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.
1XQL
Asym. Unit
Info
Asym.Unit (143 KB)
Biol.Unit 1 (138 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
EFFECT OF A Y265F MUTANT ON THE TRANSAMINATION BASED CYCLOSERINE INACTIVATION OF ALANINE RACEMASE
Authors
:
T. D. Fenn, T. Holyoak, G. F. Stamper, D. Ringe
Date
:
12 Oct 04 (Deposition) - 18 Jan 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Alanine Racemase, Cycloserine, Tim Barrel, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. D. Fenn, T. Holyoak, G. F. Stamper, D. Ringe
Effect Of A Y265F Mutant On The Transamination-Based Cycloserine Inactivation Of Alanine Racemase
Biochemistry V. 44 5317 2005
[
close entry info
]
Hetero Components
(6, 12)
Info
All Hetero Components
1a: (R)-4-AMINO-ISOXAZOLIDIN-3-ONE (4AXa)
1b: (R)-4-AMINO-ISOXAZOLIDIN-3-ONE (4AXb)
2a: ACETIC ACID (ACYa)
2b: ACETIC ACID (ACYb)
3a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
3b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
4a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
4b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
5a: (5-HYDROXY-4-{[(3-HYDROXYISOXAZOL-... (PMHa)
5b: (5-HYDROXY-4-{[(3-HYDROXYISOXAZOL-... (PMHb)
6a: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOS... (PMPa)
6b: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOS... (PMPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4AX
2
Ligand/Ion
(R)-4-AMINO-ISOXAZOLIDIN-3-ONE
2
ACY
2
Ligand/Ion
ACETIC ACID
3
KCX
2
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
4
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
5
PMH
2
Ligand/Ion
(5-HYDROXY-4-{[(3-HYDROXYISOXAZOL-4-YL)AMINO]METHYL}-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE
6
PMP
2
Ligand/Ion
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:39 , TYR A:43 , ARG A:136 , HIS A:166 , ASN A:203 , SER A:204 , ARG A:219 , GLY A:221 , ILE A:222 , TYR A:354 , HOH A:661 , HOH A:670 , HOH A:695 , PHE B:265
BINDING SITE FOR RESIDUE PMP A 501
02
AC2
SOFTWARE
LYS A:39 , TYR A:43 , KCX A:129 , ARG A:136 , HIS A:166 , ASN A:203 , SER A:204 , ARG A:219 , GLY A:221 , ILE A:222 , TYR A:354 , HOH A:661 , HOH A:670 , HOH A:695 , HOH A:697 , PHE B:265 , TYR B:284 , CYS B:311 , MET B:312 , HOH B:672
BINDING SITE FOR RESIDUE PMH A 503
03
AC3
SOFTWARE
LYS A:39 , TYR A:43 , LEU A:85 , HIS A:166 , ASN A:203 , SER A:204 , ARG A:219 , GLY A:221 , ILE A:222 , TYR A:354 , HOH A:661 , HOH A:670 , HOH A:695
BINDING SITE FOR RESIDUE PLP A 504
04
AC4
SOFTWARE
LYS A:39 , ARG A:136 , PLP A:504 , HOH A:697 , PHE B:265 , TYR B:284 , CYS B:311 , MET B:312 , HOH B:672
BINDING SITE FOR RESIDUE 4AX B 505
05
AC5
SOFTWARE
VAL B:37 , LYS B:39 , TYR B:43 , ARG B:136 , HIS B:166 , ASN B:203 , SER B:204 , ARG B:219 , GLY B:221 , ILE B:222 , TYR B:354 , HOH B:605 , HOH B:643 , HOH B:678
BINDING SITE FOR RESIDUE PMP B 601
06
AC6
SOFTWARE
PHE A:265 , TYR A:284 , CYS A:311 , MET A:312 , HOH A:678 , LYS B:39 , TYR B:43 , ARG B:136 , HIS B:166 , ASN B:203 , SER B:204 , ARG B:219 , GLY B:221 , ILE B:222 , TYR B:354 , HOH B:605 , HOH B:628 , HOH B:643 , HOH B:678
BINDING SITE FOR RESIDUE PMH B 603
07
AC7
SOFTWARE
LYS B:39 , TYR B:43 , LEU B:85 , ARG B:136 , HIS B:166 , ASN B:203 , SER B:204 , ARG B:219 , GLY B:221 , ILE B:222 , TYR B:354 , HOH B:605 , HOH B:678
BINDING SITE FOR RESIDUE PLP B 604
08
AC8
SOFTWARE
PHE A:265 , TYR A:284 , MET A:312 , HOH A:678 , HOH A:746 , LYS B:39 , ARG B:136 , TYR B:354 , HOH B:628
BINDING SITE FOR RESIDUE 4AX A 605
09
AC9
SOFTWARE
LYS A:39 , ARG A:136 , PHE B:265 , CYS B:311 , MET B:312
BINDING SITE FOR RESIDUE ACY B 502
10
BC1
SOFTWARE
PHE A:265 , CYS A:311 , MET A:312 , LYS B:39 , ARG B:136
BINDING SITE FOR RESIDUE ACY A 602
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ALANINE_RACEMASE (A:36-46,B:36-46)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALANINE_RACEMASE
PS00395
Alanine racemase pyridoxal-phosphate attachment site.
ALR_GEOSE
36-46
2
A:36-46
B:36-46
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1xqlA02 (A:14-224)
1b: CATH_1xqlB02 (B:14-224)
2a: CATH_1xqlB01 (B:2-13,B:244-381)
2b: CATH_1xqlA01 (A:2-13,A:244-382)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Alanine racemase
(53)
Geobacillus stearothermophilus. Organism_taxid: 1422.
(3)
1a
1xqlA02
A:14-224
1b
1xqlB02
B:14-224
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Lyase, Ornithine Decarboxylase; Chain A, domain 1
(47)
Homologous Superfamily
:
Lyase, Ornithine Decarboxylase; Chain A, domain 1
(47)
Geobacillus stearothermophilus. Organism_taxid: 1422.
(3)
2a
1xqlB01
B:2-13,B:244-381
2b
1xqlA01
A:2-13,A:244-382
[
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 (143 KB)
Header - Asym.Unit
Biol.Unit 1 (138 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
1XQL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help