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2VR0
Asym. Unit
Info
Asym.Unit (409 KB)
Biol.Unit 1 (387 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CYTOCHROME C NITRITE REDUCTASE NRFHA COMPLEX BOUND TO THE HQNO INHIBITOR
Authors
:
M. L. Rodrigues, M. Archer
Date
:
24 Mar 08 (Deposition) - 03 Jun 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Quinol Dehydrogenase, Oxidoreductase, Hqno, Nrfh, Nrfha, Membrane Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. L. Rodrigues, K. A. Scott, M. S. P. Sansom, I. A. C. Pereira, M. Archer
Quinol Oxidation By C-Type Cytochromes: Structural Characterization Of The Menaquinol Binding Site Of Nrfha.
J. Mol. Biol. V. 381 341 2008
[
close entry info
]
Hetero Components
(3, 38)
Info
All Hetero Components
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)
2a: HEME C (HEMa)
2aa: HEME C (HEMaa)
2ab: HEME C (HEMab)
2b: HEME C (HEMb)
2c: HEME C (HEMc)
2d: HEME C (HEMd)
2e: HEME C (HEMe)
2f: HEME C (HEMf)
2g: HEME C (HEMg)
2h: HEME C (HEMh)
2i: HEME C (HEMi)
2j: HEME C (HEMj)
2k: HEME C (HEMk)
2l: HEME C (HEMl)
2m: HEME C (HEMm)
2n: HEME C (HEMn)
2o: HEME C (HEMo)
2p: HEME C (HEMp)
2q: HEME C (HEMq)
2r: HEME C (HEMr)
2s: HEME C (HEMs)
2t: HEME C (HEMt)
2u: HEME C (HEMu)
2v: HEME C (HEMv)
2w: HEME C (HEMw)
2x: HEME C (HEMx)
2y: HEME C (HEMy)
2z: HEME C (HEMz)
3a: 2-HEPTYL-4-HYDROXY QUINOLINE N-OXI... (HQOa)
3b: 2-HEPTYL-4-HYDROXY QUINOLINE N-OXI... (HQOb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
8
Ligand/Ion
CALCIUM ION
2
HEM
28
Ligand/Ion
HEME C
3
HQO
2
Ligand/Ion
2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE
[
close Hetero Component info
]
Sites
(38, 38)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:116 , ALA A:118 , ILE A:131 , ARG A:133 , CYS A:147 , CYS A:150 , LYS A:151 , CYS A:232 , HIS A:233 , TYR A:236 , HIS A:298 , ASN A:429 , HEM A:1003 , HOH A:2023
BINDING SITE FOR RESIDUE HEM A1001
02
AC2
SOFTWARE
TYR A:39 , PHE A:57 , GLN A:60 , TYR A:61 , TYR A:64 , GLY A:186 , CYS A:187 , CYS A:190 , HIS A:191 , MET A:196 , LEU A:198 , ARG A:221 , ARG A:225 , MET A:321 , ILE A:332 , SER A:333 , HIS A:335 , TRP A:337 , HEM A:1003 , GLU C:126 , VAL C:127
BINDING SITE FOR RESIDUE HEM A1002
03
AC3
SOFTWARE
GLY A:78 , SER A:79 , ALA A:118 , ARG A:119 , GLY A:120 , HIS A:121 , TYR A:123 , ALA A:124 , ASP A:127 , CYS A:150 , ILE A:185 , THR A:189 , VAL A:228 , CYS A:229 , CYS A:232 , HIS A:233 , HIS A:320 , TRP A:337 , THR A:338 , HEM A:1001 , HEM A:1002 , HEM A:1004 , CA A:1007
BINDING SITE FOR RESIDUE HEM A1003
04
AC4
SOFTWARE
THR A:74 , LYS A:77 , GLY A:78 , GLU A:117 , HIS A:233 , GLU A:300 , TRP A:304 , HIS A:309 , VAL A:314 , THR A:315 , CYS A:316 , CYS A:319 , HIS A:320 , SER A:339 , MET A:341 , GLN A:369 , ASN A:429 , PHE A:433 , HIS A:434 , HEM A:1003 , CA A:1007
BINDING SITE FOR RESIDUE HEM A1004
05
AC5
SOFTWARE
HIS A:309 , CYS A:319 , PRO A:340 , MET A:346 , CYS A:349 , CYS A:352 , HIS A:353 , ARG A:364 , HIS B:353 , LYS B:356 , HEM B:1005 , ASP C:138 , ARG C:141
BINDING SITE FOR RESIDUE HEM A1005
06
AC6
SOFTWARE
GLU A:235 , TYR A:236 , LYS A:295 , GLN A:297 , HOH A:2014
BINDING SITE FOR RESIDUE CA A1006
07
AC7
SOFTWARE
GLY A:78 , GLU A:117 , ALA A:118 , HEM A:1003 , HEM A:1004
BINDING SITE FOR RESIDUE CA A1007
08
AC8
SOFTWARE
ARG B:116 , ALA B:118 , PHE B:128 , ILE B:131 , ARG B:133 , CYS B:147 , CYS B:150 , LYS B:151 , CYS B:232 , HIS B:233 , TYR B:236 , PHE B:238 , HIS B:298 , ASN B:429 , HEM B:1003 , HOH B:2008 , HOH B:2040 , HOH B:2041
BINDING SITE FOR RESIDUE HEM B1001
09
AC9
SOFTWARE
TYR B:39 , PHE B:57 , GLN B:60 , TYR B:64 , GLY B:186 , CYS B:187 , CYS B:190 , HIS B:191 , MET B:196 , LEU B:198 , ARG B:221 , ARG B:225 , MET B:321 , TYR B:323 , SER B:333 , HIS B:335 , TRP B:337 , HEM B:1003 , ALA C:157
BINDING SITE FOR RESIDUE HEM B1002
10
BC1
SOFTWARE
GLY B:78 , SER B:79 , ALA B:118 , ARG B:119 , GLY B:120 , HIS B:121 , TYR B:123 , ALA B:124 , ASP B:127 , CYS B:150 , ILE B:185 , VAL B:228 , CYS B:229 , CYS B:232 , HIS B:233 , HIS B:320 , MET B:321 , TRP B:337 , THR B:338 , HEM B:1001 , HEM B:1002 , HEM B:1004 , CA B:1007 , HOH B:2029
BINDING SITE FOR RESIDUE HEM B1003
11
BC2
SOFTWARE
THR B:74 , LYS B:77 , GLY B:78 , GLU B:117 , ALA B:118 , HIS B:233 , GLU B:300 , TRP B:304 , HIS B:309 , VAL B:314 , THR B:315 , CYS B:316 , CYS B:319 , HIS B:320 , SER B:339 , GLN B:369 , ASN B:429 , PHE B:433 , HIS B:434 , HEM B:1003 , HEM B:1005 , CA B:1007 , HOH B:2029
BINDING SITE FOR RESIDUE HEM B1004
12
BC3
SOFTWARE
HIS A:353 , LYS A:356 , HEM A:1005 , HIS B:309 , VAL B:314 , ASP B:318 , PRO B:340 , CYS B:349 , CYS B:352 , HIS B:353 , ARG B:364 , VAL B:365 , PHE B:433 , PRO B:436 , HEM B:1004 , MET C:148
BINDING SITE FOR RESIDUE HEM B1005
13
BC4
SOFTWARE
GLU B:235 , TYR B:236 , LYS B:295 , GLN B:297 , HOH B:2016
BINDING SITE FOR RESIDUE CA B1006
14
BC5
SOFTWARE
GLY B:78 , GLU B:117 , ALA B:118 , HEM B:1003 , HEM B:1004
BINDING SITE FOR RESIDUE CA B1007
15
BC6
SOFTWARE
THR C:37 , CYS C:43 , CYS C:46 , MET C:49 , ASN C:67 , ASP C:89 , MET C:92 , ASN C:93 , ALA C:104 , GLY C:105 , THR C:108 , HEM C:1002 , HQO C:1005
BINDING SITE FOR RESIDUE HEM C1001
16
BC7
SOFTWARE
ARG C:40 , CYS C:43 , MET C:49 , VAL C:52 , GLY C:53 , HIS C:56 , HIS C:61 , SER C:65 , CYS C:66 , CYS C:69 , HIS C:70 , ILE C:102 , ALA C:104 , LYS C:109 , THR C:137 , GLN C:144 , HIS C:145 , HEM C:1001
BINDING SITE FOR RESIDUE HEM C1002
17
BC8
SOFTWARE
GLY C:60 , HIS C:61 , ASP C:68 , CYS C:69 , ASN C:115 , CYS C:116 , CYS C:119 , HIS C:120 , HIS C:140 , VAL C:143 , HEM C:1004 , LYS D:329 , CYS F:119 , HIS F:120 , MET F:122 , THR F:123 , HEM F:1003
BINDING SITE FOR RESIDUE HEM C1003
18
BC9
SOFTWARE
TYR A:323 , THR A:324 , ARG A:325 , LYS A:331 , ARG A:347 , GLN A:351 , CYS C:116 , HIS C:120 , ASN C:124 , SER C:129 , CYS C:136 , CYS C:139 , HIS C:140 , HEM C:1003 , ARG D:325 , LYS D:329 , HEM F:1004
BINDING SITE FOR RESIDUE HEM C1004
19
CC1
SOFTWARE
MET C:34 , PHE C:42 , ASN C:67 , LYS C:82 , ALA C:85 , GLY C:86 , ASP C:89 , HEM C:1001
BINDING SITE FOR RESIDUE HQO C1005
20
CC2
SOFTWARE
TYR D:115 , ARG D:116 , ALA D:118 , PHE D:128 , ILE D:131 , ARG D:133 , CYS D:147 , CYS D:150 , LYS D:151 , CYS D:232 , HIS D:233 , TYR D:236 , HIS D:298 , ASN D:429 , HEM D:1003 , HOH D:2007 , HOH D:2019 , HOH D:2020
BINDING SITE FOR RESIDUE HEM D1001
21
CC3
SOFTWARE
TYR D:39 , PHE D:57 , GLN D:60 , TYR D:61 , TYR D:64 , GLY D:186 , CYS D:187 , CYS D:190 , HIS D:191 , MET D:196 , ARG D:221 , ARG D:225 , MET D:321 , SER D:333 , HIS D:335 , TRP D:337 , HEM D:1003 , GLU F:126 , VAL F:127
BINDING SITE FOR RESIDUE HEM D1002
22
CC4
SOFTWARE
GLY D:78 , SER D:79 , ALA D:118 , ARG D:119 , GLY D:120 , HIS D:121 , TYR D:123 , ALA D:124 , ASP D:127 , CYS D:150 , LYS D:151 , ILE D:185 , THR D:189 , VAL D:228 , CYS D:229 , CYS D:232 , HIS D:233 , HIS D:320 , MET D:321 , TRP D:337 , THR D:338 , HEM D:1001 , HEM D:1002 , HEM D:1004 , CA D:1007
BINDING SITE FOR RESIDUE HEM D1003
23
CC5
SOFTWARE
THR D:74 , LYS D:77 , GLY D:78 , GLU D:117 , HIS D:233 , GLU D:300 , TRP D:304 , HIS D:309 , VAL D:314 , THR D:315 , CYS D:316 , CYS D:319 , HIS D:320 , SER D:339 , GLN D:369 , ASN D:429 , PHE D:433 , HIS D:434 , HEM D:1003 , HEM D:1005 , CA D:1007
BINDING SITE FOR RESIDUE HEM D1004
24
CC6
SOFTWARE
HIS D:309 , VAL D:314 , MET D:346 , ALA D:348 , CYS D:349 , CYS D:352 , HIS D:353 , ARG D:364 , HEM D:1004 , HIS E:353 , LYS E:356 , ARG F:141
BINDING SITE FOR RESIDUE HEM D1005
25
CC7
SOFTWARE
GLU D:235 , TYR D:236 , ASP D:283 , LYS D:295 , GLN D:297
BINDING SITE FOR RESIDUE CA D1006
26
CC8
SOFTWARE
GLY D:78 , GLU D:117 , ALA D:118 , HEM D:1003 , HEM D:1004
BINDING SITE FOR RESIDUE CA D1007
27
CC9
SOFTWARE
ARG E:116 , ALA E:118 , ASP E:127 , ILE E:131 , ARG E:133 , CYS E:147 , CYS E:150 , LYS E:151 , CYS E:232 , HIS E:233 , VAL E:234 , TYR E:236 , HIS E:298 , ASN E:429 , HEM E:1003 , HOH E:2005 , HOH E:2013
BINDING SITE FOR RESIDUE HEM E1001
28
DC1
SOFTWARE
TYR E:39 , GLN E:60 , TYR E:64 , GLY E:186 , CYS E:187 , CYS E:190 , HIS E:191 , MET E:196 , ARG E:221 , ARG E:225 , MET E:321 , TYR E:323 , ILE E:332 , SER E:333 , HIS E:335 , TRP E:337 , HEM E:1003 , ALA F:157
BINDING SITE FOR RESIDUE HEM E1002
29
DC2
SOFTWARE
GLY E:78 , SER E:79 , ALA E:118 , ARG E:119 , GLY E:120 , HIS E:121 , ALA E:124 , ASP E:127 , CYS E:150 , LYS E:151 , ILE E:185 , THR E:189 , VAL E:228 , CYS E:229 , CYS E:232 , HIS E:233 , HIS E:320 , MET E:321 , TRP E:337 , THR E:338 , HEM E:1001 , HEM E:1002 , HEM E:1004 , CA E:1007
BINDING SITE FOR RESIDUE HEM E1003
30
DC3
SOFTWARE
THR E:74 , LYS E:77 , GLY E:78 , GLU E:117 , GLU E:300 , TRP E:304 , HIS E:309 , VAL E:314 , THR E:315 , CYS E:316 , CYS E:319 , HIS E:320 , SER E:339 , PRO E:340 , MET E:341 , GLN E:369 , ASN E:429 , PHE E:433 , HIS E:434 , HEM E:1003 , CA E:1007 , HOH E:2009
BINDING SITE FOR RESIDUE HEM E1004
31
DC4
SOFTWARE
HIS D:353 , LYS D:356 , HIS E:309 , VAL E:314 , ASP E:318 , PRO E:340 , CYS E:349 , CYS E:352 , HIS E:353 , ARG E:364 , VAL E:365 , PRO E:436 , HOH E:2014 , MET F:148
BINDING SITE FOR RESIDUE HEM E1005
32
DC5
SOFTWARE
GLU E:235 , TYR E:236 , LYS E:295 , GLN E:297
BINDING SITE FOR RESIDUE CA E1006
33
DC6
SOFTWARE
GLY E:78 , GLU E:117 , ALA E:118 , HEM E:1003 , HEM E:1004
BINDING SITE FOR RESIDUE CA E1007
34
DC7
SOFTWARE
THR F:37 , CYS F:43 , CYS F:46 , MET F:49 , CYS F:66 , ASN F:67 , HIS F:70 , ASP F:89 , MET F:92 , LEU F:103 , ALA F:104 , GLY F:105 , THR F:108 , HEM F:1002 , HQO F:1005
BINDING SITE FOR RESIDUE HEM F1001
35
DC8
SOFTWARE
ARG F:40 , CYS F:43 , MET F:49 , VAL F:52 , HIS F:56 , HIS F:61 , SER F:65 , CYS F:66 , CYS F:69 , HIS F:70 , ALA F:104 , LYS F:109 , THR F:137 , VAL F:143 , GLN F:144 , HIS F:145 , HEM F:1001
BINDING SITE FOR RESIDUE HEM F1002
36
DC9
SOFTWARE
LYS A:329 , CYS C:119 , HIS C:120 , MET C:122 , THR C:123 , HEM C:1003 , GLY F:60 , HIS F:61 , ASP F:68 , CYS F:69 , VAL F:112 , ASN F:115 , CYS F:116 , CYS F:119 , HIS F:120 , HIS F:140 , HOH F:2003
BINDING SITE FOR RESIDUE HEM F1003
37
EC1
SOFTWARE
ARG A:325 , LYS A:329 , HEM C:1004 , TYR D:323 , THR D:324 , ARG D:325 , LYS D:331 , ARG D:347 , GLN D:351 , HIS F:120 , ASN F:124 , SER F:129 , CYS F:136 , CYS F:139 , HIS F:140
BINDING SITE FOR RESIDUE HEM F1004
38
EC2
SOFTWARE
THR F:37 , ASN F:67 , LYS F:82 , ALA F:85 , GLY F:86 , ASP F:89 , HEM F:1001
BINDING SITE FOR RESIDUE HQO F1005
[
close Site info
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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[
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2vr0a_ (A:)
1b: SCOP_d2vr0b_ (B:)
1c: SCOP_d2vr0d_ (D:)
1d: SCOP_d2vr0e_ (E:)
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Protein Domains
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Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Multiheme cytochromes
(149)
Superfamily
:
Multiheme cytochromes
(149)
Family
:
Di-heme elbow motif
(53)
Protein domain
:
automated matches
(16)
Desulfovibrio vulgaris [TaxId: 882]
(2)
1a
d2vr0a_
A:
1b
d2vr0b_
B:
1c
d2vr0d_
D:
1d
d2vr0e_
E:
[
close SCOP info
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_2vr0C00 (C:15-158)
1b: CATH_2vr0F00 (F:14-159)
2a: CATH_2vr0A02 (A:355-478)
2b: CATH_2vr0B02 (B:355-478)
2c: CATH_2vr0D02 (D:355-478)
2d: CATH_2vr0E02 (E:355-478)
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Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Multiheme cytochrome fold
(2)
Homologous Superfamily
:
Di-heme elbow motif domain
(2)
Desulfovibrio vulgaris. Organism_taxid: 882. Strain: hildenborough.
(1)
1a
2vr0C00
C:15-158
1b
2vr0F00
F:14-159
Architecture
:
Up-down Bundle
(3216)
Topology
:
Butyryl-CoA Dehydrogenase, subunit A; domain 3
(76)
Homologous Superfamily
:
Butyryl-CoA Dehydrogenase, subunit A, domain 3
(37)
Desulfovibrio vulgaris. Organism_taxid: 882. Strain: hildenborough.
(1)
2a
2vr0A02
A:355-478
2b
2vr0B02
B:355-478
2c
2vr0D02
D:355-478
2d
2vr0E02
E:355-478
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Cytochrom_C552_2vr0E01 (E:50-514)
1b: PFAM_Cytochrom_C552_2vr0E02 (E:50-514)
1c: PFAM_Cytochrom_C552_2vr0E03 (E:50-514)
1d: PFAM_Cytochrom_C552_2vr0E04 (E:50-514)
2a: PFAM_Cytochrom_NNT_2vr0F01 (F:14-150)
2b: PFAM_Cytochrom_NNT_2vr0F02 (F:14-150)
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Clan
:
Multiheme_cytos
(34)
Family
:
Cytochrom_C552
(6)
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
(1)
1a
Cytochrom_C552-2vr0E01
E:50-514
1b
Cytochrom_C552-2vr0E02
E:50-514
1c
Cytochrom_C552-2vr0E03
E:50-514
1d
Cytochrom_C552-2vr0E04
E:50-514
Family
:
Cytochrom_NNT
(1)
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
(1)
2a
Cytochrom_NNT-2vr0F01
F:14-150
2b
Cytochrom_NNT-2vr0F02
F:14-150
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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)
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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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