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.
5CH7
Biol. Unit 3
Info
Asym.Unit (656 KB)
Biol.Unit 1 (226 KB)
Biol.Unit 2 (219 KB)
Biol.Unit 3 (224 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE PERCHLORATE REDUCTASE PCRAB - PHE164 GATE SWITCH INTERMEDIATE - FROM AZOSPIRA SUILLUM PS
Authors
:
C. -L. Tsai, J. A. Tainer
Date
:
10 Jul 15 (Deposition) - 09 Mar 16 (Release) - 11 May 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Keywords
:
Electron-Shuttling Protein, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. D. Youngblut, C. L. Tsai, I. C. Clark, H. K. Carlson, A. P. Maglaqui, P. S. Gau-Pan, S. A. Redford, A. Wong, J. A. Tainer, J. D. Coates
Perchlorate Reductase Is Distinguished By Active Site Aromatic Gate Residues.
J. Biol. Chem. V. 291 9190 2016
[
close entry info
]
Hetero Components
(6, 13)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
3a: FE3-S4 CLUSTER (F3Sa)
3b: FE3-S4 CLUSTER (F3Sb)
3c: FE3-S4 CLUSTER (F3Sc)
4a: GLYCEROL (GOLa)
5a: PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3... (MD1a)
5b: PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3... (MD1b)
5c: PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3... (MD1c)
6a: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDa)
6b: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDb)
6c: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,... (MGDc)
7a: MOLYBDENUM ATOM (MOa)
7b: MOLYBDENUM ATOM (MOb)
7c: MOLYBDENUM ATOM (MOc)
8a: SODIUM ION (NAa)
8b: SODIUM ION (NAb)
8c: SODIUM ION (NAc)
8d: SODIUM ION (NAd)
9a: IRON/SULFUR CLUSTER (SF4a)
9b: IRON/SULFUR CLUSTER (SF4b)
9c: IRON/SULFUR CLUSTER (SF4c)
9d: IRON/SULFUR CLUSTER (SF4d)
9e: IRON/SULFUR CLUSTER (SF4e)
9f: IRON/SULFUR CLUSTER (SF4f)
9g: IRON/SULFUR CLUSTER (SF4g)
9h: IRON/SULFUR CLUSTER (SF4h)
9i: IRON/SULFUR CLUSTER (SF4i)
9j: IRON/SULFUR CLUSTER (SF4j)
9k: IRON/SULFUR CLUSTER (SF4k)
9l: IRON/SULFUR CLUSTER (SF4l)
10a: SULFITE ION (SO3a)
10b: SULFITE ION (SO3b)
10c: SULFITE ION (SO3c)
10d: SULFITE ION (SO3d)
10e: SULFITE ION (SO3e)
11a: ZINC ION (ZNa)
11b: ZINC ION (ZNb)
11c: ZINC ION (ZNc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
-1
Ligand/Ion
ACETATE ION
2
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
3
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
4
GOL
-1
Ligand/Ion
GLYCEROL
5
MD1
1
Ligand/Ion
PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YLESTER GUANYLATE ESTER
6
MGD
1
Ligand/Ion
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINEDINUCLEOTIDE
7
MO
-1
Ligand/Ion
MOLYBDENUM ATOM
8
NA
-1
Ligand/Ion
SODIUM ION
9
SF4
4
Ligand/Ion
IRON/SULFUR CLUSTER
10
SO3
1
Ligand/Ion
SULFITE ION
11
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(17, 17)
Info
All Sites
01: AE8 (SOFTWARE)
02: AG2 (SOFTWARE)
03: AG3 (SOFTWARE)
04: AG4 (SOFTWARE)
05: AG5 (SOFTWARE)
06: AG6 (SOFTWARE)
07: AG7 (SOFTWARE)
08: AG8 (SOFTWARE)
09: AG9 (SOFTWARE)
10: AH1 (SOFTWARE)
11: AH2 (SOFTWARE)
12: AH3 (SOFTWARE)
13: AH4 (SOFTWARE)
14: AH5 (SOFTWARE)
15: AH6 (SOFTWARE)
16: AH7 (SOFTWARE)
17: AH8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AE8
SOFTWARE
GLU C:495 , ASN C:553 , HOH C:1173 , HOH C:1195 , HOH C:1221 , TRP E:806 , ARG F:103
binding site for residue EDO C 1006
02
AG2
SOFTWARE
HIS E:32 , CYS E:36 , ALA E:39 , CYS E:40 , HIS E:42 , GLY E:73 , CYS E:74
binding site for residue SF4 E 1001
03
AG3
SOFTWARE
ASP E:170 , MGD E:1003 , MD1 E:1004
binding site for residue MO E 1002
04
AG4
SOFTWARE
LYS E:76 , ASP E:170 , TRP E:200 , GLY E:201 , ASN E:203 , GLN E:206 , THR E:207 , ARG E:208 , ILE E:228 , SER E:229 , PRO E:230 , ASP E:231 , ASN E:233 , GLY E:248 , ASP E:250 , GLY E:421 , GLY E:422 , GLY E:423 , TRP E:427 , ILE E:458 , GLY E:459 , ASN E:761 , PRO E:763 , HIS E:764 , SER E:765 , ARG E:766 , SER E:768 , VAL E:769 , HIS E:770 , ARG E:830 , ARG E:882 , MO E:1002 , MD1 E:1004 , HOH E:1141 , HOH E:1156 , HOH E:1390 , HOH E:1392 , HOH E:1404
binding site for residue MGD E 1003
05
AG5
SOFTWARE
LEU E:33 , ASN E:35 , TYR E:168 , ASP E:170 , HIS E:426 , TYR E:536 , ARG E:537 , GLY E:538 , ASN E:539 , GLN E:543 , LYS E:545 , ILE E:564 , ASN E:565 , ILE E:566 , ARG E:567 , ASP E:569 , SER E:581 , TRP E:584 , LYS E:587 , ASP E:615 , SER E:762 , HIS E:764 , VAL E:769 , HIS E:770 , SER E:771 , THR E:772 , HIS E:835 , GLN E:849 , CYS E:852 , GLN E:881 , ARG E:882 , MO E:1002 , MGD E:1003 , HOH E:1205 , HOH E:1250 , HOH E:1385
binding site for residue MD1 E 1004
06
AG6
SOFTWARE
TRP A:806 , ARG B:103 , ARG B:105 , GLU E:495 , ASN E:553 , HOH E:1151 , HOH E:1301 , HOH E:1343
binding site for residue EDO E 1005
07
AG7
SOFTWARE
THR E:185 , LYS E:462 , THR E:593 , SER E:594 , HIS E:596 , ASN E:697 , TYR E:708
binding site for residue EDO E 1006
08
AG8
SOFTWARE
GLU E:808 , TRP E:810 , LYS E:815 , LYS E:889
binding site for residue EDO E 1007
09
AG9
SOFTWARE
HIS E:81 , ZN E:1010 , LYS F:33
binding site for residue SO3 E 1008
10
AH1
SOFTWARE
VAL E:777 , HOH E:1615
binding site for residue NA E 1009
11
AH2
SOFTWARE
HIS E:81 , ASP E:82 , SO3 E:1008 , LYS F:33
binding site for residue ZN E 1010
12
AH3
SOFTWARE
CYS F:149 , ASN F:151 , CYS F:170 , LYS F:171 , GLY F:172 , ALA F:173 , GLN F:174 , ALA F:175 , CYS F:176
binding site for residue F3S F 401
13
AH4
SOFTWARE
CYS F:137 , ASN F:138 , CYS F:140 , CYS F:145 , CYS F:180
binding site for residue SF4 F 402
14
AH5
SOFTWARE
CYS F:21 , ILE F:22 , CYS F:24 , GLN F:25 , CYS F:27 , ARG F:47 , CYS F:216
binding site for residue SF4 F 403
15
AH6
SOFTWARE
TYR F:14 , CYS F:31 , TRP F:35 , ARG F:47 , CYS F:197 , GLY F:199 , CYS F:200 , CYS F:212
binding site for residue SF4 F 404
16
AH7
SOFTWARE
GLY F:85 , ILE F:86 , PHE F:88 , PRO F:108 , THR F:109 , PRO F:110 , ARG F:111 , SER F:112
binding site for residue EDO F 405
17
AH8
SOFTWARE
PHE F:97 , HOH F:512
binding site for residue EDO F 406
[
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
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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 E
Chain F
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 (656 KB)
Header - Asym.Unit
Biol.Unit 1 (226 KB)
Header - Biol.Unit 1
Biol.Unit 2 (219 KB)
Header - Biol.Unit 2
Biol.Unit 3 (224 KB)
Header - Biol.Unit 3
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
5CH7
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help