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.
4L3Y
Biol. Unit 1
Info
Asym.Unit (225 KB)
Biol.Unit 1 (618 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
NITRITE COMPLEX OF TVNIR, HIGH DOSE DATA SET (NO COMPLEX)
Authors
:
A. A. Trofimov, K. M. Polyakov, V. A. Lazarenko, A. N. Popov, T. V. Tikhon A. V. Tikhonov, V. O. Popov
Date
:
07 Jun 13 (Deposition) - 11 Jun 14 (Release) - 11 Jun 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Hemes C, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. A. Trofimov, K. M. Polyakov, V. A. Lazarenko, A. N. Popov, T. V. Tikhonova, A. V. Tikhonov, V. O. Popov
Investigation Of The X-Ray-Induced Nitrite Reduction Catalysed By Cytochrome C Nitrite Reductase From The Bacterium Thioalkalivibrio Nitratireducens
To Be Published
[
close entry info
]
Hetero Components
(5, 93)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
3a: HEME C (HECa)
3b: HEME C (HECb)
3c: HEME C (HECc)
3d: HEME C (HECd)
3e: HEME C (HECe)
3f: HEME C (HECf)
3g: HEME C (HECg)
3h: HEME C (HECh)
3i: HEME C (HECi)
3j: HEME C (HECj)
3k: HEME C (HECk)
3l: HEME C (HECl)
3m: HEME C (HECm)
3n: HEME C (HECn)
3o: HEME C (HECo)
3p: HEME C (HECp)
4a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
4b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
5a: NITRITE ION (NO2a)
5b: NITRITE ION (NO2b)
5c: NITRITE ION (NO2c)
5d: NITRITE ION (NO2d)
5e: NITRITE ION (NO2e)
5f: NITRITE ION (NO2f)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
GOL
15
Ligand/Ion
GLYCEROL
3
HEC
48
Ligand/Ion
HEME C
4
MPD
6
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
5
NO2
18
Ligand/Ion
NITRITE ION
6
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(35, 35)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
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 , HEC A:603 , NO2 A:609 , HOH A:714 , HOH A:800 , HOH A:801 , HOH A:806 , HOH A:918 , HOH A:1175
BINDING SITE FOR RESIDUE HEC A 601
02
AC2
SOFTWARE
CYS A:66 , HIS A:70 , GLN A:73 , LEU A:225 , CYS A:227 , CYS A:230 , HIS A:231 , ALA A:290 , MET A:384 , TYR A:395 , THR A:396 , HIS A:398 , HEC A:607 , HOH A:779 , HOH A:863 , HOH A:879
BINDING SITE FOR RESIDUE HEC A 602
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 , LYS A:188 , MET A:229 , CYS A:296 , CYS A:299 , HIS A:300 , HIS A:383 , MET A:384 , HEC A:601 , HEC A:604 , CA A:611 , HOH A:704 , HOH A:719 , HOH A:797
BINDING SITE FOR RESIDUE HEC A 603
04
AC4
SOFTWARE
HIS A:300 , PHE A:367 , HIS A:372 , VAL A:377 , 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 , HEC A:603 , HEC A:605 , CA A:611 , GOL A:613 , HOH A:797 , HOH A:807 , HOH A:908 , HOH A:915 , HOH A:987 , HOH A:1029
BINDING SITE FOR RESIDUE HEC A 604
05
AC5
SOFTWARE
ASN A:141 , TRP A:142 , GLN A:143 , HIS A:372 , PRO A:403 , ALA A:410 , CYS A:411 , CYS A:414 , HIS A:415 , TRP A:418 , ILE A:427 , HEC A:604 , HOH A:940
BINDING SITE FOR RESIDUE HEC A 605
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 , HEC A:607 , HEC A:608 , HOH A:758 , HOH A:1178 , HOH A:1215
BINDING SITE FOR RESIDUE HEC A 606
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 , CYS A:227 , HIS A:231 , ALA A:236 , HEC A:602 , HEC A:606 , HOH A:1163 , HOH A:1167 , HOH A:1223 , HOH A:1282 , THR B:68
BINDING SITE FOR RESIDUE HEC A 607
08
AC8
SOFTWARE
GLN A:13 , CYS A:14 , CYS A:17 , HIS A:18 , HIS A:39 , HIS A:44 , ALA A:48 , SER A:49 , SER A:50 , ARG A:52 , MET A:53 , ARG A:56 , PRO A:57 , THR A:59 , LEU A:194 , ARG A:276 , GLY A:277 , HEC A:606 , HOH A:760 , HOH A:777 , HOH A:1000 , HOH A:1212 , HOH A:1217
BINDING SITE FOR RESIDUE HEC A 608
09
AC9
SOFTWARE
TYR A:303 , HIS A:361 , HEC A:601 , HOH A:916 , HOH A:1175
BINDING SITE FOR RESIDUE NO2 A 609
10
BC1
SOFTWARE
GLU A:302 , TYR A:303 , LYS A:358 , GLN A:360 , HOH A:866 , HOH A:962
BINDING SITE FOR RESIDUE CA A 610
11
BC2
SOFTWARE
PRO A:116 , HEC A:603 , HEC A:604 , GOL A:613 , HOH A:908 , HOH A:925 , HOH A:1029
BINDING SITE FOR RESIDUE CA A 611
12
BC3
SOFTWARE
ARG A:87 , VAL A:128 , GLN A:138 , PHE A:139 , TRP A:142 , TYR A:433 , ARG A:497 , HOH A:1098
BINDING SITE FOR RESIDUE MPD A 612
13
BC4
SOFTWARE
ARG A:96 , GLU A:115 , PRO A:116 , ASN A:486 , HEC A:604 , CA A:611 , HOH A:807 , HOH A:1029 , HOH A:1033
BINDING SITE FOR RESIDUE GOL A 613
14
BC5
SOFTWARE
ASP A:101 , ALA A:110 , PHE A:111 , GLN A:175 , TRP A:444 , ILE A:504 , LYS A:508 , HOH A:716 , HOH A:935
BINDING SITE FOR RESIDUE GOL A 614
15
BC6
SOFTWARE
ASP A:251 , LYS A:271 , ARG A:322 , HOH A:842
BINDING SITE FOR RESIDUE GOL A 615
16
BC7
SOFTWARE
THR A:351 , LYS A:447 , ASN A:515 , HOH A:743 , HOH A:896 , HOH A:1061 , HOH A:1165
BINDING SITE FOR RESIDUE SO4 A 616
17
BC8
SOFTWARE
SER A:212 , GLU A:213 , VAL A:214 , NO2 A:618 , HOH A:819 , HOH A:959 , HOH A:1047 , HOH A:1106
BINDING SITE FOR RESIDUE NO2 A 617
18
BC9
SOFTWARE
VAL A:214 , NO2 A:617 , HOH A:903 , HOH A:1047 , HOH A:1106
BINDING SITE FOR RESIDUE NO2 A 618
19
CC1
SOFTWARE
HIS B:113 , ALA B:114 , ASP B:125 , HIS B:126 , VAL B:129 , ARG B:131 , 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 , HEC B:603 , NO2 B:609 , HOH B:739 , HOH B:827 , HOH B:828 , HOH B:833 , HOH B:946 , HOH B:1205
BINDING SITE FOR RESIDUE HEC B 601
20
CC2
SOFTWARE
CYS B:66 , 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 , HEC B:607 , HOH B:805 , HOH B:890 , HOH B:906 , HOH B:1180 , HOH B:1264
BINDING SITE FOR RESIDUE HEC B 602
21
CC3
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 , LYS B:188 , MET B:229 , CYS B:296 , CYS B:299 , HIS B:300 , HIS B:383 , MET B:384 , HEC B:601 , HEC B:604 , CA B:611 , HOH B:729 , HOH B:745 , HOH B:824 , HOH B:1059
BINDING SITE FOR RESIDUE HEC B 603
22
CC4
SOFTWARE
PHE B:367 , HIS B:372 , VAL B:377 , 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 , HEC B:603 , HEC B:605 , CA B:611 , GOL B:613 , HOH B:824 , HOH B:834 , HOH B:936 , HOH B:943 , HOH B:1016 , HOH B:1059
BINDING SITE FOR RESIDUE HEC B 604
23
CC5
SOFTWARE
ASN B:141 , TRP B:142 , GLN B:143 , VAL B:371 , HIS B:372 , ASN B:375 , PRO B:403 , ALA B:410 , CYS B:411 , CYS B:414 , HIS B:415 , TRP B:418 , ILE B:427 , HEC B:604
BINDING SITE FOR RESIDUE HEC B 605
24
CC6
SOFTWARE
CYS B:14 , PHE B:15 , HIS B:18 , HIS B:25 , 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:607 , HEC B:608 , HOH B:784 , HOH B:1202
BINDING SITE FOR RESIDUE HEC B 606
25
CC7
SOFTWARE
THR A:68 , 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 , HEC B:602 , HEC B:606 , HOH B:708 , HOH B:1193 , HOH B:1197 , HOH B:1257 , HOH B:1272
BINDING SITE FOR RESIDUE HEC B 607
26
CC8
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 , ARG B:51 , ARG B:52 , MET B:53 , ARG B:56 , PRO B:57 , THR B:59 , LEU B:194 , GLN B:275 , ARG B:276 , HEC B:606 , HOH B:786 , HOH B:803 , HOH B:1029 , HOH B:1202 , HOH B:1255 , HOH B:1283
BINDING SITE FOR RESIDUE HEC B 608
27
CC9
SOFTWARE
TYR B:303 , HIS B:361 , HEC B:601 , HOH B:944 , HOH B:1205
BINDING SITE FOR RESIDUE NO2 B 609
28
DC1
SOFTWARE
GLU B:302 , TYR B:303 , LYS B:358 , GLN B:360 , HOH B:893 , HOH B:990
BINDING SITE FOR RESIDUE CA B 610
29
DC2
SOFTWARE
PRO B:116 , HEC B:603 , HEC B:604 , GOL B:613 , HOH B:936 , HOH B:953 , HOH B:1059
BINDING SITE FOR RESIDUE CA B 611
30
DC3
SOFTWARE
ARG B:87 , VAL B:128 , GLN B:138 , PHE B:139 , TRP B:142 , ARG B:497 , HOH B:1128
BINDING SITE FOR RESIDUE MPD B 612
31
DC4
SOFTWARE
ARG B:96 , GLU B:115 , PRO B:116 , ASN B:486 , HEC B:604 , CA B:611 , HOH B:830 , HOH B:834 , HOH B:1059 , HOH B:1063
BINDING SITE FOR RESIDUE GOL B 613
32
DC5
SOFTWARE
ASP B:101 , ALA B:110 , GLN B:175 , TRP B:444 , ILE B:504 , LYS B:508 , HOH B:742 , HOH B:963
BINDING SITE FOR RESIDUE GOL B 614
33
DC6
SOFTWARE
THR B:351 , LYS B:447 , ASN B:515 , HOH B:769 , HOH B:1091 , HOH B:1236
BINDING SITE FOR RESIDUE SO4 B 615
34
DC7
SOFTWARE
GLN B:169 , GLU B:213 , VAL B:214 , NO2 B:617 , HOH B:931 , HOH B:1077 , HOH B:1136
BINDING SITE FOR RESIDUE NO2 B 616
35
DC8
SOFTWARE
SER B:212 , GLU B:213 , VAL B:214 , NO2 B:616 , HOH B:846 , HOH B:987 , HOH B:1077 , HOH B:1136
BINDING SITE FOR RESIDUE NO2 B 617
[
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 A
Chain B
Asymmetric Unit 1
Asymmetric Unit 2
Asymmetric Unit 3
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 (225 KB)
Header - Asym.Unit
Biol.Unit 1 (618 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
4L3Y
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
