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.
5AG1
Asym. Unit
Info
Asym.Unit (165 KB)
Biol.Unit 1 (83 KB)
Biol.Unit 2 (80 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
DYP-TYPE PEROXIDASE OF AURICULARIA AURICULA-JUDAE (AAUDYPI) WITH MESO-NITRATED HEME
Authors
:
E. Strittmatter, K. Piontek, D. A. Plattner
Date
:
27 Jan 15 (Deposition) - 02 Mar 16 (Release) - 02 Mar 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Oxidoreductase, Dyp, Fungal, Heme, Glycoprotein, Nitration
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Strittmatter, K. Piontek, D. A. Plattner
Crystallographic Trapping Of A Covalently Modified Heme In A Dye-Decolorizing Peroxidase
To Be Published
[
close entry info
]
Hetero Components
(6, 21)
Info
All Hetero Components
1a: CACODYLATE ION (CACa)
1b: CACODYLATE ION (CACb)
2a: FORMIC ACID (FMTa)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
4a: DELTA-MESO NITROHEME (N7Ha)
4b: DELTA-MESO NITROHEME (N7Hb)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6a: NITRITE ION (NO2a)
6b: NITRITE ION (NO2b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CAC
2
Ligand/Ion
CACODYLATE ION
2
FMT
1
Ligand/Ion
FORMIC ACID
3
GOL
8
Ligand/Ion
GLYCEROL
4
N7H
2
Ligand/Ion
DELTA-MESO NITROHEME
5
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
NO2
2
Ligand/Ion
NITRITE ION
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:286 , HIS A:287 , ALA A:288 , HOH A:2375
BINDING SITE FOR RESIDUE CAC A1449
02
AC2
SOFTWARE
HIS B:287 , ALA B:288
BINDING SITE FOR RESIDUE CAC B1449
03
AC3
SOFTWARE
ASP A:126 , GLN A:130 , HOH A:2218 , HOH A:2474 , HOH A:2475 , SER B:152 , PRO B:339 , GOL B:1453
BINDING SITE FOR RESIDUE GOL A1450
04
AC4
SOFTWARE
LYS A:21 , SER A:152 , PRO A:339 , GLU A:340 , HOH A:2244 , HOH A:2410 , HOH A:2412 , ASP B:126 , ASP B:129 , GLN B:130
BINDING SITE FOR RESIDUE GOL B1450
05
AC5
SOFTWARE
ARG A:154 , GLU A:158 , PHE A:164 , GLY A:165 , ASN A:227 , LYS A:257 , HOH A:2307 , HOH A:2476
BINDING SITE FOR RESIDUE GOL A1451
06
AC6
SOFTWARE
ARG A:445 , PRO B:201 , ILE B:202 , THR B:203 , HOH B:2407
BINDING SITE FOR RESIDUE GOL B1451
07
AC7
SOFTWARE
ARG B:251 , SER B:294 , ASP B:295 , GLN B:296 , SER B:297 , GLY B:410 , LEU B:412 , PRO B:413 , SER B:416 , HOH B:2317
BINDING SITE FOR RESIDUE GOL B1452
08
AC8
SOFTWARE
GOL A:1450 , HOH A:2211 , SER B:150 , SER B:152 , TYR B:337 , GLY B:338 , HOH B:2180
BINDING SITE FOR RESIDUE GOL B1453
09
AC9
SOFTWARE
ALA A:272 , ASP A:276 , ARG A:279 , HOH A:2358
BINDING SITE FOR RESIDUE GOL A1452
10
BC1
SOFTWARE
GLY A:196 , ALA A:197 , THR A:198 , ASN A:199 , ASP A:200
BINDING SITE FOR RESIDUE GOL A1453
11
BC2
SOFTWARE
GLU A:162 , PHE A:166 , LEU A:167 , ASP A:168 , GLY A:169 , ILE A:170 , ALA A:171 , GLN A:221 , VAL A:253 , ARG A:255 , HIS A:304 , THR A:308 , ARG A:309 , ARG A:311 , ARG A:332 , LEU A:357 , PHE A:359 , PHE A:370 , ILE A:398 , NO2 A:1460 , HOH A:2339 , HOH A:2365 , HOH A:2372 , HOH A:2483
BINDING SITE FOR RESIDUE N7H A1458
12
BC3
SOFTWARE
GLU B:162 , PHE B:166 , LEU B:167 , ASP B:168 , GLY B:169 , ILE B:170 , ALA B:171 , LEU B:219 , GLN B:221 , VAL B:253 , ARG B:255 , HIS B:304 , THR B:308 , ARG B:309 , ARG B:311 , ARG B:332 , PHE B:359 , PHE B:370 , ILE B:398 , VAL B:426 , NO2 B:1457 , HOH B:2273 , HOH B:2302 , HOH B:2309 , HOH B:2409
BINDING SITE FOR RESIDUE N7H B1456
13
BC4
SOFTWARE
ASN A:30 , SER A:141
BINDING SITE FOR RESIDUE FMT A1459
14
BC5
SOFTWARE
ASP A:168 , ARG A:332 , LEU A:357 , PHE A:359 , N7H A:1458 , HOH A:2259
BINDING SITE FOR RESIDUE NO2 A1460
15
BC6
SOFTWARE
ASP B:168 , ARG B:332 , PHE B:359 , N7H B:1456 , HOH B:2201 , HOH B:2344
BINDING SITE FOR RESIDUE NO2 B1457
16
BC7
SOFTWARE
GLN A:278 , ASN A:282 , PRO A:320 , HOH A:2367 , HOH A:2477 , HOH A:2478
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1454 THROUGH NAG A1457 BOUND TO ASN A 282
17
BC8
SOFTWARE
LYS A:228 , ASP A:232 , ALA A:347 , ASN A:349 , HOH A:2309 , HOH A:2479
BINDING SITE FOR MONO-SACCHARIDE NAG A1455 BOUND TO ASN A 349
18
BC9
SOFTWARE
ASN A:415 , SER A:417 , HOH A:2459 , HOH A:2463 , HOH A:2480 , HOH A:2481 , HOH A:2482
BINDING SITE FOR MONO-SACCHARIDE NAG A1456 BOUND TO ASN A 415
19
CC1
SOFTWARE
GLN B:278 , ARG B:279 , ASN B:282 , PRO B:320 , HOH B:2304 , HOH B:2306 , HOH B:2408
BINDING SITE FOR MONO-SACCHARIDE NAG B1454 BOUND TO ASN B 282
20
CC2
SOFTWARE
LYS B:228 , ASP B:232 , ALA B:347 , ASN B:349 , HOH B:2352
BINDING SITE FOR MONO-SACCHARIDE NAG B1455 BOUND TO ASN B 349
[
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
(0, 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.
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 (165 KB)
Header - Asym.Unit
Biol.Unit 1 (83 KB)
Header - Biol.Unit 1
Biol.Unit 2 (80 KB)
Header - Biol.Unit 2
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
5AG1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
