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.
4KFE
Biol. Unit 3
Info
Asym.Unit (1.3 MB)
Biol.Unit 1 (447 KB)
Biol.Unit 2 (449 KB)
Biol.Unit 3 (448 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 HANSENULA POLYMORPHA COPPER AMINE OXIDASE-1 REDUCED BY METHYLAMINE AT PH 7.0
Authors
:
B. J. Johnson, E. T. Yukl, V. J. Klema, C. M. Wilmot
Date
:
26 Apr 13 (Deposition) - 21 Aug 13 (Release) - 21 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
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
:
Amine Oxidase, Oxidoreductase, Peroxisome
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. J. Johnson, E. T. Yukl, V. J. Klema, J. P. Klinman, C. M. Wilmot
Structural Evidence For The Semiquinone In A Copper Amine Oxidase From Hansenula Polymorpha: Implications For The Catalytic Mechanism
J. Biol. Chem. 2013
[
close entry info
]
Hetero Components
(4, 19)
Info
All Hetero Components
1a: COPPER (II) ION (CUa)
1b: COPPER (II) ION (CUb)
1c: COPPER (II) ION (CUc)
1d: COPPER (II) ION (CUd)
1e: COPPER (II) ION (CUe)
1f: COPPER (II) ION (CUf)
2a: FORMYL GROUP (FORa)
2b: FORMYL GROUP (FORb)
2c: FORMYL GROUP (FORc)
3a: GLYCEROL (GOLa)
3aa: GLYCEROL (GOLaa)
3ab: GLYCEROL (GOLab)
3ac: GLYCEROL (GOLac)
3ad: GLYCEROL (GOLad)
3ae: GLYCEROL (GOLae)
3af: GLYCEROL (GOLaf)
3ag: GLYCEROL (GOLag)
3ah: GLYCEROL (GOLah)
3ai: GLYCEROL (GOLai)
3aj: GLYCEROL (GOLaj)
3ak: GLYCEROL (GOLak)
3al: GLYCEROL (GOLal)
3am: GLYCEROL (GOLam)
3an: GLYCEROL (GOLan)
3ao: GLYCEROL (GOLao)
3ap: GLYCEROL (GOLap)
3aq: GLYCEROL (GOLaq)
3ar: GLYCEROL (GOLar)
3as: GLYCEROL (GOLas)
3at: GLYCEROL (GOLat)
3au: GLYCEROL (GOLau)
3av: GLYCEROL (GOLav)
3aw: GLYCEROL (GOLaw)
3ax: GLYCEROL (GOLax)
3ay: GLYCEROL (GOLay)
3az: GLYCEROL (GOLaz)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
3o: GLYCEROL (GOLo)
3p: GLYCEROL (GOLp)
3q: GLYCEROL (GOLq)
3r: GLYCEROL (GOLr)
3s: GLYCEROL (GOLs)
3t: GLYCEROL (GOLt)
3u: GLYCEROL (GOLu)
3v: GLYCEROL (GOLv)
3w: GLYCEROL (GOLw)
3x: GLYCEROL (GOLx)
3y: GLYCEROL (GOLy)
3z: GLYCEROL (GOLz)
4a: HYDROGEN PEROXIDE (PEOa)
4b: HYDROGEN PEROXIDE (PEOb)
4c: HYDROGEN PEROXIDE (PEOc)
4d: HYDROGEN PEROXIDE (PEOd)
4e: HYDROGEN PEROXIDE (PEOe)
4f: HYDROGEN PEROXIDE (PEOf)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
5c: PHOSPHATE ION (PO4c)
6a: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYa)
6b: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYb)
6c: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYc)
6d: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYd)
6e: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYe)
6f: 3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHE... (TYYf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CU
-1
Ligand/Ion
COPPER (II) ION
2
FOR
-1
Mod. Residue
FORMYL GROUP
3
GOL
14
Ligand/Ion
GLYCEROL
4
PEO
2
Ligand/Ion
HYDROGEN PEROXIDE
5
PO4
1
Ligand/Ion
PHOSPHATE ION
6
TYY
2
Mod. Amino Acid
3-(4-HYDROXY-3-IMINO-6-OXO-CYCLOHEXA-1,4-DIENYL)-ALANINE
[
close Hetero Component info
]
Sites
(25, 25)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC9 (SOFTWARE)
03: BC1 (SOFTWARE)
04: BC2 (SOFTWARE)
05: BC3 (SOFTWARE)
06: BC5 (SOFTWARE)
07: FC7 (SOFTWARE)
08: FC8 (SOFTWARE)
09: FC9 (SOFTWARE)
10: GC1 (SOFTWARE)
11: GC2 (SOFTWARE)
12: GC3 (SOFTWARE)
13: GC4 (SOFTWARE)
14: GC5 (SOFTWARE)
15: GC6 (SOFTWARE)
16: GC7 (SOFTWARE)
17: GC8 (SOFTWARE)
18: GC9 (SOFTWARE)
19: HC1 (SOFTWARE)
20: HC2 (SOFTWARE)
21: HC3 (SOFTWARE)
22: HC4 (SOFTWARE)
23: HC5 (SOFTWARE)
24: HC6 (SOFTWARE)
25: HC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
GLN A:66 , GLN A:70 , GLY A:72 , HOH A:955 , HOH A:1353 , TYR F:534 , GLU F:651
BINDING SITE FOR RESIDUE GOL A 804
02
AC9
SOFTWARE
TYR A:160 , LYS A:561 , SER A:591 , HOH A:1246 , LYS F:561 , ASP F:593 , GOL F:811 , HOH F:994
BINDING SITE FOR RESIDUE GOL A 809
03
BC1
SOFTWARE
GLU A:110 , HOH A:1149 , HOH A:1509 , ALA F:133 , ILE F:204 , ILE F:206
BINDING SITE FOR RESIDUE GOL A 810
04
BC2
SOFTWARE
LYS A:68 , HOH F:1601
BINDING SITE FOR RESIDUE GOL A 811
05
BC3
SOFTWARE
GLY A:142 , PRO A:144 , GLU A:147 , TYR A:177 , HOH A:1624 , HOH E:1357
BINDING SITE FOR RESIDUE GOL A 812
06
BC5
SOFTWARE
ASP A:131 , ALA A:133 , VAL A:203 , ILE A:204 , HOH A:1645 , GLU F:110 , HOH F:1432
BINDING SITE FOR RESIDUE GOL A 814
07
FC7
SOFTWARE
HIS E:456 , HIS E:458 , HIS E:624 , PEO E:802 , HOH E:1432
BINDING SITE FOR RESIDUE CU E 801
08
FC8
SOFTWARE
TYY E:405 , LEU E:429 , HIS E:456 , HIS E:458 , HIS E:624 , MET E:634 , CU E:801 , HOH E:903
BINDING SITE FOR RESIDUE PEO E 802
09
FC9
SOFTWARE
GLY E:142 , PRO E:144 , GLU E:147 , TYR E:177 , LYS E:217 , HOH E:1248
BINDING SITE FOR RESIDUE GOL E 803
10
GC1
SOFTWARE
PHE E:252 , LYS E:253 , MET E:254 , ILE E:342 , HIS E:343 , HOH E:1486
BINDING SITE FOR RESIDUE GOL E 804
11
GC2
SOFTWARE
GLU E:58 , PRO E:59 , ARG E:295 , TYR E:575 , ASP E:577 , ASN E:578 , HOH E:948 , HOH E:957 , HOH E:1477 , HOH E:1502
BINDING SITE FOR RESIDUE GOL E 805
12
GC3
SOFTWARE
HIS E:23 , TYR E:64 , LYS E:68 , LYS E:265 , ASP E:280
BINDING SITE FOR RESIDUE GOL E 806
13
GC4
SOFTWARE
GLU E:368 , LYS E:393 , ARG E:420 , ASP E:422 , ARG E:424 , HOH E:1036 , HOH E:1308 , HOH E:1441 , GLY F:371
BINDING SITE FOR RESIDUE GOL E 807
14
GC5
SOFTWARE
HIS F:456 , HIS F:458 , HIS F:624 , PEO F:802 , HOH F:1395
BINDING SITE FOR RESIDUE CU F 801
15
GC6
SOFTWARE
TYY F:405 , HIS F:456 , HIS F:458 , HIS F:624 , MET F:634 , CU F:801 , HOH F:983 , HOH F:1395
BINDING SITE FOR RESIDUE PEO F 802
16
GC7
SOFTWARE
HIS F:23 , TYR F:64 , LYS F:68 , LYS F:265 , ASP F:280 , HOH F:946
BINDING SITE FOR RESIDUE GOL F 803
17
GC8
SOFTWARE
GLY E:371 , LYS F:393 , VAL F:412 , ASP F:422 , ARG F:424 , GOL F:805 , HOH F:1036 , HOH F:1525
BINDING SITE FOR RESIDUE GOL F 804
18
GC9
SOFTWARE
GLY E:371 , ARG E:390 , CYS F:338 , LYS F:339 , HIS F:366 , GLU F:368 , GOL F:804 , HOH F:1334
BINDING SITE FOR RESIDUE GOL F 805
19
HC1
SOFTWARE
PRO E:484 , PRO F:442
BINDING SITE FOR RESIDUE GOL F 806
20
HC2
SOFTWARE
PHE F:252 , LYS F:253 , MET F:254 , HIS F:343 , HOH F:1203
BINDING SITE FOR RESIDUE GOL F 807
21
HC3
SOFTWARE
PRO F:484
BINDING SITE FOR RESIDUE GOL F 808
22
HC4
SOFTWARE
HIS F:218 , LYS F:219 , HOH F:1528
BINDING SITE FOR RESIDUE PO4 F 809
23
HC5
SOFTWARE
LEU F:512 , ASP F:604 , GLY F:605 , HOH F:1069 , HOH F:1375 , HOH F:1596
BINDING SITE FOR RESIDUE GOL F 810
24
HC6
SOFTWARE
LYS A:561 , ASP A:593 , GOL A:809 , TYR F:160 , LEU F:558 , LYS F:561 , SER F:591 , HOH F:994 , HOH F:1489
BINDING SITE FOR RESIDUE GOL F 811
25
HC7
SOFTWARE
GLU F:58 , PRO F:59 , TYR F:575 , ASN F:578 , HOH F:924 , HOH F:987 , HOH F:1182
BINDING SITE FOR RESIDUE GOL F 812
[
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 (1.3 MB)
Header - Asym.Unit
Biol.Unit 1 (447 KB)
Header - Biol.Unit 1
Biol.Unit 2 (449 KB)
Header - Biol.Unit 2
Biol.Unit 3 (448 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
4KFE
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help