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.
1QMF
Asym. Unit
Info
Asym.Unit (95 KB)
Biol.Unit 1 (90 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PENICILLIN-BINDING PROTEIN 2X (PBP-2X) ACYL-ENZYME COMPLEX
Authors
:
E. J. Gordon, N. Mouz, E. Duee, O. Dideberg
Date
:
28 Sep 99 (Deposition) - 25 May 00 (Release) - 17 Apr 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Peptidoglycan Synthesis, Cell Wall, Cell Cycle
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. J. Gordon, N. Mouz, E. Duee, O. Dideberg
The Crystal Structure Of The Penicillin Binding Protein 2X From Streptococcus Pneumoniae And Its Acyl-Enzyme Form: Implication In Drug Resistance
J. Mol. Biol. V. 299 501 2000
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: 2-[CARBOXY-(2-FURAN-2-YL-2-METHOXY... (CESa)
2a: CEFUROXIME (OCT-3-ENE FORM) (KEFa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CES
1
Ligand/Ion
2-[CARBOXY-(2-FURAN-2-YL-2-METHOXYIMINO-ACETYLAMINO)-METHYL]-5-METHYL-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID
2
KEF
1
Ligand/Ion
CEFUROXIME (OCT-3-ENE FORM)
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
VAL A:423 , PRO A:424 , ARG A:426 , VAL A:662 , HOH A:2057
BINDING SITE FOR RESIDUE KEF A 900
2
AC2
SOFTWARE
GLU A:334 , SER A:337 , TRP A:374 , SER A:395 , ASN A:397 , PHE A:450 , GLN A:452 , SER A:548 , GLY A:549 , THR A:550 , GLN A:552
BINDING SITE FOR LIGAND CES A 800 BOUND TO SER A 337
[
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: PASTA (A:633-691|A:692-750)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PASTA
PS51178
PASTA domain profile.
PBPX_STRPN
632-691
692-750
2
A:633-691
A:692-750
[
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
(3, 4)
Info
All SCOP Domains
1a: SCOP_d1qmfa3 (A:71-263)
2a: SCOP_d1qmfa1 (A:633-692)
2b: SCOP_d1qmfa2 (A:693-750)
3a: SCOP_d1qmfa4 (A:264-620)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Penicillin binding protein dimerisation domain
(32)
Superfamily
:
Penicillin binding protein dimerisation domain
(32)
Family
:
Penicillin binding protein dimerisation domain
(12)
Protein domain
:
Penicillin-binding protein 2x (pbp-2x), N-terminal domain
(6)
Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313]
(6)
1a
d1qmfa3
A:71-263
Fold
:
Penicillin-binding protein 2x (pbp-2x), c-terminal domain
(10)
Superfamily
:
Penicillin-binding protein 2x (pbp-2x), c-terminal domain
(10)
Family
:
Penicillin-binding protein 2x (pbp-2x), c-terminal domain
(10)
Protein domain
:
Penicillin-binding protein 2x (pbp-2x), c-terminal domain
(10)
Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313]
(10)
2a
d1qmfa1
A:633-692
2b
d1qmfa2
A:693-750
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
beta-lactamase/transpeptidase-like
(515)
Superfamily
:
beta-lactamase/transpeptidase-like
(515)
Family
:
beta-Lactamase/D-ala carboxypeptidase
(411)
Protein domain
:
Penicillin-binding protein 2x (pbp-2x), transpeptidase domain
(10)
Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313]
(10)
3a
d1qmfa4
A:264-620
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1qmfA02 (A:264-480,A:495-620)
2a: CATH_1qmfA01 (A:71-92,A:183-263,A:481-494)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Beta-lactamase
(339)
Homologous Superfamily
:
DD-peptidase/beta-lactamase superfamily
(335)
Streptococcus pneumoniae. Organism_taxid: 1313. Strain: mc1061.
(2)
1a
1qmfA02
A:264-480,A:495-620
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Penicillin-binding protein 2a (Domain 2)
(7)
Homologous Superfamily
:
Penicillin-binding protein 2a (Domain 2)
(7)
Streptococcus pneumoniae. Organism_taxid: 1313. Strain: mc1061.
(2)
2a
1qmfA01
A:71-92,A:183-263,A:481-494
[
close CATH info
]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_Transpeptidase_1qmfA01 (A:289-609)
2a: PFAM_PASTA_1qmfA02 (A:694-750)
3a: PFAM_PBP_dimer_1qmfA03 (A:71-234)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Beta-lactamase
(210)
Family
:
Transpeptidase
(31)
Streptococcus pneumoniae
(9)
1a
Transpeptidase-1qmfA01
A:289-609
Clan
:
no clan defined [family: PASTA]
(12)
Family
:
PASTA
(12)
Streptococcus pneumoniae
(7)
2a
PASTA-1qmfA02
A:694-750
Clan
:
no clan defined [family: PBP_dimer]
(15)
Family
:
PBP_dimer
(15)
Streptococcus pneumoniae
(7)
3a
PBP_dimer-1qmfA03
A:71-234
[
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
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 (95 KB)
Header - Asym.Unit
Biol.Unit 1 (90 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
1QMF
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help