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.
1LW5
Asym. Unit
Info
Asym.Unit (243 KB)
Biol.Unit 1 (231 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY STRUCTURE OF L-THREONINE ALDOLASE (LOW-SPECIFICITY) IN COMPLEX WITH GLYCINE
Authors
:
C. L. Kielkopf, S. K. Burley, New York Sgx Research Center For Str Genomics (Nysgxrc)
Date
:
30 May 02 (Deposition) - 11 Dec 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Pyridoxal-5-Phosphate, Plp, Enzyme, Product Complex, Threonine, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. L. Kielkopf, S. K. Burley
X-Ray Structures Of Threonine Aldolase Complexes: Structura Basis Of Substrate Recognition
Biochemistry V. 41 11711 2002
[
close entry info
]
Hetero Components
(6, 73)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
3a: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPa)
3b: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPb)
3c: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPc)
3d: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPd)
4a: SELENOMETHIONINE (MSEa)
4aa: SELENOMETHIONINE (MSEaa)
4ab: SELENOMETHIONINE (MSEab)
4ac: SELENOMETHIONINE (MSEac)
4ad: SELENOMETHIONINE (MSEad)
4ae: SELENOMETHIONINE (MSEae)
4af: SELENOMETHIONINE (MSEaf)
4ag: SELENOMETHIONINE (MSEag)
4ah: SELENOMETHIONINE (MSEah)
4ai: SELENOMETHIONINE (MSEai)
4aj: SELENOMETHIONINE (MSEaj)
4ak: SELENOMETHIONINE (MSEak)
4al: SELENOMETHIONINE (MSEal)
4am: SELENOMETHIONINE (MSEam)
4an: SELENOMETHIONINE (MSEan)
4ao: SELENOMETHIONINE (MSEao)
4ap: SELENOMETHIONINE (MSEap)
4aq: SELENOMETHIONINE (MSEaq)
4ar: SELENOMETHIONINE (MSEar)
4as: SELENOMETHIONINE (MSEas)
4at: SELENOMETHIONINE (MSEat)
4au: SELENOMETHIONINE (MSEau)
4av: SELENOMETHIONINE (MSEav)
4aw: SELENOMETHIONINE (MSEaw)
4ax: SELENOMETHIONINE (MSEax)
4ay: SELENOMETHIONINE (MSEay)
4az: SELENOMETHIONINE (MSEaz)
4b: SELENOMETHIONINE (MSEb)
4ba: SELENOMETHIONINE (MSEba)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
4m: SELENOMETHIONINE (MSEm)
4n: SELENOMETHIONINE (MSEn)
4o: SELENOMETHIONINE (MSEo)
4p: SELENOMETHIONINE (MSEp)
4q: SELENOMETHIONINE (MSEq)
4r: SELENOMETHIONINE (MSEr)
4s: SELENOMETHIONINE (MSEs)
4t: SELENOMETHIONINE (MSEt)
4u: SELENOMETHIONINE (MSEu)
4v: SELENOMETHIONINE (MSEv)
4w: SELENOMETHIONINE (MSEw)
4x: SELENOMETHIONINE (MSEx)
4y: SELENOMETHIONINE (MSEy)
4z: SELENOMETHIONINE (MSEz)
5a: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PH... (PLGa)
5b: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PH... (PLGb)
5c: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PH... (PLGc)
6a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
6
Ligand/Ion
CALCIUM ION
2
CL
6
Ligand/Ion
CHLORIDE ION
3
LLP
4
Mod. Amino Acid
2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
4
MSE
53
Mod. Amino Acid
SELENOMETHIONINE
5
PLG
3
Ligand/Ion
N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
6
PLP
1
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR B:8 , THR B:10 , SER B:198 , ALA B:203 , GLN C:232
BINDING SITE FOR RESIDUE CA C 1004
02
AC2
SOFTWARE
THR A:8 , THR A:10 , SER A:198 , ALA A:203 , GLN D:232
BINDING SITE FOR RESIDUE CA A 1005
03
AC3
SOFTWARE
GLN A:232 , THR D:8 , THR D:10 , SER D:198 , ALA D:203
BINDING SITE FOR RESIDUE CA A 1006
04
AC4
SOFTWARE
GLN B:232 , THR C:8 , THR C:10 , SER C:198 , ALA C:203
BINDING SITE FOR RESIDUE CA B 1007
05
AC5
SOFTWARE
ASP A:322 , ASN B:326 , GLU B:329 , HOH B:1038 , HOH B:1142 , HOH B:1146 , HOH B:1203
BINDING SITE FOR RESIDUE CA B 1008
06
AC6
SOFTWARE
ASN A:288 , SER A:343 , ASN D:326 , GLU D:329 , HOH D:1214 , HOH D:1215
BINDING SITE FOR RESIDUE CA D 1009
07
AC7
SOFTWARE
GLN A:71 , ARG A:72 , HOH A:1207 , GLN B:71 , ARG B:72
BINDING SITE FOR RESIDUE CL A 1010
08
AC8
SOFTWARE
ARG C:72 , GLN D:71 , ARG D:72
BINDING SITE FOR RESIDUE CL D 1011
09
AC9
SOFTWARE
LYS B:11 , ARG B:17 , VAL C:25
BINDING SITE FOR RESIDUE CL B 1012
10
BC1
SOFTWARE
GLU B:24 , VAL B:25 , LYS C:11 , ARG C:17
BINDING SITE FOR RESIDUE CL B 1013
11
BC2
SOFTWARE
LYS A:11 , ARG A:17 , VAL D:25
BINDING SITE FOR RESIDUE CL D 1014
12
BC3
SOFTWARE
GLU A:24 , VAL A:25 , LYS D:11 , ARG D:17
BINDING SITE FOR RESIDUE CL D 1015
13
BC4
SOFTWARE
SER B:6 , SER B:57 , GLY B:58 , THR B:59 , HIS B:83 , GLU B:135 , ASP B:168 , ALA B:170 , ARG B:171 , MSE B:194 , LLP B:199 , ARG B:316 , HOH B:1031 , HOH B:1037 , HOH B:1046 , HOH B:1073 , HOH B:1167 , ARG C:231 , HOH C:1066
BINDING SITE FOR RESIDUE PLG B 1000
14
BC5
SOFTWARE
ARG B:231 , HOH B:1043 , SER C:6 , SER C:57 , GLY C:58 , THR C:59 , ASN C:62 , HIS C:83 , GLU C:135 , ASN C:139 , ASP C:168 , ALA C:170 , ARG C:171 , MSE C:194 , LLP C:199 , ARG C:316 , HOH C:1019 , HOH C:1022 , HOH C:1030 , HOH C:1042 , HOH C:1118 , HOH C:1143 , HOH C:1182
BINDING SITE FOR RESIDUE PLG C 1001
15
BC6
SOFTWARE
ARG A:231 , HOH A:1013 , HOH A:1105 , SER D:6 , SER D:57 , GLY D:58 , THR D:59 , ASN D:62 , HIS D:83 , GLU D:135 , ASN D:139 , ASP D:168 , ALA D:170 , ARG D:171 , MSE D:194 , LLP D:199 , ARG D:316 , HOH D:1062 , HOH D:1079 , HOH D:1093 , HOH D:1102 , HOH D:1126
BINDING SITE FOR RESIDUE PLG D 1002
16
BC7
SOFTWARE
SER B:57 , GLY B:58 , THR B:59 , ASN B:62 , HIS B:83 , GLU B:88 , GLU B:135 , ASP B:168 , ALA B:170 , ARG B:171 , LLP B:199 , HOH B:1031 , HOH B:1037 , HOH B:1046 , HOH B:1167 , ARG C:231 , HOH C:1066
BINDING SITE FOR RESIDUE PLP B 1003
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d1lw5a_ (A:)
1b: SCOP_d1lw5b_ (B:)
1c: SCOP_d1lw5c_ (C:)
1d: SCOP_d1lw5d_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PLP-dependent transferase-like
(627)
Superfamily
:
PLP-dependent transferases
(625)
Family
:
AAT-like
(184)
Protein domain
:
Low-specificity threonine aldolase
(6)
Thermotoga maritima [TaxId: 2336]
(5)
1a
d1lw5a_
A:
1b
d1lw5b_
B:
1c
d1lw5c_
C:
1d
d1lw5d_
D:
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1lw5A01 (A:2-246)
1b: CATH_1lw5C01 (C:2-246)
1c: CATH_1lw5D01 (D:2-246)
1d: CATH_1lw5B01 (B:2-246)
2a: CATH_1lw5A02 (A:248-330)
2b: CATH_1lw5B02 (B:248-330)
2c: CATH_1lw5C02 (C:248-330)
2d: CATH_1lw5D02 (D:248-330)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aspartate Aminotransferase; domain 2
(384)
Homologous Superfamily
:
Type I PLP-dependent aspartate aminotransferase-like (Major domain)
(384)
Thermotoga maritima. Organism_taxid: 2336.
(8)
1a
1lw5A01
A:2-246
1b
1lw5C01
C:2-246
1c
1lw5D01
D:2-246
1d
1lw5B01
B:2-246
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aspartate Aminotransferase, domain 1
(355)
Homologous Superfamily
:
Aspartate Aminotransferase, domain 1
(354)
Thermotoga maritima. Organism_taxid: 2336.
(8)
2a
1lw5A02
A:248-330
2b
1lw5B02
B:248-330
2c
1lw5C02
C:248-330
2d
1lw5D02
D:248-330
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Beta_elim_lyase_1lw5D01 (D:3-288)
1b: PFAM_Beta_elim_lyase_1lw5D02 (D:3-288)
1c: PFAM_Beta_elim_lyase_1lw5D03 (D:3-288)
1d: PFAM_Beta_elim_lyase_1lw5D04 (D:3-288)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PLP_aminotran
(240)
Family
:
Beta_elim_lyase
(13)
Thermotoga maritima
(4)
1a
Beta_elim_lyase-1lw5D01
D:3-288
1b
Beta_elim_lyase-1lw5D02
D:3-288
1c
Beta_elim_lyase-1lw5D03
D:3-288
1d
Beta_elim_lyase-1lw5D04
D:3-288
[
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 (243 KB)
Header - Asym.Unit
Biol.Unit 1 (231 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
1LW5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help