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.
PLEASE WAIT...
Getting 'Exon' information from database.
3S7W
Asym. Unit
Info
Asym.Unit (219 KB)
Biol.Unit 1 (604 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE TVNIRB FORM OF THIOALKALIVIBRIO NITRATIREDUCENS CYTOCHROME C NITRITE REDUCTASE WITH AN OXIDIZED GLN360 IN A COMPLEX WITH HYDROXYLAMINE
Authors
:
A. A. Trofimov, K. M. Polyakov, T. V. Tikhonova, V. O. Popov
Date
:
27 May 11 (Deposition) - 27 Jul 11 (Release) - 27 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.79
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Eight Hemes C, Oxidoreductase, Tyr-Cys (Ce2-S) And Tyr-Gln (Ce1-Cg) Bonds
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. A. Trofimov, K. M. Polyakov, T. V. Tikhonova, V. O. Popov
Structure Of The Tvnirb Form Of Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase With An Oxidized Gln360 In A Complex With Hydroxylamine
To Be Published
[
close entry info
]
Hetero Components
(5, 31)
Info
All Hetero Components
1a: AZIDE ION (AZIa)
1b: AZIDE ION (AZIb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
4a: HEME C (HECa)
4b: HEME C (HECb)
4c: HEME C (HECc)
4d: HEME C (HECd)
4e: HEME C (HECe)
4f: HEME C (HECf)
4g: HEME C (HECg)
4h: HEME C (HECh)
4i: HEME C (HECi)
4j: HEME C (HECj)
4k: HEME C (HECk)
4l: HEME C (HECl)
4m: HEME C (HECm)
4n: HEME C (HECn)
4o: HEME C (HECo)
4p: HEME C (HECp)
5a: NITRITE ION (NO2a)
5b: NITRITE ION (NO2b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AZI
2
Ligand/Ion
AZIDE ION
2
CA
4
Ligand/Ion
CALCIUM ION
3
GOL
7
Ligand/Ion
GLYCEROL
4
HEC
16
Ligand/Ion
HEME C
5
NO2
2
Ligand/Ion
NITRITE ION
[
close Hetero Component info
]
Sites
(31, 31)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
NO2 A:1 , HIS A:113 , ALA A:114 , ASP A:125 , HIS A:126 , VAL A:129 , ARG A:131 , CYS A:184 , CYS A:187 , LYS A:188 , ARG A:242 , CYS A:299 , HIS A:300 , TYR A:303 , CYS A:305 , HIS A:361 , ASN A:486 , HOH A:549 , HOH A:724 , HOH A:725 , HOH A:731 , HOH A:965 , HEC A:1006 , HOH A:1011
BINDING SITE FOR RESIDUE HEC A 1004
02
AC2
SOFTWARE
HIS A:70 , GLN A:73 , LEU A:225 , CYS A:227 , CYS A:230 , HIS A:231 , MET A:384 , TYR A:395 , THR A:396 , HIS A:398 , HOH A:812 , HOH A:836 , HEC A:1003
BINDING SITE FOR RESIDUE HEC A 1005
03
AC3
SOFTWARE
SER A:84 , PRO A:116 , ARG A:117 , HIS A:119 , PHE A:121 , MET A:122 , ASP A:125 , CYS A:187 , MET A:229 , CYS A:296 , CYS A:299 , HIS A:300 , HIS A:383 , MET A:384 , CA A:525 , HOH A:532 , HOH A:577 , HOH A:719 , HEC A:1004 , HEC A:1007
BINDING SITE FOR RESIDUE HEC A 1006
04
AC4
SOFTWARE
GOL A:3 , HIS A:300 , PHE A:367 , HIS A:372 , ALA A:378 , CYS A:379 , CYS A:382 , HIS A:383 , THR A:402 , ARG A:404 , LYS A:431 , ASN A:486 , PHE A:490 , HIS A:491 , CA A:525 , HOH A:719 , HOH A:720 , HOH A:732 , HOH A:894 , HEC A:1006 , HOH A:1025
BINDING SITE FOR RESIDUE HEC A 1007
05
AC5
SOFTWARE
ASN A:141 , TRP A:142 , GLN A:143 , VAL A:371 , HIS A:372 , PRO A:403 , ALA A:410 , CYS A:411 , CYS A:414 , HIS A:415 , TRP A:418 , ILE A:427 , PHE A:490 , HOH A:607 , HOH A:992
BINDING SITE FOR RESIDUE HEC A 1008
06
AC6
SOFTWARE
CYS A:14 , PHE A:15 , HIS A:18 , HIS A:25 , VAL A:33 , ASN A:34 , CYS A:35 , CYS A:38 , HIS A:39 , THR A:59 , LEU A:194 , PHE A:228 , PRO A:233 , HIS A:234 , ARG A:239 , PHE A:274 , ARG A:276 , ARG A:282 , HOH A:936 , HOH A:949 , HEC A:1001 , HEC A:1003
BINDING SITE FOR RESIDUE HEC A 1002
07
AC7
SOFTWARE
LYS A:29 , HIS A:30 , HIS A:37 , ALA A:65 , CYS A:66 , THR A:68 , CYS A:69 , HIS A:70 , HIS A:231 , ALA A:236 , HOH A:876 , HOH A:877 , HOH A:935 , HOH A:980 , HOH A:991 , HEC A:1002 , HEC A:1005 , HOH A:1072 , THR B:68
BINDING SITE FOR RESIDUE HEC A 1003
08
AC8
SOFTWARE
GLN A:13 , CYS A:14 , CYS A:17 , HIS A:18 , HIS A:39 , HIS A:44 , VAL A:45 , ALA A:48 , SER A:49 , SER A:50 , ARG A:51 , ARG A:52 , MET A:53 , ARG A:56 , PRO A:57 , THR A:59 , GLN A:275 , ARG A:276 , HOH A:666 , HOH A:695 , HOH A:949 , HEC A:1002 , HOH A:1041 , HOH A:1057
BINDING SITE FOR RESIDUE HEC A 1001
09
AC9
SOFTWARE
PHE A:109 , ARG A:131 , TYR A:303 , HIS A:361 , HOH A:730 , HOH A:965 , HEC A:1004 , HOH A:1011 , HOH A:1012
BINDING SITE FOR RESIDUE NO2 A 1
10
BC1
SOFTWARE
GLU A:302 , TYR A:303 , LYS A:358 , GLN A:360 , HOH A:815 , HOH A:816
BINDING SITE FOR RESIDUE CA A 2
11
BC2
SOFTWARE
ARG A:96 , GLU A:115 , PRO A:116 , ASN A:486 , CA A:525 , HOH A:727 , HEC A:1007
BINDING SITE FOR RESIDUE GOL A 3
12
BC3
SOFTWARE
ASP A:101 , ALA A:110 , PHE A:111 , GLN A:175 , TRP A:444 , ILE A:504 , LYS A:508 , HOH A:564 , HOH A:620
BINDING SITE FOR RESIDUE GOL A 4
13
BC4
SOFTWARE
GLN A:138 , PHE A:139 , ASN A:141 , TRP A:142
BINDING SITE FOR RESIDUE GOL A 524
14
BC5
SOFTWARE
GOL A:3 , PRO A:116 , HOH A:595 , HOH A:894 , HEC A:1006 , HEC A:1007
BINDING SITE FOR RESIDUE CA A 525
15
BC6
SOFTWARE
SER A:76 , GLU A:79 , SER A:397
BINDING SITE FOR RESIDUE AZI A 526
16
BC7
SOFTWARE
NO2 B:1 , HIS B:113 , ALA B:114 , ASP B:125 , HIS B:126 , VAL B:129 , ARG B:131 , ALA B:179 , CYS B:184 , CYS B:187 , LYS B:188 , ARG B:242 , CYS B:299 , HIS B:300 , TYR B:303 , CYS B:305 , HIS B:361 , ASN B:486 , HOH B:585 , HOH B:732 , HOH B:733 , HOH B:739 , HOH B:972 , HEC B:1006 , HOH B:1019
BINDING SITE FOR RESIDUE HEC B 1004
17
BC8
SOFTWARE
HIS B:70 , GLN B:73 , LEU B:225 , CYS B:227 , CYS B:230 , HIS B:231 , MET B:384 , TYR B:395 , THR B:396 , HIS B:398 , HOH B:598 , HOH B:820 , HOH B:844 , HOH B:930 , HOH B:946 , HEC B:1003
BINDING SITE FOR RESIDUE HEC B 1005
18
BC9
SOFTWARE
SER B:84 , PRO B:116 , ARG B:117 , HIS B:119 , PHE B:121 , MET B:122 , ASP B:125 , CYS B:187 , MET B:229 , CYS B:296 , CYS B:299 , HIS B:300 , HIS B:383 , MET B:384 , CA B:526 , HOH B:571 , HOH B:596 , HOH B:727 , HEC B:1004 , HEC B:1007
BINDING SITE FOR RESIDUE HEC B 1006
19
CC1
SOFTWARE
GOL B:3 , HIS B:300 , PHE B:367 , HIS B:372 , ALA B:378 , CYS B:379 , CYS B:382 , HIS B:383 , THR B:402 , ARG B:404 , LYS B:431 , ASN B:486 , PHE B:490 , HIS B:491 , CA B:526 , HOH B:727 , HOH B:728 , HOH B:902 , HEC B:1006
BINDING SITE FOR RESIDUE HEC B 1007
20
CC2
SOFTWARE
ASN B:141 , TRP B:142 , GLN B:143 , VAL B:371 , HIS B:372 , PRO B:403 , ALA B:410 , CYS B:411 , CYS B:414 , HIS B:415 , TRP B:418 , ILE B:427 , PHE B:490 , HOH B:680 , HOH B:1000 , HOH B:1059
BINDING SITE FOR RESIDUE HEC B 1008
21
CC3
SOFTWARE
CYS B:14 , PHE B:15 , HIS B:18 , ILE B:21 , VAL B:33 , ASN B:34 , CYS B:35 , CYS B:38 , HIS B:39 , LEU B:194 , PHE B:228 , PRO B:233 , HIS B:234 , ARG B:239 , PHE B:274 , ARG B:276 , ARG B:282 , HEC B:1001 , HEC B:1003 , HOH B:1053 , HOH B:1055 , HOH B:1069
BINDING SITE FOR RESIDUE HEC B 1002
22
CC4
SOFTWARE
LYS B:29 , HIS B:30 , HIS B:37 , ALA B:65 , CYS B:66 , THR B:68 , CYS B:69 , HIS B:70 , CYS B:227 , HIS B:231 , ALA B:236 , HOH B:541 , HOH B:884 , HOH B:885 , HOH B:942 , HOH B:988 , HOH B:999 , HEC B:1002 , HEC B:1005
BINDING SITE FOR RESIDUE HEC B 1003
23
CC5
SOFTWARE
GLN B:13 , CYS B:14 , CYS B:17 , HIS B:18 , HIS B:39 , HIS B:44 , VAL B:45 , ALA B:48 , SER B:49 , SER B:50 , ARG B:52 , MET B:53 , ARG B:56 , PRO B:57 , THR B:59 , LEU B:194 , ARG B:276 , GLY B:277 , HOH B:568 , HOH B:674 , HOH B:703 , HEC B:1002 , HOH B:1052
BINDING SITE FOR RESIDUE HEC B 1001
24
CC6
SOFTWARE
TYR B:303 , HIS B:361 , HOH B:738 , HOH B:972 , HEC B:1004 , HOH B:1019 , HOH B:1020
BINDING SITE FOR RESIDUE NO2 B 1
25
CC7
SOFTWARE
GLU B:302 , TYR B:303 , LYS B:358 , GLN B:360 , HOH B:823 , HOH B:824
BINDING SITE FOR RESIDUE CA B 2
26
CC8
SOFTWARE
ARG B:96 , GLU B:115 , PRO B:116 , ASN B:486 , CA B:526 , HOH B:735 , HEC B:1007
BINDING SITE FOR RESIDUE GOL B 3
27
CC9
SOFTWARE
ASP B:101 , ALA B:110 , GLN B:175 , TRP B:444 , ILE B:504 , LYS B:508 , HOH B:591 , HOH B:633
BINDING SITE FOR RESIDUE GOL B 4
28
DC1
SOFTWARE
GLN B:138 , PHE B:139 , ASN B:141 , TRP B:142
BINDING SITE FOR RESIDUE GOL B 524
29
DC2
SOFTWARE
ASP B:168 , GLN B:169 , GLU B:213 , VAL B:214 , HOH B:754 , HOH B:768
BINDING SITE FOR RESIDUE GOL B 525
30
DC3
SOFTWARE
GOL B:3 , PRO B:116 , HOH B:610 , HOH B:902 , HEC B:1006 , HEC B:1007
BINDING SITE FOR RESIDUE CA B 526
31
DC4
SOFTWARE
VAL B:58 , THR B:59 , HOH B:589 , HOH B:703
BINDING SITE FOR RESIDUE AZI B 527
[
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, 2)
Info
All PROSITE Patterns/Profiles
1: MULTIHEME_CYTC (A:9-420,B:9-420)
;
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.
NIR_THIND
37-448
2
A:9-420
B:9-420
[
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.
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 A
Chain B
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 (219 KB)
Header - Asym.Unit
Biol.Unit 1 (604 KB)
Header - Biol.Unit 1
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
3S7W
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
