
SOFTWARE
PHE L:181 , MET L:185 , LEU L:189 , PHE M:59 , SER M:63 , SER M:123 , TRP M:127 , ILE M:144 , PHE M:148 , SER M:271 , MET M:275 , BCB M:400 , BPB M:401 , HOH M:776
BINDING SITE FOR RESIDUE BPB M 402
34
DC7
SOFTWARE
GLY M:117 , THR M:121 , GLY M:159 , VAL M:173 , GLY M:176 , ILE M:177 , HIS M:180 , BCB M:400
BINDING SITE FOR RESIDUE NS5 M 600
35
DC8
SOFTWARE
HOH H:504 , ASN L:199 , HIS M:143 , ARG M:265 , HOH M:653 , HOH M:677 , SO4 M:818
BINDING SITE FOR RESIDUE SO4 M 801
36
DC9
SOFTWARE
TRP M:23 , TYR M:50 , ALA M:53 , SER M:54 , SER M:133 , LDA M:704 , HOH M:745 , HOH M:783 , HOH M:809
BINDING SITE FOR RESIDUE SO4 M 802
37
EC1
SOFTWARE
LEU H:246 , HOH H:540 , HTO L:709 , ALA M:1 , ARG M:226 , HOH M:561 , HOH M:689
BINDING SITE FOR RESIDUE SO4 M 804
38
EC2
SOFTWARE
SER M:35 , TYR M:36 , TRP M:37
BINDING SITE FOR RESIDUE SO4 M 805
39
EC3
SOFTWARE
PRO M:15 , HIS M:16 , HOH M:834
BINDING SITE FOR RESIDUE SO4 M 816
40
EC4
SOFTWARE
HIS M:143 , TRP M:146 , TRP M:268 , SO4 M:801
BINDING SITE FOR RESIDUE SO4 M 818
41
EC5
SOFTWARE
PRO M:106 , LEU M:107 , HIS M:108
BINDING SITE FOR RESIDUE SO4 M 819
42
EC6
SOFTWARE
ASP L:60 , TYR M:195 , CYS M:197 , PRO M:198 , GLY M:201 , HIS M:299
BINDING SITE FOR RESIDUE LDA M 702
43
EC7
SOFTWARE
SER M:54 , SO4 M:802
BINDING SITE FOR RESIDUE LDA M 704
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(2, 3)
Info
All PROSITE Patterns/Profiles
1: MULTIHEME_CYTC (C:82-314)
2: REACTION_CENTER (L:166-192,M:193-219)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MULTIHEME_CYTC
PS51008
Multiheme cytochrome c family profile.
CYCR_BLAVI
102-334
1
C:82-314
2
REACTION_CENTER
PS00244
Photosynthetic reaction center proteins signature.
RCEL_BLAVI
167-193
1
L:166-192
RCEM_BLAVI
194-220
1
M:193-219
[
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]
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
(4, 5)
Info
All SCOP Domains
1a: SCOP_d3g7fc_ (C:)
2a: SCOP_d3g7fh2 (H:37-258)
3a: SCOP_d3g7fl_ (L:)
3b: SCOP_d3g7fm_ (M:)
4a: SCOP_d3g7fh1 (H:1-36)
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Folds
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Superfamilies
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)
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)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Multiheme cytochromes
(149)
Superfamily
:
Multiheme cytochromes
(149)
Family
:
Photosynthetic reaction centre (cytochrome subunit)
(20)
Protein domain
:
Photosynthetic reaction centre (cytochrome subunit)
(19)
Rhodopseudomonas viridis [TaxId: 1079]
(18)
1a
d3g7fc_
C:
Class
:
All beta proteins
(24004)
Fold
:
PRC-barrel domain
(113)
Superfamily
:
PRC-barrel domain
(113)
Family
:
Photosynthetic reaction centre, H-chain, cytoplasmic domain
(108)
Protein domain
:
automated matches
(10)
Blastochloris viridis [TaxId: 1079]
(4)
2a
d3g7fh2
H:37-258
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Bacterial photosystem II reaction centre, L and M subunits
(187)
Superfamily
:
Bacterial photosystem II reaction centre, L and M subunits
(187)
Family
:
Bacterial photosystem II reaction centre, L and M subunits
(187)
Protein domain
:
automated matches
(44)
Blastochloris viridis [TaxId: 1079]
(7)
3a
d3g7fl_
L:
3b
d3g7fm_
M:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Photosystem II reaction centre subunit H, transmembrane region
(108)
Family
:
automated matches
(10)
Protein domain
:
automated matches
(10)
Blastochloris viridis [TaxId: 1079]
(4)
4a
d3g7fh1
H:1-36
[
close SCOP info
]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_3g7fH02 (H:120-258)
2a: CATH_3g7fH01 (H:2-119)
3a: CATH_3g7fC02 (C:143-205,C:221-313)
3b: CATH_3g7fC01 (C:24-142,C:314-332)
4a: CATH_3g7fM01 (M:1-143)
4b: CATH_3g7fM02 (M:144-302)
4c: CATH_3g7fL01 (L:1-165)
4d: CATH_3g7fL02 (L:166-273)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Photosynthetic Reaction Center; Chain H, domain 2
(93)
Homologous Superfamily
:
Photosynthetic Reaction Center, subunit H, domain 2
(93)
Blastochloris viridis. Organism_taxid: 1079.
(10)
1a
3g7fH02
H:120-258
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Photosynthetic Reaction Center; Chain H, domain 1
(93)
Homologous Superfamily
:
Photosynthetic Reaction Center, subunit H, domain 1
(93)
Blastochloris viridis. Organism_taxid: 1079.
(10)
2a
3g7fH01
H:2-119
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Photosynthetic Reaction Center, subunit C; domain 2
(18)
Homologous Superfamily
:
Photosynthetic Reaction Center, subunit C, domain 2
(18)
Blastochloris viridis. Organism_taxid: 1079.
(10)
3a
3g7fC02
C:143-205,C:221-313
3b
3g7fC01
C:24-142,C:314-332
Architecture
:
Up-down Bundle
(3216)
Topology
:
Photosynthetic Reaction Center, subunit M; domain 1
(93)
Homologous Superfamily
:
Membrane spanning alpha-helix pairs
(93)
Blastochloris viridis. Organism_taxid: 1079.
(10)
4a
3g7fM01
M:1-143
4b
3g7fM02
M:144-302
4c
3g7fL01
L:1-165
4d
3g7fL02
L:166-273
[
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
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain C
Chain H
Chain L
Chain M
Asymmetric Unit 1
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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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In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
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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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