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.
2BMK
Asym. Unit
Info
Asym.Unit (147 KB)
Biol.Unit 1 (73 KB)
Biol.Unit 2 (74 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
FAB FRAGMENT OF PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH PHOSPHOPYRIDOXYL-D-ALANINE
Authors
:
B. Golinelli-Pimpaneau, P. Christen
Date
:
14 Mar 05 (Deposition) - 03 Mar 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,H,L
Biol. Unit 1: A,B (1x)
Biol. Unit 2: H,L (1x)
Keywords
:
Catalytic Antibody, Transamination, Pyridoxal-Phosphate, Hapten, Phosphopyridoxyl-L-Lysine, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Golinelli-Pimpaneau, C. Luthi, P. Christen
Structural Basis For D-Amino Acid Transamination By The Pyridoxal 5'-Phosphate-Dependent Catalytic Antibody 15A9.
J. Biol. Chem. V. 281 23969 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 8)
Info
All Hetero Components
1a: IODIDE ION (IODa)
1b: IODIDE ION (IODb)
1c: IODIDE ION (IODc)
1d: IODIDE ION (IODd)
1e: IODIDE ION (IODe)
1f: IODIDE ION (IODf)
2a: N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE (PDDa)
2b: N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE (PDDb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IOD
6
Ligand/Ion
IODIDE ION
2
PDD
2
Ligand/Ion
N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR B:32 , GLY B:97 , TYR B:99 , TRP B:100E
BINDING SITE FOR RESIDUE IOD B1215
2
AC2
SOFTWARE
ASN B:52A , ASN B:53
BINDING SITE FOR RESIDUE IOD B1216
3
AC3
SOFTWARE
THR B:68
BINDING SITE FOR RESIDUE IOD B1218
4
AC4
SOFTWARE
THR H:68 , ASN H:82A
BINDING SITE FOR RESIDUE IOD H1215
5
AC5
SOFTWARE
GLY H:97 , TYR H:99 , ASN H:100A , TRP H:100E
BINDING SITE FOR RESIDUE IOD H1216
6
AC6
SOFTWARE
GLY H:26 , PHE H:27
BINDING SITE FOR RESIDUE IOD H1217
7
AC7
SOFTWARE
TYR A:32 , HIS A:34 , ARG A:91 , SER A:92 , TYR A:94 , TYR B:33 , ARG B:52 , ASP B:95 , LYS B:96 , HOH B:2080 , HOH B:2081 , HOH B:2082
BINDING SITE FOR RESIDUE PDD B1217
8
AC8
SOFTWARE
TYR H:33 , ARG H:52 , ASP H:95 , TYR L:32 , HIS L:34 , ARG L:91 , SER L:92 , TYR L:94 , HOH L:2096 , HOH L:2097
BINDING SITE FOR RESIDUE PDD L1215
[
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
(4, 8)
Info
All SCOP Domains
1a: SCOP_d2bmka1 (A:1-107)
1b: SCOP_d2bmkl1 (L:1-107)
2a: SCOP_d2bmka2 (A:108-214)
2b: SCOP_d2bmkl2 (L:108-214)
3a: SCOP_d2bmkb2 (B:114-214)
3b: SCOP_d2bmkh2 (H:114-214)
4a: SCOP_d2bmkb1 (B:1-113)
4b: SCOP_d2bmkh1 (H:1-113)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Mouse (Mus musculus) [TaxId: 10090]
(360)
1a
d2bmka1
A:1-107
1b
d2bmkl1
L:1-107
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Mouse (Mus musculus) [TaxId: 10090]
(309)
2a
d2bmka2
A:108-214
2b
d2bmkl2
L:108-214
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma
(608)
Mouse (Mus musculus) [TaxId: 10090]
(414)
3a
d2bmkb2
B:114-214
3b
d2bmkh2
H:114-214
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Mouse (Mus musculus), cluster 1 [TaxId: 10090]
(57)
4a
d2bmkb1
B:1-113
4b
d2bmkh1
H:1-113
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_2bmkA02 (A:109-214)
1b: CATH_2bmkL02 (L:109-214)
1c: CATH_2bmkA01 (A:1-108)
1d: CATH_2bmkL01 (L:1-108)
1e: CATH_2bmkB02 (B:114-214)
1f: CATH_2bmkH02 (H:114-214)
1g: CATH_2bmkB01 (B:1-113)
1h: CATH_2bmkH01 (H:1-113)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Mouse (Mus musculus)
(152)
1a
2bmkA02
A:109-214
1b
2bmkL02
L:109-214
1c
2bmkA01
A:1-108
1d
2bmkL01
L:1-108
1e
2bmkB02
B:114-214
1f
2bmkH02
H:114-214
1g
2bmkB01
B:1-113
1h
2bmkH01
H:1-113
[
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 H
Chain L
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 (147 KB)
Header - Asym.Unit
Biol.Unit 1 (73 KB)
Header - Biol.Unit 1
Biol.Unit 2 (74 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
2BMK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help