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.
2EJ3
Asym. Unit
Info
Asym.Unit (158 KB)
Biol.Unit 1 (302 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 T.TH.HB8 BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE COMPLEXED WITH GABAPENTIN
Authors
:
M. Goto
Date
:
14 Mar 07 (Deposition) - 18 Mar 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (2x)
Keywords
:
Plp-Dependent Enzyme, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Goto
Crystal Structure Of T. Th. Hb8 Branched-Chain Amino Acid Aminotransferase Complexed With Gabapentin
To Be Published
[
close entry info
]
Hetero Components
(3, 11)
Info
All Hetero Components
1a: [1-(AMINOMETHYL)CYCLOHEXYL]ACETIC ... (GBNa)
1b: [1-(AMINOMETHYL)CYCLOHEXYL]ACETIC ... (GBNb)
1c: [1-(AMINOMETHYL)CYCLOHEXYL]ACETIC ... (GBNc)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
2c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
2d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
2e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
3a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
3b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
3c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GBN
3
Ligand/Ion
[1-(AMINOMETHYL)CYCLOHEXYL]ACETIC ACID
2
MPD
5
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
PLP
3
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:59 , ARG A:148 , LYS A:159 , TYR A:164 , GLU A:193 , GLY A:196 , LEU A:216 , GLY A:218 , ILE A:219 , THR A:220 , GLY A:255 , THR A:256 , HOH A:2443 , HOH A:2446
BINDING SITE FOR RESIDUE PLP A 413
02
AC2
SOFTWARE
ARG B:59 , LYS B:159 , TYR B:164 , GLU B:193 , GLY B:196 , LEU B:216 , GLY B:218 , ILE B:219 , THR B:220 , GLY B:255 , THR B:256 , HOH B:928 , HOH B:958
BINDING SITE FOR RESIDUE PLP B 913
03
AC3
SOFTWARE
ARG C:59 , ARG C:148 , LYS C:159 , TYR C:164 , GLU C:193 , GLY C:196 , LEU C:216 , GLY C:218 , ILE C:219 , THR C:220 , GLY C:255 , THR C:256 , HOH C:1425 , HOH C:1447
BINDING SITE FOR RESIDUE PLP C 1413
04
AC4
SOFTWARE
ARG A:97 , GLY A:196 , GLU A:197 , GLY A:255 , THR A:256 , ALA A:257 , ALA A:258 , HOH A:2539 , HOH A:2554 , TYR C:31
BINDING SITE FOR RESIDUE GBN A 2414
05
AC5
SOFTWARE
ARG B:97 , GLY B:196 , GLU B:197 , GLY B:255 , THR B:256 , ALA B:257 , ALA B:258 , HOH B:983 , HOH B:984 , HOH B:1091
BINDING SITE FOR RESIDUE GBN B 914
06
AC6
SOFTWARE
TYR A:31 , ARG C:97 , GLY C:196 , GLU C:197 , GLY C:255 , THR C:256 , ALA C:257 , ALA C:258 , HOH C:1457 , HOH C:1469 , HOH C:1572
BINDING SITE FOR RESIDUE GBN C 1414
07
AC7
SOFTWARE
ASP A:230 , GLU A:297 , HOH A:2472 , HOH A:2502 , GLU C:289 , ARG C:294 , ARG C:295
BINDING SITE FOR RESIDUE MPD A 2416
08
AC8
SOFTWARE
ARG A:52 , GLU A:55 , GLU A:217 , ILE A:219 , ASP A:222 , HOH A:2524 , HOH A:2532 , ARG C:203 , ASP C:204
BINDING SITE FOR RESIDUE MPD A 1417
09
AC9
SOFTWARE
LEU B:107 , TRP B:124 , TRP B:126
BINDING SITE FOR RESIDUE MPD B 915
10
BC1
SOFTWARE
ARG A:203 , ASP A:204 , ARG B:52 , GLU B:55 , GLU B:217 , GLY B:218 , ASP B:222 , HOH B:967
BINDING SITE FOR RESIDUE MPD B 917
11
BC2
SOFTWARE
ARG B:203 , ASP B:204 , ARG C:52 , GLU C:55 , GLU C:217 , ASP C:222 , HOH C:1521 , HOH C:1569
BINDING SITE FOR RESIDUE MPD C 1416
[
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, 3)
Info
All SCOP Domains
1a: SCOP_d2ej3a_ (A:)
1b: SCOP_d2ej3b_ (B:)
1c: SCOP_d2ej3c_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
D-aminoacid aminotransferase-like PLP-dependent enzymes
(46)
Superfamily
:
D-aminoacid aminotransferase-like PLP-dependent enzymes
(46)
Family
:
automated matches
(13)
Protein domain
:
automated matches
(13)
Thermus thermophilus HB8 [TaxId: 300852]
(4)
1a
d2ej3a_
A:
1b
d2ej3b_
B:
1c
d2ej3c_
C:
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_2ej3B01 (B:5-130)
1b: CATH_2ej3A01 (A:5-126)
1c: CATH_2ej3C01 (C:5-126)
2a: CATH_2ej3B02 (B:131-294)
2b: CATH_2ej3A02 (A:135-294)
2c: CATH_2ej3C02 (C:137-294)
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
:
[code=3.30.470.10, no name defined]
(39)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(4)
1a
2ej3B01
B:5-130
1b
2ej3A01
A:5-126
1c
2ej3C01
C:5-126
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
D-amino Acid Aminotransferase; Chain A, domain 2
(39)
Homologous Superfamily
:
D-amino Acid Aminotransferase, subunit A, domain 2
(39)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(4)
2a
2ej3B02
B:131-294
2b
2ej3A02
A:135-294
2c
2ej3C02
C:137-294
[
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
Chain C
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 (158 KB)
Header - Asym.Unit
Biol.Unit 1 (302 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
2EJ3
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help