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.
3KED
Asym. Unit
Info
Asym.Unit (161 KB)
Biol.Unit 1 (154 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 AMINOPEPTIDASE N IN COMPLEX WITH 2,4-DIAMINOBUTYRIC ACID
Authors
:
A. Addlagatta, R. Gumpena
Date
:
25 Oct 09 (Deposition) - 03 Nov 10 (Release) - 29 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Aminopeptidase, Thermolysin Like Active Site, Amino Switch, Inhibitor, Ligand Design, Cell Inner Membrane, Cell Membrane, Hydrolase, Membrane, Metal-Binding, Metalloprotease, Protease
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Gumpena, C. Kishor, R. J. Ganji, A. Addlagatta
Discovery Of Alpha, Beta- And Alpha, Gamma-Diamino Acid Scaffolds For The Inhibition Of M1 Family Aminopeptidases
Chemmedchem V. 6 1971 2011
[
close entry info
]
Hetero Components
(5, 16)
Info
All Hetero Components
1a: 2,4-DIAMINOBUTYRIC ACID (DABa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
3a: MALONIC ACID (MLAa)
3b: MALONIC ACID (MLAb)
3c: MALONIC ACID (MLAc)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DAB
1
Ligand/Ion
2,4-DIAMINOBUTYRIC ACID
2
GOL
9
Ligand/Ion
GLYCEROL
3
MLA
3
Ligand/Ion
MALONIC ACID
4
NA
2
Ligand/Ion
SODIUM ION
5
ZN
1
Ligand/Ion
ZINC 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
HIS A:297 , HIS A:301 , GLU A:320 , DAB A:880
BINDING SITE FOR RESIDUE ZN A 875
02
AC2
SOFTWARE
GLU A:121 , MET A:260 , ALA A:262 , MET A:263 , GLU A:264 , HIS A:297 , GLU A:298 , HIS A:301 , LYS A:319 , GLU A:320 , TYR A:381 , ZN A:875 , MLA A:991
BINDING SITE FOR RESIDUE DAB A 880
03
AC3
SOFTWARE
SER A:332 , ASP A:333 , GLY A:335 , HOH A:949 , HOH A:1126
BINDING SITE FOR RESIDUE NA A 951
04
AC4
SOFTWARE
ASP A:452 , HOH A:1210
BINDING SITE FOR RESIDUE NA A 952
05
AC5
SOFTWARE
LEU A:532 , TRP A:546 , LEU A:554 , ASP A:566 , SER A:570
BINDING SITE FOR RESIDUE GOL A 970
06
AC6
SOFTWARE
SER A:63 , VAL A:64 , TRP A:71 , TRP A:74 , ARG A:669 , VAL A:670 , GLU A:671 , GOL A:972 , GOL A:975 , HOH A:980
BINDING SITE FOR RESIDUE GOL A 971
07
AC7
SOFTWARE
VAL A:62 , SER A:63 , TRP A:74 , ARG A:669 , GLU A:671 , GOL A:971
BINDING SITE FOR RESIDUE GOL A 972
08
AC8
SOFTWARE
LEU A:378 , TYR A:381 , GLU A:382 , MLA A:991
BINDING SITE FOR RESIDUE GOL A 973
09
AC9
SOFTWARE
ARG A:681 , ALA A:707 , ASN A:708 , ASN A:709 , ASP A:712 , HOH A:1290
BINDING SITE FOR RESIDUE GOL A 974
10
BC1
SOFTWARE
THR A:72 , TRP A:74 , VAL A:670 , GLU A:671 , GOL A:971 , HOH A:1222
BINDING SITE FOR RESIDUE GOL A 975
11
BC2
SOFTWARE
HIS A:11 , GLN A:467 , ARG A:468 , THR A:469 , GLN A:479 , PRO A:480
BINDING SITE FOR RESIDUE GOL A 976
12
BC3
SOFTWARE
GLU A:123 , ASP A:312 , TRP A:313 , PHE A:314
BINDING SITE FOR RESIDUE GOL A 977
13
BC4
SOFTWARE
GLU A:409 , ASP A:412 , LEU A:589 , SER A:590 , LEU A:591 , HOH A:1343 , HOH A:1344
BINDING SITE FOR RESIDUE GOL A 978
14
BC5
SOFTWARE
ARG A:641 , GLU A:642 , THR A:645 , ARG A:686 , ALA A:722 , HOH A:1186 , HOH A:1283
BINDING SITE FOR RESIDUE MLA A 990
15
BC6
SOFTWARE
ARG A:293 , ASP A:327 , TYR A:381 , DAB A:880 , GOL A:973
BINDING SITE FOR RESIDUE MLA A 991
16
BC7
SOFTWARE
GLU A:69 , PRO A:70 , TRP A:71 , THR A:72 , PRO A:224 , ARG A:279 , THR A:280 , TYR A:288 , HOH A:994
BINDING SITE FOR RESIDUE MLA A 992
[
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, 1)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:294-303)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZINC_PROTEASE
PS00142
Neutral zinc metallopeptidases, zinc-binding region signature.
AMPN_ECOLI
294-303
1
A:294-303
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Peptidase_M1_3kedA01 (A:19-384)
2a: PFAM_DUF3458_3kedA02 (A:457-827)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M1
(15)
Escherichia coli (strain K12)
(2)
1a
Peptidase_M1-3kedA01
A:19-384
Clan
:
TPR
(230)
Family
:
DUF3458
(4)
Escherichia coli (strain K12)
(2)
2a
DUF3458-3kedA02
A:457-827
[
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 (161 KB)
Header - Asym.Unit
Biol.Unit 1 (154 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
3KED
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
