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.
2FPG
Biol. Unit 1
Info
Asym.Unit (113 KB)
Biol.Unit 1 (108 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 PIG GTP-SPECIFIC SUCCINYL-COA SYNTHETASE IN COMPLEX WITH GDP
Authors
:
M. E. Fraser
Date
:
16 Jan 06 (Deposition) - 21 Feb 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.96
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Active Site Histidine Residue, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. E. Fraser, K. Hayakawa, M. S. Hume, D. G. Ryan, E. R. Brownie
Interactions Of Gtp With The Atp-Grasp Domain Of Gtp-Specific Succinyl-Coa Synthetase
J. Biol. Chem. V. 281 11058 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
2a: POTASSIUM ION (Ka)
3a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GDP
1
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
2
K
-1
Ligand/Ion
POTASSIUM ION
3
PO4
1
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN B:206 , ASP B:220 , LYS B:222 , GDP B:397
BINDING SITE FOR RESIDUE K B 396
2
AC2
SOFTWARE
SER A:162 , GLY A:163 , THR A:164 , HIS A:259 , HOH A:406 , GLY B:272 , ALA B:273 , GLY B:274
BINDING SITE FOR RESIDUE PO4 A 401
3
AC3
SOFTWARE
GLN B:20 , GLY B:52 , GLY B:53 , ARG B:54 , GLY B:55 , VAL B:67 , LEU B:69 , ALA B:108 , LEU B:109 , GLU B:114 , ASP B:220 , LYS B:222 , K B:396
BINDING SITE FOR RESIDUE GDP B 397
[
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
(3, 3)
Info
All PROSITE Patterns/Profiles
1: SUCCINYL_COA_LIG_1 (A:160-189)
2: SUCCINYL_COA_LIG_2 (A:248-261)
3: SUCCINYL_COA_LIG_3 (B:264-289)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SUCCINYL_COA_LIG_1
PS01216
ATP-citrate lyase / succinyl-CoA ligases family signature 1.
SUCA_PIG
200-229
1
A:160-189
2
SUCCINYL_COA_LIG_2
PS00399
ATP-citrate lyase / succinyl-CoA ligases family active site.
SUCA_PIG
288-301
1
A:248-261
3
SUCCINYL_COA_LIG_3
PS01217
ATP-citrate lyase / succinyl-CoA ligases family signature 3.
SUCB2_PIG
302-327
1
B:264-289
[
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
(4, 4)
Info
All SCOP Domains
1a: SCOP_d2fpgb2 (B:1-245)
2a: SCOP_d2fpga2 (A:131-306)
3a: SCOP_d2fpgb1 (B:246-393)
4a: SCOP_d2fpga1 (A:2-130)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ATP-grasp
(191)
Superfamily
:
Glutathione synthetase ATP-binding domain-like
(158)
Family
:
Succinyl-CoA synthetase, beta-chain, N-terminal domain
(17)
Protein domain
:
Succinyl-CoA synthetase, beta-chain, N-terminal domain
(17)
Pig (Sus scrofa) [TaxId: 9823]
(6)
1a
d2fpgb2
B:1-245
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Succinyl-CoA synthetase domains
(39)
Family
:
Succinyl-CoA synthetase domains
(38)
Protein domain
:
Succinyl-CoA synthetase, alpha-chain, C-terminal domain
(20)
Pig (Sus scrofa) [TaxId: 9823]
(6)
2a
d2fpga2
A:131-306
Protein domain
:
Succinyl-CoA synthetase, beta-chain, C-terminal domain
(17)
Pig (Sus scrofa) [TaxId: 9823]
(6)
3a
d2fpgb1
B:246-393
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
CoA-binding domain
(29)
Protein domain
:
Succinyl-CoA synthetase, alpha-chain, N-terminal (CoA-binding) domain
(20)
Pig (Sus scrofa) [TaxId: 9823]
(6)
4a
d2fpga1
A:2-130
[
close SCOP info
]
CATH Domains
(4, 5)
Info
all CATH domains
1a: CATH_2fpgB01 (B:1-20,B:112-246)
2a: CATH_2fpgB02 (B:21-111)
3a: CATH_2fpgA02 (A:132-301)
3b: CATH_2fpgB03 (B:247-392)
4a: CATH_2fpgA01 (A:9-131)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
D-amino Acid Aminotransferase; Chain A, domain 1
(175)
Homologous Superfamily
:
ATP-grasp fold, B domain
(118)
Pig (Sus scrofa)
(6)
1a
2fpgB01
B:1-20,B:112-246
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
ATP-grasp fold, A domain
(109)
Pig (Sus scrofa)
(6)
2a
2fpgB02
B:21-111
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.261, no name defined]
(20)
Pig (Sus scrofa)
(6)
3a
2fpgA02
A:132-301
3b
2fpgB03
B:247-392
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Pig (Sus scrofa)
(21)
4a
2fpgA01
A:9-131
[
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
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 (113 KB)
Header - Asym.Unit
Biol.Unit 1 (108 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
2FPG
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
