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.
3NXK
Biol. Unit 1
Info
Asym.Unit (833 KB)
Biol.Unit 1 (422 KB)
Biol.Unit 2 (408 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 PROBABLE CYTOPLASMIC L-ASPARAGINASE FROM CAMPYLOBACTER JEJUNI
Authors
:
Y. Kim, M. Makowska-Grzyska, N. Maltseva, L. Papazisi, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious D (Csgid)
Date
:
14 Jul 10 (Deposition) - 04 Aug 10 (Release) - 04 Aug 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha-Beta-Alpha Sandwich, Cytoplasmic L- Asparaginase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Kim, M. Makowska-Grzyska, N. Maltseva, L. Papazisi, W. F. Anderson A. Joachimiak
Crystal Structure Of Probable Cytoplasmic L-Asparaginase From Campylobacter Jejuni
To Be Published
[
close entry info
]
Hetero Components
(4, 37)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
1c: ACETIC ACID (ACYc)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
3ab: SELENOMETHIONINE (MSEab)
3ac: SELENOMETHIONINE (MSEac)
3ad: SELENOMETHIONINE (MSEad)
3ae: SELENOMETHIONINE (MSEae)
3af: SELENOMETHIONINE (MSEaf)
3ag: SELENOMETHIONINE (MSEag)
3ah: SELENOMETHIONINE (MSEah)
3ai: SELENOMETHIONINE (MSEai)
3aj: SELENOMETHIONINE (MSEaj)
3ak: SELENOMETHIONINE (MSEak)
3al: SELENOMETHIONINE (MSEal)
3am: SELENOMETHIONINE (MSEam)
3an: SELENOMETHIONINE (MSEan)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
3y: SELENOMETHIONINE (MSEy)
3z: SELENOMETHIONINE (MSEz)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
4k: SULFATE ION (SO4k)
4l: SULFATE ION (SO4l)
4m: SULFATE ION (SO4m)
4n: SULFATE ION (SO4n)
4o: SULFATE ION (SO4o)
4p: SULFATE ION (SO4p)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
2
Ligand/Ion
ACETIC ACID
2
GOL
7
Ligand/Ion
GLYCEROL
3
MSE
20
Mod. Amino Acid
SELENOMETHIONINE
4
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(18, 18)
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: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:15 , THR A:16 , ASP A:62 , SER A:63 , GLY A:94 , THR A:95 , ASP A:96 , HOH A:873
BINDING SITE FOR RESIDUE SO4 A 341
02
AC2
SOFTWARE
SER A:111 , ASP A:112 , LYS A:113 , LYS A:205 , HOH A:899
BINDING SITE FOR RESIDUE SO4 A 342
03
AC3
SOFTWARE
THR A:318 , SER A:319 , LYS F:213
BINDING SITE FOR RESIDUE ACY A 343
04
AC4
SOFTWARE
ASN A:144 , GLY A:191 , LYS A:192 , VAL A:193 , PHE A:194
BINDING SITE FOR RESIDUE GOL A 344
05
AC5
SOFTWARE
GLY B:15 , THR B:16 , ASP B:62 , SER B:63 , GLY B:94 , THR B:95 , ASP B:96
BINDING SITE FOR RESIDUE SO4 B 341
06
AC6
SOFTWARE
SER B:111 , ASP B:112 , LYS B:113 , LYS B:205
BINDING SITE FOR RESIDUE SO4 B 342
07
AC7
SOFTWARE
TYR B:327 , LYS B:330 , TYR B:331
BINDING SITE FOR RESIDUE GOL B 343
08
AC8
SOFTWARE
ILE B:256 , LYS B:261 , ASP B:262 , LYS B:265 , HOH B:697 , ASN C:65
BINDING SITE FOR RESIDUE GOL B 344
09
AC9
SOFTWARE
GLU B:292 , LYS B:322 , GLN B:325 , GLU B:326 , LEU B:329 , HOH B:365
BINDING SITE FOR RESIDUE GOL B 345
10
BC1
SOFTWARE
GLY C:15 , THR C:16 , ASP C:62 , SER C:63 , GLY C:94 , THR C:95 , ASP C:96 , HOH C:387 , HOH C:823
BINDING SITE FOR RESIDUE SO4 C 341
11
BC2
SOFTWARE
SER C:111 , ASP C:112 , LYS C:205
BINDING SITE FOR RESIDUE SO4 C 342
12
BC3
SOFTWARE
THR C:318 , SER C:319
BINDING SITE FOR RESIDUE GOL C 343
13
BC4
SOFTWARE
TYR A:196 , LYS C:201 , CYS C:284 , GLU C:300 , ASP C:301
BINDING SITE FOR RESIDUE ACY C 344
14
BC5
SOFTWARE
GLY D:15 , THR D:16 , ASP D:62 , SER D:63 , GLY D:94 , THR D:95 , ASP D:96 , HOH D:358 , HOH D:800
BINDING SITE FOR RESIDUE SO4 D 341
15
BC6
SOFTWARE
SER D:111 , ASP D:112 , HOH D:1038
BINDING SITE FOR RESIDUE SO4 D 342
16
BC7
SOFTWARE
THR D:318 , SER D:319 , ASP D:320
BINDING SITE FOR RESIDUE GOL D 343
17
BC8
SOFTWARE
LYS D:261 , LYS D:265 , ASP D:291
BINDING SITE FOR RESIDUE GOL D 344
18
CC7
SOFTWARE
LYS A:213 , THR F:318 , SER F:319
BINDING SITE FOR RESIDUE ACY F 343
[
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
(1, 8)
Info
all PFAM domains
1a: PFAM_Asparaginase_3nxkH01 (H:7-325)
1b: PFAM_Asparaginase_3nxkH02 (H:7-325)
1c: PFAM_Asparaginase_3nxkH03 (H:7-325)
1d: PFAM_Asparaginase_3nxkH04 (H:7-325)
1e: PFAM_Asparaginase_3nxkH05 (H:7-325)
1f: PFAM_Asparaginase_3nxkH06 (H:7-325)
1g: PFAM_Asparaginase_3nxkH07 (H:7-325)
1h: PFAM_Asparaginase_3nxkH08 (H:7-325)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Asparaginase]
(13)
Family
:
Asparaginase
(13)
Campylobacter jejuni
(1)
1a
Asparaginase-3nxkH01
H:7-325
1b
Asparaginase-3nxkH02
H:7-325
1c
Asparaginase-3nxkH03
H:7-325
1d
Asparaginase-3nxkH04
H:7-325
1e
Asparaginase-3nxkH05
H:7-325
1f
Asparaginase-3nxkH06
H:7-325
1g
Asparaginase-3nxkH07
H:7-325
1h
Asparaginase-3nxkH08
H:7-325
[
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
Chain D
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 (833 KB)
Header - Asym.Unit
Biol.Unit 1 (422 KB)
Header - Biol.Unit 1
Biol.Unit 2 (408 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
3NXK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help