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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1O7J
Asym. Unit
Info
Asym.Unit (655 KB)
Biol.Unit 1 (648 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ATOMIC RESOLUTION STRUCTURE OF ERWINIA CHRYSANTHEMI L-ASPARAGINASE
Authors
:
J. Lubkowski, M. Dauter, K. Aghaiypour, A. Wlodawer, Z. Dauter
Date
:
07 Nov 02 (Deposition) - 04 Dec 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
L-Asparaginase, Atomic Resolution, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Lubkowski, M. Dauter, K. Aghaiypour, A. Wlodawer, Z. Dauter
Atomic Resolution Structure Of Erwinia Chrysanthemi L-Asparaginase
Acta Crystallogr. , Sect. D V. 59 84 2003
[
close entry info
]
Hetero Components
(3, 22)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
12
Ligand/Ion
1,2-ETHANEDIOL
2
GOL
2
Ligand/Ion
GLYCEROL
3
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(22, 22)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:14 , THR A:15 , ALA A:61 , SER A:62 , GLY A:94 , THR A:95 , ASP A:96 , HOH A:2111 , HOH A:2114
BINDING SITE FOR RESIDUE SO4 A1328
02
AC2
SOFTWARE
MET A:60 , ALA A:61 , ASN A:64 , HOH A:2029 , HOH A:2343
BINDING SITE FOR RESIDUE SO4 A1329
03
AC3
SOFTWARE
GLY B:14 , THR B:15 , ALA B:31 , ALA B:61 , SER B:62 , GLY B:94 , THR B:95 , ASP B:96 , HOH B:2094 , HOH B:2095
BINDING SITE FOR RESIDUE SO4 B1328
04
AC4
SOFTWARE
LEU B:267 , LEU B:290 , GLY B:292 , HOH B:2307 , HOH B:2308 , HOH B:2309 , HOH B:2310 , THR D:314 , SER D:315 , HOH D:2330
BINDING SITE FOR RESIDUE SO4 B1329
05
AC5
SOFTWARE
GLY C:14 , THR C:15 , ALA C:61 , SER C:62 , GLY C:94 , THR C:95 , ASP C:96 , HOH C:2353
BINDING SITE FOR RESIDUE SO4 C1328
06
AC6
SOFTWARE
MET C:60 , ALA C:61 , ASN C:64 , HOH C:2354 , HOH C:2355
BINDING SITE FOR RESIDUE SO4 C1329
07
AC7
SOFTWARE
GLY D:14 , THR D:15 , ALA D:61 , SER D:62 , GLY D:94 , THR D:95 , ASP D:96 , HOH D:2127 , HOH D:2131
BINDING SITE FOR RESIDUE SO4 D1328
08
AC8
SOFTWARE
MET D:60 , ALA D:61 , ASN D:64 , HOH D:2344 , HOH D:2345 , HOH D:2346
BINDING SITE FOR RESIDUE SO4 D1329
09
AC9
SOFTWARE
LYS A:243 , EDO A:1332 , EDO A:1335 , THR C:312
BINDING SITE FOR RESIDUE EDO A1331
10
BC1
SOFTWARE
LYS A:243 , EDO A:1331 , EDO A:1333 , ASP C:210 , HOH C:2330
BINDING SITE FOR RESIDUE EDO A1332
11
BC2
SOFTWARE
LYS A:243 , EDO A:1332 , EDO A:1334 , ASP C:210 , ARG C:212
BINDING SITE FOR RESIDUE EDO A1333
12
BC3
SOFTWARE
LYS A:243 , GLY A:270 , EDO A:1333 , EDO A:1335
BINDING SITE FOR RESIDUE EDO A1334
13
BC4
SOFTWARE
LYS A:243 , EDO A:1331 , EDO A:1334 , HOH A:2348
BINDING SITE FOR RESIDUE EDO A1335
14
BC5
SOFTWARE
GLN B:75 , EDO B:1331 , THR D:205
BINDING SITE FOR RESIDUE EDO B1330
15
BC6
SOFTWARE
GLN B:75 , ARG B:212 , EDO B:1330 , EDO B:1332 , ARG D:206
BINDING SITE FOR RESIDUE EDO B1331
16
BC7
SOFTWARE
ASN B:78 , ARG B:212 , EDO B:1331
BINDING SITE FOR RESIDUE EDO B1332
17
BC8
SOFTWARE
VAL D:69 , LYS D:72 , EDO D:1332 , EDO D:1333 , EDO D:1334
BINDING SITE FOR RESIDUE EDO D1331
18
BC9
SOFTWARE
LYS D:72 , EDO D:1331 , EDO D:1333
BINDING SITE FOR RESIDUE EDO D1332
19
CC1
SOFTWARE
LYS D:72 , EDO D:1331 , EDO D:1332 , EDO D:1334
BINDING SITE FOR RESIDUE EDO D1333
20
CC2
SOFTWARE
LYS D:72 , EDO D:1331 , EDO D:1333
BINDING SITE FOR RESIDUE EDO D1334
21
CC3
SOFTWARE
ASP A:68 , SER A:216 , LEU A:217 , HOH A:2344 , HOH A:2345 , HOH A:2346 , THR C:215
BINDING SITE FOR RESIDUE GOL A1330
22
CC4
SOFTWARE
ASN A:180 , GLU A:181 , ARG C:178 , HOH C:2202 , ARG D:159 , ASN D:180 , TYR D:184 , HOH D:2347
BINDING SITE FOR RESIDUE GOL D1330
[
close Site info
]
SAPs(SNPs)/Variants
(4, 16)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_ASPG_DICCH_001 (I156I, chain A/B/C/D, )
2: VAR_ASPG_DICCH_002 (R178R, chain A/B/C/D, )
3: VAR_ASPG_DICCH_003 (L267L, chain A/B/C/D, )
4: VAR_ASPG_DICCH_004 (M274M, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_ASPG_DICCH_001
*
L
177
I
ASPG_DICCH
---
---
A/B/C/D
I
156
I
2
UniProt
VAR_ASPG_DICCH_002
*
K
199
R
ASPG_DICCH
---
---
A/B/C/D
R
178
R
3
UniProt
VAR_ASPG_DICCH_003
*
M
288
L
ASPG_DICCH
---
---
A/B/C/D
L
267
L
4
UniProt
VAR_ASPG_DICCH_004
*
I
295
M
ASPG_DICCH
---
---
A/B/C/D
M
274
M
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 12)
Info
All PROSITE Patterns/Profiles
1: ASN_GLN_ASE_3 (A:5-327,B:5-327,C:5-327,D:5-327)
2: ASN_GLN_ASE_1 (A:9-17,B:9-17,C:9-17,D:9-17)
3: ASN_GLN_ASE_2 (A:88-98,B:88-98,C:88-98,D:88-98)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ASN_GLN_ASE_3
PS51732
Asparaginase / glutaminase domain profile.
ASPG_DICCH
26-348
4
A:5-327
B:5-327
C:5-327
D:5-327
2
ASN_GLN_ASE_1
PS00144
Asparaginase / glutaminase active site signature 1.
ASPG_DICCH
30-38
4
A:9-17
B:9-17
C:9-17
D:9-17
3
ASN_GLN_ASE_2
PS00917
Asparaginase / glutaminase active site signature 2.
ASPG_DICCH
109-119
4
A:88-98
B:88-98
C:88-98
D:88-98
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d1o7ja_ (A:)
1b: SCOP_d1o7jb_ (B:)
1c: SCOP_d1o7jc_ (C:)
1d: SCOP_d1o7jd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Glutaminase/Asparaginase
(37)
Superfamily
:
Glutaminase/Asparaginase
(37)
Family
:
Glutaminase/Asparaginase
(33)
Protein domain
:
Asparaginase type II
(17)
Erwinia chrysanthemi [TaxId: 556]
(8)
1a
d1o7ja_
A:
1b
d1o7jb_
B:
1c
d1o7jc_
C:
1d
d1o7jd_
D:
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1o7jA01 (A:3-218)
1b: CATH_1o7jB01 (B:3-218)
1c: CATH_1o7jC01 (C:3-218)
1d: CATH_1o7jD01 (D:3-218)
2a: CATH_1o7jA02 (A:219-327)
2b: CATH_1o7jB02 (B:219-327)
2c: CATH_1o7jC02 (C:219-327)
2d: CATH_1o7jD02 (D:219-327)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1170, no name defined]
(27)
Erwinia chrysanthemi. Organism_taxid: 556
(3)
1a
1o7jA01
A:3-218
1b
1o7jB01
B:3-218
1c
1o7jC01
C:3-218
1d
1o7jD01
D:3-218
Homologous Superfamily
:
[code=3.40.50.40, no name defined]
(27)
Erwinia chrysanthemi. Organism_taxid: 556
(3)
2a
1o7jA02
A:219-327
2b
1o7jB02
B:219-327
2c
1o7jC02
C:219-327
2d
1o7jD02
D:219-327
[
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
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 (655 KB)
Header - Asym.Unit
Biol.Unit 1 (648 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
1O7J
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help