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.
2HDR
Asym. Unit
Info
Asym.Unit (127 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (63 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
AMPC BETA-LACTAMASE IN COMPLEX WITH 4-AMINO-3-HYDROXYBENZOIC ACID
Authors
:
K. Babaoglu, B. K. Shoichet
Date
:
20 Jun 06 (Deposition) - 07 Nov 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Ampc Fragment-Based Drug Design Beta-Lactamase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Babaoglu, B. K. Shoichet
Deconstructing Fragment-Based Inhibitor Discovery
Nat. Chem. Biol. V. 2 720 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 16)
Info
All Hetero Components
1a: 4-AMINO-3-HYDROXYBENZOIC ACID (4A3a)
1b: 4-AMINO-3-HYDROXYBENZOIC ACID (4A3b)
1c: 4-AMINO-3-HYDROXYBENZOIC ACID (4A3c)
1d: 4-AMINO-3-HYDROXYBENZOIC ACID (4A3d)
1e: 4-AMINO-3-HYDROXYBENZOIC ACID (4A3e)
1f: 4-AMINO-3-HYDROXYBENZOIC ACID (4A3f)
1g: 4-AMINO-3-HYDROXYBENZOIC ACID (4A3g)
1h: 4-AMINO-3-HYDROXYBENZOIC ACID (4A3h)
1i: 4-AMINO-3-HYDROXYBENZOIC ACID (4A3i)
1j: 4-AMINO-3-HYDROXYBENZOIC ACID (4A3j)
1k: 4-AMINO-3-HYDROXYBENZOIC ACID (4A3k)
1l: 4-AMINO-3-HYDROXYBENZOIC ACID (4A3l)
1m: 4-AMINO-3-HYDROXYBENZOIC ACID (4A3m)
1n: 4-AMINO-3-HYDROXYBENZOIC ACID (4A3n)
1o: 4-AMINO-3-HYDROXYBENZOIC ACID (4A3o)
2a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4A3
15
Ligand/Ion
4-AMINO-3-HYDROXYBENZOIC ACID
2
PO4
1
Ligand/Ion
PHOSPHATE ION
[
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
SER A:64 , TYR A:150 , THR A:316 , ALA A:318 , HOH A:536
BINDING SITE FOR RESIDUE PO4 A 401
02
AC2
SOFTWARE
VAL A:191 , GLU A:196 , TYR A:199 , HIS A:210 , HOH A:522 , HOH A:544
BINDING SITE FOR RESIDUE 4A3 A 501
03
AC3
SOFTWARE
VAL B:191 , GLU B:196 , TYR B:199 , HIS B:210 , HOH B:525 , HOH B:567
BINDING SITE FOR RESIDUE 4A3 B 502
04
AC4
SOFTWARE
GLN A:120 , ASN A:152 , SER A:212 , TYR A:221 , THR A:319 , GLY A:320 , HOH A:557 , HOH A:581
BINDING SITE FOR RESIDUE 4A3 A 503
05
AC5
SOFTWARE
PRO B:140 , TRP B:142 , ALA B:143 , HOH B:520
BINDING SITE FOR RESIDUE 4A3 B 504
06
AC6
SOFTWARE
GLN B:120 , ASN B:152 , VAL B:211 , SER B:212 , TYR B:221 , GLY B:320 , HOH B:573 , HOH B:600
BINDING SITE FOR RESIDUE 4A3 B 505
07
AC7
SOFTWARE
LYS A:239 , PRO A:240 , LEU A:241 , ARG A:309 , LYS B:246 , THR B:247 , GLN B:250
BINDING SITE FOR RESIDUE 4A3 A 506
08
AC8
SOFTWARE
THR A:302 , TYR B:259 , TRP B:260 , ILE B:301 , THR B:302 , PRO B:303 , PRO B:304 , HOH B:571
BINDING SITE FOR RESIDUE 4A3 B 507
09
AC9
SOFTWARE
ALA A:141 , TRP A:142 , ALA A:143 , HOH A:538
BINDING SITE FOR RESIDUE 4A3 A 508
10
BC1
SOFTWARE
PRO A:277 , VAL A:278 , PRO A:280 , TRP A:354 , ASN A:358 , 4A3 A:511
BINDING SITE FOR RESIDUE 4A3 A 509
11
BC2
SOFTWARE
ILE A:48 , GLY A:206 , HOH A:653
BINDING SITE FOR RESIDUE 4A3 A 510
12
BC3
SOFTWARE
PRO A:277 , VAL A:278 , ASN A:279 , 4A3 A:509
BINDING SITE FOR RESIDUE 4A3 A 511
13
BC4
SOFTWARE
TRP A:93 , GLU A:95 , SER A:128 , SER A:129 , LEU A:132 , ASN B:279 , ASP B:281 , ASN B:285
BINDING SITE FOR RESIDUE 4A3 B 512
14
BC5
SOFTWARE
VAL A:125 , LYS A:126 , PRO A:213 , GLY A:214 , ALA A:215 , HOH A:563
BINDING SITE FOR RESIDUE 4A3 A 513
15
BC6
SOFTWARE
GLY A:167 , LEU A:168 , SER A:169 , GLN A:172 , TRP B:354 , GLN B:355 , ASN B:358
BINDING SITE FOR RESIDUE 4A3 B 514
16
BC7
SOFTWARE
THR B:97 , LYS B:99 , ASN B:102 , TRP B:188 , ASN B:190 , PRO B:192
BINDING SITE FOR RESIDUE 4A3 B 515
[
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: BETA_LACTAMASE_C (A:60-67,B:60-67)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BETA_LACTAMASE_C
PS00336
Beta-lactamase class-C active site.
AMPC_ECOLI
76-83
2
A:60-67
B:60-67
[
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, 2)
Info
All SCOP Domains
1a: SCOP_d2hdra_ (A:)
1b: SCOP_d2hdrb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
:
AMPC beta-Lactamase, class C
(85)
Escherichia coli, cephalosporinase [TaxId: 562]
(73)
1a
d2hdra_
A:
1b
d2hdrb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2hdrA00 (A:4-361)
1b: CATH_2hdrB00 (B:4-361)
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)
Escherichia coli k12. Organism_taxid: 83333. Strain: k-12.
(4)
1a
2hdrA00
A:4-361
1b
2hdrB00
B:4-361
[
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
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 (127 KB)
Header - Asym.Unit
Biol.Unit 1 (62 KB)
Header - Biol.Unit 1
Biol.Unit 2 (63 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
2HDR
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help