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.
PLEASE WAIT...
Getting 'Exon' information from database.
1SCU
Asym. Unit
Info
Asym.Unit (216 KB)
Biol.Unit 1 (207 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE CRYSTAL STRUCTURE OF SUCCINYL-COA SYNTHETASE FROM ESCHERICHIA COLI AT 2.5 ANGSTROMS RESOLUTION
Authors
:
W. T. Wolodko, M. E. Fraser, M. N. G. James, W. A. Bridger
Date
:
18 Nov 93 (Deposition) - 20 Apr 95 (Release) - 21 Apr 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,D,E
Biol. Unit 1: A,B,D,E (1x)
Keywords
:
Ligase (Atp-Binding)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. T. Wolodko, M. E. Fraser, M. N. James, W. A. Bridger
The Crystal Structure Of Succinyl-Coa Synthetase From Escherichia Coli At 2. 5-A Resolution.
J. Biol. Chem. V. 269 10883 1994
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: COENZYME A (COAa)
1b: COENZYME A (COAb)
2a: N1-PHOSPHONOHISTIDINE (NEPa)
2b: N1-PHOSPHONOHISTIDINE (NEPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
COA
2
Ligand/Ion
COENZYME A
2
NEP
2
Mod. Amino Acid
N1-PHOSPHONOHISTIDINE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:14 , THR A:16 , GLY A:17 , SER A:18 , GLN A:19 , VAL A:38 , THR A:39 , PRO A:40 , LYS A:42 , TYR A:71 , VAL A:72 , PRO A:73 , SER A:80 , ILE A:95 , THR A:96 , GLU A:97 , ASN A:122 , CYS A:123 , PRO A:124 , HOH A:293 , HOH A:294 , ARG B:161 , ARG E:29 , GLU E:33 , SER E:36 , LYS E:66
BINDING SITE FOR RESIDUE COA A 289
2
AC2
SOFTWARE
GLU B:33 , SER B:36 , LYS B:66 , GLY D:14 , THR D:16 , GLY D:17 , SER D:18 , GLN D:19 , VAL D:38 , PRO D:40 , LYS D:42 , TYR D:71 , VAL D:72 , PRO D:73 , SER D:80 , ILE D:95 , THR D:96 , GLU D:97 , ASN D:122 , CYS D:123 , HOH D:298 , HOH D:303
BINDING SITE FOR RESIDUE COA D 289
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: SUCCINYL_COA_LIG_1 (A:151-180,D:151-180,A:151-180,D:15...)
2: SUCCINYL_COA_LIG_2 (A:235-248,D:235-248,A:235-248,D:23...)
3: SUCCINYL_COA_LIG_3 (B:257-282,E:257-282)
;
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.
SUCD_ECO57
152-181
2
A:151-180
D:151-180
SUCD_ECOL6
152-181
2
A:151-180
D:151-180
SUCD_ECOLI
152-181
2
A:151-180
D:151-180
2
SUCCINYL_COA_LIG_2
PS00399
ATP-citrate lyase / succinyl-CoA ligases family active site.
SUCD_ECO57
236-249
2
A:235-248
D:235-248
SUCD_ECOL6
236-249
2
A:235-248
D:235-248
SUCD_ECOLI
236-249
2
A:235-248
D:235-248
3
SUCCINYL_COA_LIG_3
PS01217
ATP-citrate lyase / succinyl-CoA ligases family signature 3.
SUCC_ECOLI
257-282
2
B:257-282
E:257-282
[
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
(4, 8)
Info
All SCOP Domains
1a: SCOP_d1scub2 (B:1-238)
1b: SCOP_d1scue2 (E:1-238)
2a: SCOP_d1scua2 (A:122-288)
2b: SCOP_d1scud2 (D:122-288)
3a: SCOP_d1scub1 (B:239-388)
3b: SCOP_d1scue1 (E:239-388)
4a: SCOP_d1scua1 (A:1-121)
4b: SCOP_d1scud1 (D:1-121)
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)
Escherichia coli [TaxId: 562]
(11)
1a
d1scub2
B:1-238
1b
d1scue2
E:1-238
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)
Escherichia coli [TaxId: 562]
(11)
2a
d1scua2
A:122-288
2b
d1scud2
D:122-288
Protein domain
:
Succinyl-CoA synthetase, beta-chain, C-terminal domain
(17)
Escherichia coli [TaxId: 562]
(11)
3a
d1scub1
B:239-388
3b
d1scue1
E:239-388
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)
Escherichia coli [TaxId: 562]
(11)
4a
d1scua1
A:1-121
4b
d1scud1
D:1-121
[
close SCOP info
]
CATH Domains
(4, 10)
Info
all CATH domains
1a: CATH_1scuB01 (B:1-20,B:105-239)
1b: CATH_1scuE01 (E:1-20,E:105-239)
2a: CATH_1scuB02 (B:21-104)
2b: CATH_1scuE02 (E:21-104)
3a: CATH_1scuD02 (D:123-288)
3b: CATH_1scuA02 (A:123-288)
3c: CATH_1scuB03 (B:240-388)
3d: CATH_1scuE03 (E:240-388)
4a: CATH_1scuA01 (A:1-122)
4b: CATH_1scuD01 (D:1-122)
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)
Escherichia coli. Organism_taxid: 562.
(2)
1a
1scuB01
B:1-20,B:105-239
1b
1scuE01
E:1-20,E:105-239
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
ATP-grasp fold, A domain
(109)
Escherichia coli. Organism_taxid: 562.
(2)
2a
1scuB02
B:21-104
2b
1scuE02
E:21-104
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.261, no name defined]
(20)
Escherichia coli. Organism_taxid: 562.
(1)
3a
1scuD02
D:123-288
3b
1scuA02
A:123-288
3c
1scuB03
B:240-388
3d
1scuE03
E:240-388
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Escherichia coli. Organism_taxid: 562.
(1)
4a
1scuA01
A:1-122
4b
1scuD01
D:1-122
[
close CATH info
]
Pfam Domains
(3, 8)
Info
all PFAM domains
1a: PFAM_ATP_grasp_2_1scuE01 (E:2-203)
1b: PFAM_ATP_grasp_2_1scuE02 (E:2-203)
2a: PFAM_CoA_binding_1scuD01 (D:5-98)
2b: PFAM_CoA_binding_1scuD02 (D:5-98)
3a: PFAM_Ligase_CoA_1scuE03 (E:262-382)
3b: PFAM_Ligase_CoA_1scuE04 (E:262-382)
3c: PFAM_Ligase_CoA_1scuD03 (D:150-271)
3d: PFAM_Ligase_CoA_1scuD04 (D:150-271)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
ATP-grasp
(83)
Family
:
ATP-grasp_2
(10)
Escherichia coli (strain K12)
(8)
1a
ATP-grasp_2-1scuE01
E:2-203
1b
ATP-grasp_2-1scuE02
E:2-203
Clan
:
NADP_Rossmann
(1239)
Family
:
CoA_binding
(18)
Escherichia coli (strain K12)
(6)
2a
CoA_binding-1scuD01
D:5-98
2b
CoA_binding-1scuD02
D:5-98
Clan
:
Succ_CoA_synth
(13)
Family
:
Ligase_CoA
(13)
Escherichia coli (strain K12)
(8)
3a
Ligase_CoA-1scuE03
E:262-382
3b
Ligase_CoA-1scuE04
E:262-382
3c
Ligase_CoA-1scuD03
D:150-271
3d
Ligase_CoA-1scuD04
D:150-271
[
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 D
Chain E
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 (216 KB)
Header - Asym.Unit
Biol.Unit 1 (207 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
1SCU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
