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.
2D32
Biol. Unit 1
Info
Asym.Unit (348 KB)
Biol.Unit 1 (339 KB)
Biol.Unit 2 (1006 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 MICHAELIS COMPLEX OF GAMMA-GLUTAMYLCYSTEINE SYNTHETASE
Authors
:
T. Hibi, M. Nakayama, H. Nii, Y. Kurokawa, H. Katano, J. Oda
Date
:
25 Sep 05 (Deposition) - 14 Nov 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B,C,D (3x)
Keywords
:
Glutathione Homeostasis, Peptide Synthesis, Phosphoryl Transfer, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Hibi, M. Nakayama, H. Nii, Y. Kurokawa, H. Katano, J. Oda
Structural Basis Of Efficient Coupling Peptide Ligation And Atp Hydrolysis By Gamma-Gluatamylcysteine Synthetase
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 12)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
1b: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPb)
1c: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPc)
1d: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPd)
2a: CYSTEINE (CYSa)
2b: CYSTEINE (CYSb)
2c: CYSTEINE (CYSc)
2d: CYSTEINE (CYSd)
3a: GLUTAMIC ACID (GLUa)
3b: GLUTAMIC ACID (GLUb)
3c: GLUTAMIC ACID (GLUc)
3d: GLUTAMIC ACID (GLUd)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
4h: MAGNESIUM ION (MGh)
4i: MAGNESIUM ION (MGi)
4j: MAGNESIUM ION (MGj)
4k: MAGNESIUM ION (MGk)
4l: MAGNESIUM ION (MGl)
4m: MAGNESIUM ION (MGm)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ANP
4
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
CYS
4
Mod. Amino Acid
CYSTEINE
3
GLU
4
Mod. Amino Acid
GLUTAMIC ACID
4
MG
-1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(25, 25)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:29 , ASP A:60 , GLU A:67 , GLU A:1519 , ANP A:1521 , HOH A:1727
BINDING SITE FOR RESIDUE MG A 1522
02
AC2
SOFTWARE
GLU A:27 , HIS A:150 , GLU A:328 , ANP A:1521
BINDING SITE FOR RESIDUE MG A 1523
03
AC3
SOFTWARE
GLU A:27 , GLU A:67 , ANP A:1521 , HOH A:1768
BINDING SITE FOR RESIDUE MG A 1524
04
AC4
SOFTWARE
ASN A:442 , ASP A:444 , HOH A:1579 , HOH A:1581 , HOH A:1708 , HOH A:1837
BINDING SITE FOR RESIDUE MG A 1525
05
AC5
SOFTWARE
GLU B:29 , ASP B:60 , GLU B:67 , GLU B:2519 , ANP B:2521 , HOH B:2568
BINDING SITE FOR RESIDUE MG B 2522
06
AC6
SOFTWARE
GLU B:27 , HIS B:150 , GLU B:328 , ANP B:2521
BINDING SITE FOR RESIDUE MG B 2523
07
AC7
SOFTWARE
GLU B:27 , GLU B:67 , ANP B:2521
BINDING SITE FOR RESIDUE MG B 2524
08
AC8
SOFTWARE
GLU C:29 , ASP C:60 , GLU C:67 , GLU C:3519 , ANP C:3521 , HOH C:3594
BINDING SITE FOR RESIDUE MG C 3522
09
AC9
SOFTWARE
GLU C:27 , HIS C:150 , GLU C:328 , ANP C:3521
BINDING SITE FOR RESIDUE MG C 3523
10
BC1
SOFTWARE
GLU C:27 , GLU C:67 , ANP C:3521
BINDING SITE FOR RESIDUE MG C 3524
11
BC2
SOFTWARE
GLU D:29 , ASP D:60 , GLU D:67 , GLU D:4519 , ANP D:4521 , HOH D:4526
BINDING SITE FOR RESIDUE MG D 4522
12
BC3
SOFTWARE
GLU D:27 , HIS D:150 , GLU D:328 , ANP D:4521
BINDING SITE FOR RESIDUE MG D 4523
13
BC4
SOFTWARE
GLU D:27 , GLU D:67 , ANP D:4521 , HOH D:4711
BINDING SITE FOR RESIDUE MG D 4524
14
BC5
SOFTWARE
GLU A:29 , ASP A:60 , ILE A:146 , SER A:147 , GLY A:148 , HIS A:150 , ARG A:235 , ARG A:330 , CYS A:1520 , ANP A:1521 , MG A:1522 , HOH A:1786
BINDING SITE FOR RESIDUE GLU A 1519
15
BC6
SOFTWARE
ASP A:60 , TYR A:131 , ASN A:297 , GLU A:1519 , HOH A:1828
BINDING SITE FOR RESIDUE CYS A 1520
16
BC7
SOFTWARE
GLN A:23 , GLY A:25 , LEU A:26 , GLU A:27 , GLU A:67 , ILE A:69 , THR A:70 , PRO A:71 , VAL A:72 , HIS A:150 , ASN A:152 , SER A:154 , LYS A:306 , GLU A:325 , TYR A:326 , GLU A:328 , ARG A:330 , GLU A:1519 , MG A:1522 , MG A:1523 , MG A:1524 , HOH A:1752 , HOH A:1768 , HOH A:1828 , HOH A:1838
BINDING SITE FOR RESIDUE ANP A 1521
17
BC8
SOFTWARE
GLU B:29 , ASP B:60 , ILE B:146 , SER B:147 , GLY B:148 , HIS B:150 , ARG B:235 , TYR B:241 , ARG B:330 , CYS B:2520 , MG B:2522 , HOH B:2553 , HOH B:2566 , HOH B:2568
BINDING SITE FOR RESIDUE GLU B 2519
18
BC9
SOFTWARE
ASP B:60 , TYR B:131 , ARG B:132 , GLN B:144 , TYR B:241 , ASN B:297 , GLU B:2519 , HOH B:2566 , HOH B:2671
BINDING SITE FOR RESIDUE CYS B 2520
19
CC1
SOFTWARE
GLN B:23 , GLY B:25 , LEU B:26 , GLU B:27 , GLU B:67 , ILE B:69 , THR B:70 , PRO B:71 , VAL B:72 , ASN B:152 , SER B:154 , LYS B:306 , GLU B:325 , TYR B:326 , GLU B:328 , MG B:2522 , MG B:2523 , MG B:2524 , HOH B:2566 , HOH B:2575 , HOH B:2610
BINDING SITE FOR RESIDUE ANP B 2521
20
CC2
SOFTWARE
GLU C:29 , ASP C:60 , ILE C:146 , SER C:147 , GLY C:148 , HIS C:150 , ARG C:235 , TYR C:241 , ARG C:330 , CYS C:3520 , MG C:3522 , HOH C:3559 , HOH C:3594
BINDING SITE FOR RESIDUE GLU C 3519
21
CC3
SOFTWARE
ASP C:60 , TYR C:131 , ASN C:297 , GLU C:3519 , ANP C:3521 , HOH C:3587
BINDING SITE FOR RESIDUE CYS C 3520
22
CC4
SOFTWARE
GLN C:23 , GLY C:25 , LEU C:26 , GLU C:27 , GLU C:67 , ILE C:69 , THR C:70 , PRO C:71 , VAL C:72 , ASN C:152 , PHE C:153 , SER C:154 , LYS C:306 , GLU C:325 , TYR C:326 , GLU C:328 , CYS C:3520 , MG C:3522 , MG C:3523 , MG C:3524 , HOH C:3590 , HOH C:3600
BINDING SITE FOR RESIDUE ANP C 3521
23
CC5
SOFTWARE
GLU D:29 , ASP D:60 , ILE D:146 , SER D:147 , GLY D:148 , HIS D:150 , ARG D:235 , TYR D:241 , ARG D:330 , CYS D:4520 , ANP D:4521 , MG D:4522 , HOH D:4526 , HOH D:4665 , HOH D:4691
BINDING SITE FOR RESIDUE GLU D 4519
24
CC6
SOFTWARE
ASP D:60 , TYR D:131 , ARG D:132 , GLU D:4519 , ANP D:4521 , HOH D:4691
BINDING SITE FOR RESIDUE CYS D 4520
25
CC7
SOFTWARE
GLN D:23 , GLY D:25 , LEU D:26 , GLU D:27 , GLU D:67 , ILE D:69 , THR D:70 , PRO D:71 , VAL D:72 , ASN D:152 , SER D:154 , LYS D:306 , GLU D:325 , TYR D:326 , GLU D:328 , GLU D:4519 , CYS D:4520 , MG D:4522 , MG D:4523 , MG D:4524 , HOH D:4647 , HOH D:4652 , HOH D:4695
BINDING SITE FOR RESIDUE ANP D 4521
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2d32a_ (A:)
1b: SCOP_d2d32b_ (B:)
1c: SCOP_d2d32c_ (C:)
1d: SCOP_d2d32d_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Glutamine synthetase/guanido kinase
(68)
Superfamily
:
Glutamine synthetase/guanido kinase
(68)
Family
:
Glutamate-cysteine ligase
(4)
Protein domain
:
automated matches
(2)
Escherichia coli [TaxId: 562]
(2)
1a
d2d32a_
A:
1b
d2d32b_
B:
1c
d2d32c_
C:
1d
d2d32d_
D:
[
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
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 (348 KB)
Header - Asym.Unit
Biol.Unit 1 (339 KB)
Header - Biol.Unit 1
Biol.Unit 2 (1006 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
2D32
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help