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.
2FG7
Asym. Unit
Info
Asym.Unit (326 KB)
Biol.Unit 1 (164 KB)
Biol.Unit 2 (160 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
N-SUCCINYL-L-ORNITHINE TRANSCARBAMYLASE FROM B. FRAGILIS COMPLEXED WITH CARBAMOYL PHOSPHATE AND N-SUCCINYL-L-NORVALINE
Authors
:
D. Shi, X. Yu, M. H. Malamy, N. M. Allewell, M. Tuchman
Date
:
21 Dec 05 (Deposition) - 23 May 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : C,D,E,X,Y,Z
Biol. Unit 1: X,Y,Z (1x)
Biol. Unit 2: C,D,E (1x)
Keywords
:
Alpha/Beta, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Shi, H. Morizono, J. Cabrera-Luque, X. Yu, L. Roth, M. H. Malamy, N. M. Allewell, M. Tuchman
Structure And Catalytic Mechanism Of A Novel N-Succinyl-L-Ornithine Transcarbamylase In Arginine Biosynthesis Of Bacteroides Fragilis.
J. Biol. Chem. V. 281 20623 2006
[
close entry info
]
Hetero Components
(3, 14)
Info
All Hetero Components
1a: PHOSPHORIC ACID MONO(FORMAMIDE)EST... (CPa)
1b: PHOSPHORIC ACID MONO(FORMAMIDE)EST... (CPb)
1c: PHOSPHORIC ACID MONO(FORMAMIDE)EST... (CPc)
1d: PHOSPHORIC ACID MONO(FORMAMIDE)EST... (CPd)
1e: PHOSPHORIC ACID MONO(FORMAMIDE)EST... (CPe)
1f: PHOSPHORIC ACID MONO(FORMAMIDE)EST... (CPf)
2a: N-(3-CARBOXYPROPANOYL)-L-NORVALINE (SN0a)
2b: N-(3-CARBOXYPROPANOYL)-L-NORVALINE (SN0b)
2c: N-(3-CARBOXYPROPANOYL)-L-NORVALINE (SN0c)
2d: N-(3-CARBOXYPROPANOYL)-L-NORVALINE (SN0d)
2e: N-(3-CARBOXYPROPANOYL)-L-NORVALINE (SN0e)
2f: N-(3-CARBOXYPROPANOYL)-L-NORVALINE (SN0f)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CP
6
Ligand/Ion
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
2
SN0
6
Ligand/Ion
N-(3-CARBOXYPROPANOYL)-L-NORVALINE
3
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(14, 14)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG X:35 , ARG Y:35 , ARG Z:35
BINDING SITE FOR RESIDUE SO4 X 400
02
AC2
SOFTWARE
ARG C:35 , ARG D:35 , ARG E:35
BINDING SITE FOR RESIDUE SO4 C 401
03
AC3
SOFTWARE
PHE X:112 , GLU X:142 , HIS X:176 , ARG X:178 , LEU X:180 , PRO X:181 , LYS X:236 , LEU X:275 , ARG X:278 , CP X:346 , HOH X:455 , TRP Z:75 , PRO Z:90
BINDING SITE FOR RESIDUE SN0 X 345
04
AC4
SOFTWARE
SER X:47 , LEU X:48 , ARG X:49 , THR X:50 , ARG X:110 , HIS X:147 , GLN X:150 , CYS X:274 , LEU X:275 , ARG X:302 , SN0 X:345 , TRP Z:75
BINDING SITE FOR RESIDUE CP X 346
05
AC5
SOFTWARE
PRO X:90 , PHE Y:112 , GLU Y:142 , HIS Y:176 , ARG Y:178 , LEU Y:180 , PRO Y:181 , LYS Y:236 , LEU Y:275 , ARG Y:278 , CP Y:348 , HOH Y:356 , HOH Y:397
BINDING SITE FOR RESIDUE SN0 Y 347
06
AC6
SOFTWARE
TRP X:75 , SER Y:47 , LEU Y:48 , ARG Y:49 , THR Y:50 , ARG Y:110 , HIS Y:147 , GLN Y:150 , CYS Y:274 , LEU Y:275 , ARG Y:302 , SN0 Y:347
BINDING SITE FOR RESIDUE CP Y 348
07
AC7
SOFTWARE
TRP Y:75 , PRO Y:90 , PHE Z:112 , GLU Z:142 , HIS Z:176 , ARG Z:178 , LEU Z:180 , PRO Z:181 , LYS Z:236 , LEU Z:275 , ARG Z:278 , CP Z:350 , HOH Z:358 , HOH Z:364 , HOH Z:396
BINDING SITE FOR RESIDUE SN0 Z 349
08
AC8
SOFTWARE
TRP Y:75 , SER Z:47 , LEU Z:48 , ARG Z:49 , THR Z:50 , ARG Z:110 , HIS Z:147 , GLN Z:150 , CYS Z:274 , LEU Z:275 , ARG Z:302 , SN0 Z:349
BINDING SITE FOR RESIDUE CP Z 350
09
AC9
SOFTWARE
PHE C:112 , GLU C:142 , HIS C:176 , ARG C:178 , LEU C:180 , PRO C:181 , LYS C:236 , ARG C:278 , CP C:352 , TRP E:75 , PRO E:90 , HOH E:370
BINDING SITE FOR RESIDUE SN0 C 351
10
BC1
SOFTWARE
SER C:47 , LEU C:48 , ARG C:49 , THR C:50 , ARG C:110 , HIS C:147 , GLN C:150 , CYS C:274 , LEU C:275 , ARG C:302 , SN0 C:351 , TRP E:75
BINDING SITE FOR RESIDUE CP C 352
11
BC2
SOFTWARE
TRP C:75 , PRO C:90 , PHE D:112 , GLU D:142 , HIS D:176 , ARG D:178 , LEU D:180 , LYS D:236 , LEU D:275 , ARG D:278 , CP D:354
BINDING SITE FOR RESIDUE SN0 D 353
12
BC3
SOFTWARE
TRP C:75 , SER D:47 , LEU D:48 , ARG D:49 , THR D:50 , ARG D:110 , HIS D:147 , GLN D:150 , CYS D:274 , LEU D:275 , ARG D:302 , SN0 D:353
BINDING SITE FOR RESIDUE CP D 354
13
BC4
SOFTWARE
TRP D:75 , PRO D:90 , PHE E:112 , GLU E:142 , HIS E:176 , ARG E:178 , LEU E:180 , PRO E:181 , LYS E:236 , LEU E:275 , ARG E:278 , CP E:356 , HOH E:387
BINDING SITE FOR RESIDUE SN0 E 355
14
BC5
SOFTWARE
TRP D:75 , SER E:47 , LEU E:48 , ARG E:49 , THR E:50 , ARG E:110 , HIS E:147 , GLN E:150 , CYS E:274 , LEU E:275 , ARG E:302 , SN0 E:355
BINDING SITE FOR RESIDUE CP E 356
[
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
(0, 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.
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d2fg7c1 (C:-1-163)
1b: SCOP_d2fg7e1 (E:-1-163)
1c: SCOP_d2fg7e2 (E:164-318)
1d: SCOP_d2fg7x1 (X:-2-163)
1e: SCOP_d2fg7x2 (X:164-318)
1f: SCOP_d2fg7y1 (Y:-2-163)
1g: SCOP_d2fg7y2 (Y:164-318)
1h: SCOP_d2fg7z1 (Z:-1-163)
1i: SCOP_d2fg7z2 (Z:164-318)
1j: SCOP_d2fg7c2 (C:164-318)
1k: SCOP_d2fg7d1 (D:-1-163)
1l: SCOP_d2fg7d2 (D:164-318)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
ATC-like
(129)
Superfamily
:
Aspartate/ornithine carbamoyltransferase
(122)
Family
:
Aspartate/ornithine carbamoyltransferase
(87)
Protein domain
:
Transcarbamylase-like protein
(4)
Bacteroides fragilis [TaxId: 817]
(4)
1a
d2fg7c1
C:-1-163
1b
d2fg7e1
E:-1-163
1c
d2fg7e2
E:164-318
1d
d2fg7x1
X:-2-163
1e
d2fg7x2
X:164-318
1f
d2fg7y1
Y:-2-163
1g
d2fg7y2
Y:164-318
1h
d2fg7z1
Z:-1-163
1i
d2fg7z2
Z:164-318
1j
d2fg7c2
C:164-318
1k
d2fg7d1
D:-1-163
1l
d2fg7d2
D:164-318
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_2fg7C02 (C:150-301)
1b: CATH_2fg7Y02 (Y:150-301)
1c: CATH_2fg7Z02 (Z:150-301)
1d: CATH_2fg7C01 (C:-1-147,C:302-318)
1e: CATH_2fg7D01 (D:-1-147,D:302-318)
1f: CATH_2fg7E01 (E:-1-147,E:302-318)
1g: CATH_2fg7Z01 (Z:-1-147,Z:302-318)
1h: CATH_2fg7X01 (X:-2-147,X:302-318)
1i: CATH_2fg7Y01 (Y:-2-147,Y:302-318)
1j: CATH_2fg7D02 (D:150-301)
1k: CATH_2fg7E02 (E:150-301)
1l: CATH_2fg7X02 (X:150-301)
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=3.40.50.1370, no name defined]
(91)
Bacteroides fragilis nctc 9343. Organism_taxid: 272559. Strain: nctc 9343.
(2)
1a
2fg7C02
C:150-301
1b
2fg7Y02
Y:150-301
1c
2fg7Z02
Z:150-301
1d
2fg7C01
C:-1-147,C:302-318
1e
2fg7D01
D:-1-147,D:302-318
1f
2fg7E01
E:-1-147,E:302-318
1g
2fg7Z01
Z:-1-147,Z:302-318
1h
2fg7X01
X:-2-147,X:302-318
1i
2fg7Y01
Y:-2-147,Y:302-318
1j
2fg7D02
D:150-301
1k
2fg7E02
E:150-301
1l
2fg7X02
X:150-301
[
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 C
Chain D
Chain E
Chain X
Chain Y
Chain Z
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 (326 KB)
Header - Asym.Unit
Biol.Unit 1 (164 KB)
Header - Biol.Unit 1
Biol.Unit 2 (160 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
2FG7
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help