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.
3QPK
Asym. Unit
Info
Asym.Unit (215 KB)
Biol.Unit 1 (107 KB)
Biol.Unit 2 (106 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PROBING OXYGEN CHANNELS IN MELANOCARPUS ALBOMYCES LACCASE
Authors
:
J. P. Kallio, J. Rouvinen, N. Hakulinen
Date
:
14 Feb 11 (Deposition) - 11 May 11 (Release) - 08 Jun 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Cu Binding, Xe Binding, Laccase, Multicopper Oxidase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. P. Kallio, J. Rouvinen, K. Kruus, N. Hakulinen
Probing The Dioxygen Route In Melanocarpus Albomyces Laccas With Pressurized Xenon Gas.
Biochemistry V. 50 4396 2011
[
close entry info
]
Hetero Components
(5, 37)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: COPPER (II) ION (CUa)
2b: COPPER (II) ION (CUb)
2c: COPPER (II) ION (CUc)
2d: COPPER (II) ION (CUd)
2e: COPPER (II) ION (CUe)
2f: COPPER (II) ION (CUf)
2g: COPPER (II) ION (CUg)
2h: COPPER (II) ION (CUh)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3o: N-ACETYL-D-GLUCOSAMINE (NAGo)
3p: N-ACETYL-D-GLUCOSAMINE (NAGp)
3q: N-ACETYL-D-GLUCOSAMINE (NAGq)
3r: N-ACETYL-D-GLUCOSAMINE (NAGr)
3s: N-ACETYL-D-GLUCOSAMINE (NAGs)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
5a: XENON (XEa)
5b: XENON (XEb)
5c: XENON (XEc)
5d: XENON (XEd)
5e: XENON (XEe)
5f: XENON (XEf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
2
Ligand/Ion
CHLORIDE ION
2
CU
8
Ligand/Ion
COPPER (II) ION
3
NAG
19
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
SO4
2
Ligand/Ion
SULFATE ION
5
XE
6
Ligand/Ion
XENON
[
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:431 , CYS A:503 , HIS A:508
BINDING SITE FOR RESIDUE CU A 601
02
AC2
SOFTWARE
HIS A:140 , HIS A:436 , HIS A:502 , HOH A:1100
BINDING SITE FOR RESIDUE CU A 602
03
AC3
SOFTWARE
HIS A:95 , TRP A:136 , HIS A:138 , HIS A:504 , HOH A:1100
BINDING SITE FOR RESIDUE CU A 603
04
AC4
SOFTWARE
HIS A:93 , HIS A:95 , HIS A:434 , HIS A:436 , CL A:610
BINDING SITE FOR RESIDUE CU A 604
05
AC5
SOFTWARE
HIS A:93 , GLY A:96 , HIS A:434 , CU A:604 , HOH A:649 , HOH A:1108 , HOH A:1232
BINDING SITE FOR RESIDUE CL A 610
06
AC6
SOFTWARE
ASN A:39 , ILE A:82 , HOH A:869 , GLU B:78 , ARG B:126 , GLU B:531
BINDING SITE FOR RESIDUE NAG A 700
07
AC7
SOFTWARE
GLU A:42 , LYS A:56 , MET A:58 , THR A:87 , ASN A:88 , ASP A:181 , ASN A:550 , TYR A:552 , HOH A:637 , NAG A:711 , HOH A:959 , HOH A:1056
BINDING SITE FOR RESIDUE NAG A 710
08
AC8
SOFTWARE
GLU A:55 , ALA A:179 , ASP A:181 , ASP A:182 , NAG A:710 , HOH A:823 , HOH A:1039 , HOH A:1177
BINDING SITE FOR RESIDUE NAG A 711
09
AC9
SOFTWARE
LEU A:167 , ASN A:201 , VAL A:217 , NAG A:721 , HOH A:746 , HOH A:752 , HOH A:795 , HOH A:1098
BINDING SITE FOR RESIDUE NAG A 720
10
BC1
SOFTWARE
NAG A:720 , HOH A:776
BINDING SITE FOR RESIDUE NAG A 721
11
BC2
SOFTWARE
ASN A:216 , THR A:218 , HIS A:311 , GLY A:318 , NAG A:731 , HOH A:911
BINDING SITE FOR RESIDUE NAG A 730
12
BC3
SOFTWARE
HIS A:311 , ALA A:313 , GLY A:314 , GLY A:317 , NAG A:730 , HOH A:873 , HOH A:896 , HOH A:1186
BINDING SITE FOR RESIDUE NAG A 731
13
BC4
SOFTWARE
TRP A:287 , ASN A:289 , THR A:291 , HIS A:305 , ALA A:307 , GLU A:323 , THR A:325 , NAG A:741 , HOH A:822 , HOH A:1006 , HOH A:1074
BINDING SITE FOR RESIDUE NAG A 740
14
BC5
SOFTWARE
TYR A:214 , TRP A:287 , HIS A:305 , GLU A:323 , HOH A:614 , NAG A:740 , HOH A:866 , HOH A:964 , HOH A:1117 , HOH A:1130 , HOH A:1161
BINDING SITE FOR RESIDUE NAG A 741
15
BC6
SOFTWARE
PRO A:355 , ASP A:356 , LEU A:359 , ASN A:376 , HOH A:819 , HOH A:898 , HOH A:1025
BINDING SITE FOR RESIDUE NAG A 750
16
BC7
SOFTWARE
MET A:433
BINDING SITE FOR RESIDUE XE A 575
17
BC8
SOFTWARE
ARG A:128 , ARG A:130 , HOH A:781 , HOH A:801 , HOH A:1048 , ARG B:492
BINDING SITE FOR RESIDUE SO4 A 577
18
BC9
SOFTWARE
ARG A:492 , ARG B:128 , ARG B:130
BINDING SITE FOR RESIDUE SO4 A 578
19
CC1
SOFTWARE
HIS B:431 , CYS B:503 , HIS B:508
BINDING SITE FOR RESIDUE CU B 601
20
CC2
SOFTWARE
HIS B:140 , HIS B:436 , HIS B:502 , HOH B:579
BINDING SITE FOR RESIDUE CU B 602
21
CC3
SOFTWARE
HIS B:95 , TRP B:136 , HIS B:138 , HIS B:504 , HOH B:579
BINDING SITE FOR RESIDUE CU B 603
22
CC4
SOFTWARE
HIS B:93 , HIS B:434 , HIS B:436 , HOH B:579 , CL B:610
BINDING SITE FOR RESIDUE CU B 604
23
CC5
SOFTWARE
HIS B:93 , GLY B:96 , HIS B:434 , CU B:604 , HOH B:754 , HOH B:1053
BINDING SITE FOR RESIDUE CL B 610
24
CC6
SOFTWARE
GLU A:78 , ARG A:126 , GLU A:531 , ASN B:39 , ILE B:82 , ASN B:84 , HOH B:1134
BINDING SITE FOR RESIDUE NAG B 700
25
CC7
SOFTWARE
GLU B:42 , LYS B:56 , MET B:58 , THR B:87 , ASN B:88 , ASP B:181 , ASN B:550 , TYR B:552 , HOH B:709 , NAG B:711 , HOH B:797 , HOH B:847 , HOH B:902 , HOH B:1046
BINDING SITE FOR RESIDUE NAG B 710
26
CC8
SOFTWARE
GLU B:55 , ALA B:179 , ASP B:181 , ASP B:182 , TYR B:552 , NAG B:710 , HOH B:774 , HOH B:807 , HOH B:927
BINDING SITE FOR RESIDUE NAG B 711
27
CC9
SOFTWARE
LEU B:167 , ASN B:201 , VAL B:217 , HOH B:613 , HOH B:724 , HOH B:728 , HOH B:770 , HOH B:792 , HOH B:1088
BINDING SITE FOR RESIDUE NAG B 720
28
DC1
SOFTWARE
ASN B:216 , THR B:218 , HIS B:311 , GLY B:317 , GLY B:318 , NAG B:731 , HOH B:943 , HOH B:1121
BINDING SITE FOR RESIDUE NAG B 730
29
DC2
SOFTWARE
HIS B:311 , ALA B:313 , GLY B:314 , NAG B:730 , HOH B:1155 , HOH B:1226
BINDING SITE FOR RESIDUE NAG B 731
30
DC3
SOFTWARE
TRP B:287 , ASN B:289 , HIS B:305 , ALA B:307 , GLU B:323 , THR B:325 , NAG B:741 , HOH B:956 , HOH B:958 , HOH B:1128 , HOH B:1136
BINDING SITE FOR RESIDUE NAG B 740
31
DC4
SOFTWARE
TYR B:214 , TRP B:287 , HIS B:305 , GLU B:323 , NAG B:740 , HOH B:833
BINDING SITE FOR RESIDUE NAG B 741
32
DC5
SOFTWARE
PRO B:355 , THR B:358 , LEU B:359 , ASN B:376 , HOH B:789 , HOH B:984 , HOH B:1142 , HOH B:1163 , HOH B:1178
BINDING SITE FOR RESIDUE NAG B 750
33
DC6
SOFTWARE
PHE B:491
BINDING SITE FOR RESIDUE XE B 574
34
DC7
SOFTWARE
MET B:433 , PHE B:501
BINDING SITE FOR RESIDUE XE B 575
35
DC8
SOFTWARE
SER B:350
BINDING SITE FOR RESIDUE XE B 576
[
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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: MULTICOPPER_OXIDASE1 (A:497-517,B:497-517)
2: MULTICOPPER_OXIDASE2 (A:502-513,B:502-513)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MULTICOPPER_OXIDASE1
PS00079
Multicopper oxidases signature 1.
LAC1_MELAO
547-567
2
A:497-517
B:497-517
2
MULTICOPPER_OXIDASE2
PS00080
Multicopper oxidases signature 2.
LAC1_MELAO
552-563
2
A:502-513
B:502-513
[
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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d3qpka1 (A:1-162)
1b: SCOP_d3qpka2 (A:163-343)
1c: SCOP_d3qpka3 (A:344-559)
1d: SCOP_d3qpkb1 (B:1-162)
1e: SCOP_d3qpkb2 (B:163-343)
1f: SCOP_d3qpkb3 (B:344-559)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Multidomain cupredoxins
(146)
Protein domain
:
Laccase
(13)
Fungus (Melanocarpus albomyces) [TaxId: 204285]
(8)
1a
d3qpka1
A:1-162
1b
d3qpka2
A:163-343
1c
d3qpka3
A:344-559
1d
d3qpkb1
B:1-162
1e
d3qpkb2
B:163-343
1f
d3qpkb3
B:344-559
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Cu_oxidase_3qpkB01 (B:166-315)
1b: PFAM_Cu_oxidase_3qpkB02 (B:166-315)
2a: PFAM_Cu_oxidase_2_3qpkB03 (B:359-523)
2b: PFAM_Cu_oxidase_2_3qpkB04 (B:359-523)
3a: PFAM_Cu_oxidase_3_3qpkB05 (B:41-160)
3b: PFAM_Cu_oxidase_3_3qpkB06 (B:41-160)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CU_oxidase
(192)
Family
:
Cu-oxidase
(74)
Melanocarpus albomyces
(2)
1a
Cu-oxidase-3qpkB01
B:166-315
1b
Cu-oxidase-3qpkB02
B:166-315
Family
:
Cu-oxidase_2
(24)
Melanocarpus albomyces
(2)
2a
Cu-oxidase_2-3qpkB03
B:359-523
2b
Cu-oxidase_2-3qpkB04
B:359-523
Family
:
Cu-oxidase_3
(79)
Melanocarpus albomyces
(2)
3a
Cu-oxidase_3-3qpkB05
B:41-160
3b
Cu-oxidase_3-3qpkB06
B:41-160
[
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 (215 KB)
Header - Asym.Unit
Biol.Unit 1 (107 KB)
Header - Biol.Unit 1
Biol.Unit 2 (106 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
3QPK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
