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.
3ZK4
Biol. Unit 1
Info
Asym.Unit (370 KB)
Biol.Unit 1 (711 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 PURPLE ACID PHOSPHATASE PPD1 ISOLATED FROM YELLOW LUPIN (LUPINUS LUTEUS) SEEDS
Authors
:
S. V. Antonyuk, R. W. Strange
Date
:
21 Jan 13 (Deposition) - 29 Jan 14 (Release) - 20 Aug 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (2x)
Keywords
:
Three-Domain Heme-Cu Nitrite Reductase, Electron Transfer, Oxidoreductase, Proton Channel, Denitrification
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. V. Antonyuk, M. Olczak, T. Olczak, J. Ciuraszkiewicz, R. W. Strange
The Structure Of A Purple Acid Phosphatase Involved In Plant Growth And Pathogen Defence Exhibits A Novel Immunoglobulin-Like Fold
Iucrj V. 1 101 2014
[
close entry info
]
Hetero Components
(4, 64)
Info
All Hetero Components
1a: FE (III) ION (FEa)
1b: FE (III) ION (FEb)
1c: FE (III) ION (FEc)
2a: ALPHA-L-FUCOSE (FUCa)
2b: ALPHA-L-FUCOSE (FUCb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
4a: MANGANESE (II) ION (MNa)
4b: MANGANESE (II) ION (MNb)
4c: MANGANESE (II) ION (MNc)
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)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
5i: N-ACETYL-D-GLUCOSAMINE (NAGi)
5j: N-ACETYL-D-GLUCOSAMINE (NAGj)
5k: N-ACETYL-D-GLUCOSAMINE (NAGk)
5l: N-ACETYL-D-GLUCOSAMINE (NAGl)
5m: N-ACETYL-D-GLUCOSAMINE (NAGm)
5n: N-ACETYL-D-GLUCOSAMINE (NAGn)
5o: N-ACETYL-D-GLUCOSAMINE (NAGo)
5p: N-ACETYL-D-GLUCOSAMINE (NAGp)
5q: N-ACETYL-D-GLUCOSAMINE (NAGq)
5r: N-ACETYL-D-GLUCOSAMINE (NAGr)
5s: N-ACETYL-D-GLUCOSAMINE (NAGs)
5t: N-ACETYL-D-GLUCOSAMINE (NAGt)
5u: N-ACETYL-D-GLUCOSAMINE (NAGu)
5v: N-ACETYL-D-GLUCOSAMINE (NAGv)
5w: N-ACETYL-D-GLUCOSAMINE (NAGw)
6a: PHOSPHATE ION (PO4a)
6b: PHOSPHATE ION (PO4b)
6c: PHOSPHATE ION (PO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FE
-1
Ligand/Ion
FE (III) ION
2
FUC
4
Ligand/Ion
ALPHA-L-FUCOSE
3
GOL
8
Ligand/Ion
GLYCEROL
4
MN
-1
Ligand/Ion
MANGANESE (II) ION
5
NAG
46
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
PO4
6
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(28, 28)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:272 , ASP A:313 , TYR A:316 , HIS A:479 , MN A:801 , PO4 A:999
BINDING SITE FOR RESIDUE FE A 800
02
AC2
SOFTWARE
ASP A:313 , ASN A:346 , HIS A:435 , HIS A:477 , FE A:800 , PO4 A:999
BINDING SITE FOR RESIDUE MN A 801
03
AC3
SOFTWARE
ARG A:266 , LYS A:541 , THR A:543 , ARG A:555 , HOH A:2604 , HOH A:2646 , HOH A:2976 , TYR B:24
BINDING SITE FOR RESIDUE GOL A 901
04
AC4
SOFTWARE
THR A:493 , ASN A:494 , ASN A:503 , ASN A:505 , HOH A:2835 , HOH A:2854 , HOH A:2977 , HOH A:2979
BINDING SITE FOR RESIDUE NAG A 903
05
AC5
SOFTWARE
ASP A:272 , ASP A:313 , TYR A:316 , ASN A:346 , HIS A:347 , HIS A:477 , HIS A:479 , FE A:800 , MN A:801 , HOH A:2679 , HOH A:2990
BINDING SITE FOR RESIDUE PO4 A 999
06
AC6
SOFTWARE
ASN A:49 , PRO A:51 , ASP A:101 , THR A:102 , HOH A:2085 , HIS C:498
BINDING SITE FOR RESIDUE GOL A1000
07
AC7
SOFTWARE
GLN A:561 , HOH A:2915 , HOH A:2995 , HOH A:2996 , HOH A:2997 , SER B:96 , SER B:106
BINDING SITE FOR RESIDUE GOL A1001
08
AC8
SOFTWARE
ASP B:272 , ASP B:313 , TYR B:316 , HIS B:479 , MN B:801 , PO4 B:999
BINDING SITE FOR RESIDUE FE B 800
09
AC9
SOFTWARE
ASP B:313 , ASN B:346 , HIS B:435 , HIS B:477 , FE B:800 , PO4 B:999
BINDING SITE FOR RESIDUE MN B 801
10
BC1
SOFTWARE
ASP B:272 , ASP B:313 , TYR B:316 , ASN B:346 , HIS B:347 , HIS B:477 , HIS B:479 , FE B:800 , MN B:801 , HOH B:2591 , HOH B:2876
BINDING SITE FOR RESIDUE PO4 B 999
11
BC2
SOFTWARE
ASP C:272 , ASP C:313 , TYR C:316 , HIS C:479 , MN C:801 , PO4 C:999
BINDING SITE FOR RESIDUE FE C 800
12
BC3
SOFTWARE
ASP C:313 , ASN C:346 , HIS C:435 , HIS C:477 , FE C:800 , PO4 C:999
BINDING SITE FOR RESIDUE MN C 801
13
BC4
SOFTWARE
ILE C:53 , ASN C:93 , HOH C:2117 , HOH C:2639
BINDING SITE FOR RESIDUE NAG C 802
14
BC5
SOFTWARE
ASN C:503 , ASN C:505 , HOH C:2552 , HOH C:2556 , HOH C:2622 , HOH C:2655
BINDING SITE FOR RESIDUE NAG C 903
15
BC6
SOFTWARE
ASP C:272 , ASP C:313 , TYR C:316 , ASN C:346 , HIS C:347 , HIS C:477 , HIS C:479 , FE C:800 , MN C:801 , HOH C:2425 , HOH C:2659 , HOH C:2660
BINDING SITE FOR RESIDUE PO4 C 999
16
BC7
SOFTWARE
GLU B:380 , SER C:388 , LYS C:417 , SER C:421 , HOH C:2457 , HOH C:2661
BINDING SITE FOR RESIDUE GOL C1000
17
BC8
SOFTWARE
ILE A:53 , TYR A:91 , ASN A:93 , HOH A:2227 , HOH A:2982 , HOH A:2983 , HOH A:2984
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 920 THROUGH NAG A 921 BOUND TO ASN A 93
18
BC9
SOFTWARE
ASN A:143 , ASN A:242 , THR A:244 , HOH A:2557 , HOH A:2989
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 940 THROUGH NAG A 941 BOUND TO ASN A 242
19
CC1
SOFTWARE
PRO A:289 , ASN A:293 , PHE A:537 , SER A:558 , HOH A:2636 , HOH A:2893 , HOH A:2968 , HOH A:2969 , HOH A:2970 , HOH A:2971 , HOH A:2972 , HOH A:2973 , HOH A:2974 , HOH A:2975
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 808 THROUGH NAG A 809 BOUND TO ASN A 293
20
CC2
SOFTWARE
PRO A:524 , ASN A:526 , HOH A:2980 , HOH A:2981
BINDING SITE FOR MONO-SACCHARIDE NAG A 905 BOUND TO ASN A 526
21
CC3
SOFTWARE
ILE B:53 , TYR B:91 , ASN B:93 , LYS B:100 , HOH B:2201 , HOH B:2854 , HOH B:2855 , HOH B:2856 , HOH B:2857
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 805 THROUGH NAG B 806 BOUND TO ASN B 93
22
CC4
SOFTWARE
ASN B:143 , ASN B:242 , THR B:244 , HOH B:2865 , HOH B:2866
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 812 THROUGH FUC B 815 BOUND TO ASN B 242
23
CC5
SOFTWARE
PRO B:289 , ASN B:293 , PHE B:537 , SER B:558 , HOH B:2553 , HOH B:2800 , HOH B:2859 , HOH B:2860 , HOH B:2861 , HOH B:2862 , HOH B:2863 , HOH B:2864
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 808 THROUGH NAG B 809 BOUND TO ASN B 293
24
CC6
SOFTWARE
ASN B:503 , ASN B:505 , HOH B:2736 , HOH B:2738 , HOH B:2761 , HOH B:2836 , HOH B:2868
BINDING SITE FOR MONO-SACCHARIDE NAG B 903 BOUND TO ASN B 505
25
CC7
SOFTWARE
PRO B:524 , ASN B:526 , HOH B:2870 , HOH B:2871 , HOH B:2872
BINDING SITE FOR MONO-SACCHARIDE NAG B 925 BOUND TO ASN B 526
26
CC8
SOFTWARE
ASN C:242 , THR C:244 , HOH C:2648 , HOH C:2650 , HOH C:2651 , HOH C:2653 , HOH C:2654
BINDING SITE FOR MONO-SACCHARIDE NAG C 814 BOUND TO ASN C 242
27
CC9
SOFTWARE
PRO C:289 , ASN C:293 , PHE C:537 , SER C:558 , HOH C:2392 , HOH C:2589 , HOH C:2642 , HOH C:2643 , HOH C:2644 , HOH C:2645
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG C 808 THROUGH NAG C 809 BOUND TO ASN C 293
28
DC1
SOFTWARE
PRO C:524 , ASN C:526 , HOH C:2572 , HOH C:2658
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG C 925 THROUGH FUC C 928 BOUND TO ASN C 526
[
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
Chain C
Asymmetric Unit 1
Asymmetric Unit 2
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 (370 KB)
Header - Asym.Unit
Biol.Unit 1 (711 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
3ZK4
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
