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.
1MWR
Biol. Unit 1
Info
Asym.Unit (213 KB)
Biol.Unit 1 (105 KB)
Biol.Unit 2 (105 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF SEMET PENICILLIN BINDING PROTEIN 2A FROM METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS STRAIN 27R (TRIGONAL FORM) AT 2.45 A RESOLUTION.
Authors
:
D. C. Lim, N. C. J. Strynadka
Date
:
01 Oct 02 (Deposition) - 06 Nov 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.45
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Penicillin Binding Protein, Beta-Lactam, D, D- Transpeptidase, D-Carboxypeptidase, Biosynthetic Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Lim, N. C. Strynadka
Structural Basis For The Beta Lactam Resistance Of Pbp2A From Methicillin-Resistant Staphylococcus Aureus.
Nat. Struct. Biol. V. 9 870 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 15)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
1b: CADMIUM ION (CDb)
1c: CADMIUM ION (CDc)
1d: CADMIUM ION (CDd)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
3ab: SELENOMETHIONINE (MSEab)
3ac: SELENOMETHIONINE (MSEac)
3ad: SELENOMETHIONINE (MSEad)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
3y: SELENOMETHIONINE (MSEy)
3z: SELENOMETHIONINE (MSEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CD
-1
Ligand/Ion
CADMIUM ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
MSE
15
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC5 (SOFTWARE)
5: AC6 (SOFTWARE)
6: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:145 , HIS B:143 , GLU B:145 , CL B:1208
BINDING SITE FOR RESIDUE CD B 1201
2
AC2
SOFTWARE
GLY A:135 , HIS A:311 , CL A:1205 , ASP B:209
BINDING SITE FOR RESIDUE CD A 1202
3
AC3
SOFTWARE
ASP A:209 , GLY B:135 , HIS B:311 , CL B:1206
BINDING SITE FOR RESIDUE CD A 1203
4
AC5
SOFTWARE
GLY A:135 , GLN A:137 , GLN A:140 , CD A:1202
BINDING SITE FOR RESIDUE CL A 1205
5
AC6
SOFTWARE
CD A:1203 , GLY B:135 , GLN B:137 , GLN B:140 , HIS B:311
BINDING SITE FOR RESIDUE CL B 1206
6
AC7
SOFTWARE
GLU A:145 , THR A:300
BINDING SITE FOR RESIDUE CL A 1207
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1mwra1 (A:27-138)
1b: SCOP_d1mwrb1 (B:27-138)
2a: SCOP_d1mwra2 (A:139-327)
2b: SCOP_d1mwrb2 (B:139-327)
3a: SCOP_d1mwra3 (A:328-668)
3b: SCOP_d1mwrb3 (B:328-668)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cystatin-like
(403)
Superfamily
:
NTF2-like
(231)
Family
:
Penicillin binding protein 2a (PBP2A), N-terminal domain
(6)
Protein domain
:
Penicillin binding protein 2a (PBP2A), N-terminal domain
(6)
Staphylococcus aureus [TaxId: 1280]
(6)
1a
d1mwra1
A:27-138
1b
d1mwrb1
B:27-138
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 2a (PBP2A), middle domain
(6)
Staphylococcus aureus [TaxId: 1280]
(6)
2a
d1mwra2
A:139-327
2b
d1mwrb2
B:139-327
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 2a (PBP2A), C-terminal domain
(6)
Staphylococcus aureus [TaxId: 1280]
(6)
3a
d1mwra3
A:328-668
3b
d1mwrb3
B:328-668
[
close SCOP info
]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_1mwrA03 (A:168-237)
1b: CATH_1mwrB03 (B:168-237)
2a: CATH_1mwrA04 (A:327-665)
2b: CATH_1mwrB04 (B:327-665)
3a: CATH_1mwrA02 (A:137-167,A:238-326)
3b: CATH_1mwrB02 (B:137-167,B:238-326)
4a: CATH_1mwrA01 (A:27-135)
4b: CATH_1mwrB01 (B:27-135)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Ribosomal Protein L30; Chain: A,
(164)
Homologous Superfamily
:
Penicillin-binding protein 2a; domain 3
(5)
Staphylococcus aureus. Organism_taxid: 1280.
(4)
1a
1mwrA03
A:168-237
1b
1mwrB03
B:168-237
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Beta-lactamase
(339)
Homologous Superfamily
:
DD-peptidase/beta-lactamase superfamily
(335)
Staphylococcus aureus. Organism_taxid: 1280.
(5)
2a
1mwrA04
A:327-665
2b
1mwrB04
B:327-665
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Penicillin-binding protein 2a (Domain 2)
(7)
Homologous Superfamily
:
Penicillin-binding protein 2a (Domain 2)
(7)
Staphylococcus aureus. Organism_taxid: 1280.
(4)
3a
1mwrA02
A:137-167,A:238-326
3b
1mwrB02
B:137-167,B:238-326
Architecture
:
Roll
(3276)
Topology
:
Nuclear Transport Factor 2; Chain: A,
(517)
Homologous Superfamily
:
NTF2-like; domain 1
(5)
Staphylococcus aureus. Organism_taxid: 1280.
(4)
4a
1mwrA01
A:27-135
4b
1mwrB01
B:27-135
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Transpeptidase_1mwrB01 (B:345-658)
1b: PFAM_Transpeptidase_1mwrB02 (B:345-658)
2a: PFAM_MecA_N_1mwrB03 (B:27-140)
2b: PFAM_MecA_N_1mwrB04 (B:27-140)
3a: PFAM_PBP_dimer_1mwrB05 (B:146-313)
3b: PFAM_PBP_dimer_1mwrB06 (B:146-313)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Beta-lactamase
(210)
Family
:
Transpeptidase
(31)
Staphylococcus aureus
(10)
1a
Transpeptidase-1mwrB01
B:345-658
1b
Transpeptidase-1mwrB02
B:345-658
Clan
:
NTF2
(66)
Family
:
MecA_N
(5)
Staphylococcus aureus
(5)
2a
MecA_N-1mwrB03
B:27-140
2b
MecA_N-1mwrB04
B:27-140
Clan
:
no clan defined [family: PBP_dimer]
(15)
Family
:
PBP_dimer
(15)
Staphylococcus aureus
(5)
3a
PBP_dimer-1mwrB05
B:146-313
3b
PBP_dimer-1mwrB06
B:146-313
[
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 (213 KB)
Header - Asym.Unit
Biol.Unit 1 (105 KB)
Header - Biol.Unit 1
Biol.Unit 2 (105 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
1MWR
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
