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.
2VD4
Asym. Unit
Info
Asym.Unit (84 KB)
Biol.Unit 1 (228 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 SMALL-MOLECULE INHIBITOR OF GLMU FROM HAEMOPHILUS INFLUENZAE REVEALS AN ALLOSTERIC BINDING SITE
Authors
:
I. Mochalkin, S. Lightle, L. Mcdowell
Date
:
28 Sep 07 (Deposition) - 15 Jan 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (3x)
Keywords
:
Glmu, Inhibitor, Magnesium, Cell Shape, Peptidoglycan Synthesis, Allosteric, Transferase, Active Site, Metal-Binding, Cell Wall Biogenesis/Degradation, Multifunctional Enzyme, Nucleotidyltransferase, Acyltransferase, Uridyltransferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Mochalkin, S. Lightle, L. Narasimhan, D. Bornemeier, M. Melnick, S. Vanderroest, L. Mcdowell
Structure Of A Small-Molecule Inhibitor Complexed With Glmu From Haemophilus Influenzae Reveals An Allosteric Binding Site.
Protein Sci. V. 17 577 2008
[
close entry info
]
Hetero Components
(5, 12)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
2a: 4-CHLORO-N-(3-METHOXYPROPYL)-N-[(3... (P21a)
3a: TETRAETHYLENE GLYCOL (PG4a)
3b: TETRAETHYLENE GLYCOL (PG4b)
4a: TRIETHYLENE GLYCOL (PGEa)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
2
Ligand/Ion
MAGNESIUM ION
2
P21
1
Ligand/Ion
4-CHLORO-N-(3-METHOXYPROPYL)-N-[(3S)-1-(2-PHENYLETHYL)PIPERIDIN-3-YL]BENZAMIDE
3
PG4
2
Ligand/Ion
TETRAETHYLENE GLYCOL
4
PGE
1
Ligand/Ion
TRIETHYLENE GLYCOL
5
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:139 , ASN A:169 , VAL A:223 , GLU A:224 , GLY A:225 , GLN A:231 , LEU A:235 , SO4 A:1458 , HOH A:2280
BINDING SITE FOR RESIDUE P21 A1454
02
AC2
SOFTWARE
LYS A:360 , ASN A:362 , HIS A:363 , HOH A:2225 , HOH A:2281 , HOH A:2282
BINDING SITE FOR RESIDUE SO4 A1455
03
AC3
SOFTWARE
LYS A:15 , HIS A:57 , GLY A:58
BINDING SITE FOR RESIDUE SO4 A1456
04
AC4
SOFTWARE
ASN A:377 , ARG A:451 , HOH A:2221 , HOH A:2284
BINDING SITE FOR RESIDUE SO4 A1457
05
AC5
SOFTWARE
ASN A:227 , GLN A:231 , P21 A:1454
BINDING SITE FOR RESIDUE SO4 A1458
06
AC6
SOFTWARE
HIS A:57 , GLU A:78 , GLN A:79 , HOH A:2285
BINDING SITE FOR RESIDUE SO4 A1459
07
AC7
SOFTWARE
ARG A:331 , ARG A:333 , PRO A:334 , HOH A:2290 , HOH A:2291
BINDING SITE FOR RESIDUE SO4 A1465
08
AC8
SOFTWARE
GLU A:49 , ASN A:50 , GLN A:70 , VAL A:71 , ASN A:72 , PHE A:92 , TYR A:387 , HOH A:2023 , HOH A:2024 , HOH A:2286
BINDING SITE FOR RESIDUE PG4 A1460
09
AC9
SOFTWARE
ASN A:72 , ASN A:386 , ASP A:388 , PHE A:402 , ALA A:423 , HOH A:2252 , HOH A:2287 , HOH A:2288
BINDING SITE FOR RESIDUE PG4 A1461
10
BC1
SOFTWARE
VAL A:153 , ASP A:157 , ASN A:159 , GLN A:162 , ASN A:189 , ASN A:191 , ALA A:192 , GLY A:194 , HOH A:2289
BINDING SITE FOR RESIDUE PGE A1462
11
BC2
SOFTWARE
ASP A:406 , HOH A:2244
BINDING SITE FOR RESIDUE MG A1463
12
BC3
SOFTWARE
ASP A:406 , HOH A:2228
BINDING SITE FOR RESIDUE MG A1464
[
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: HEXAPEP_TRANSFERASES (A:403-431)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HEXAPEP_TRANSFERASES
PS00101
Hexapeptide-repeat containing-transferases signature.
GLMU_HAEIN
403-431
1
A:403-431
[
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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2vd4a2 (A:252-453)
2a: SCOP_d2vd4a1 (A:4-251)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Single-stranded left-handed beta-helix
(154)
Superfamily
:
Trimeric LpxA-like enzymes
(147)
Family
:
automated matches
(55)
Protein domain
:
automated matches
(55)
Haemophilus influenzae [TaxId: 727]
(9)
1a
d2vd4a2
A:252-453
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleotide-diphospho-sugar transferases
(408)
Superfamily
:
Nucleotide-diphospho-sugar transferases
(408)
Family
:
automated matches
(48)
Protein domain
:
automated matches
(48)
Haemophilus influenzae [TaxId: 727]
(9)
2a
d2vd4a1
A:4-251
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2vd4A01 (A:4-227)
2a: CATH_2vd4A02 (A:228-453)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
Homologous Superfamily
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
Haemophilus influenzae. Organism_taxid: 727.
(1)
1a
2vd4A01
A:4-227
Class
:
Mainly Beta
(13760)
Architecture
:
3 Solenoid
(196)
Topology
:
UDP N-Acetylglucosamine Acyltransferase; domain 1
(90)
Homologous Superfamily
:
Hexapeptide repeat proteins
(85)
Haemophilus influenzae. Organism_taxid: 727.
(1)
2a
2vd4A02
A:228-453
[
close CATH info
]
Pfam Domains
(2, 5)
Info
all PFAM domains
1a: PFAM_NTP_transf_3_2vd4A01 (A:8-258)
2a: PFAM_Hexapep_2vd4A02 (A:394-429)
2b: PFAM_Hexapep_2vd4A03 (A:394-429)
2c: PFAM_Hexapep_2vd4A04 (A:394-429)
2d: PFAM_Hexapep_2vd4A05 (A:394-429)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GT-A
(172)
Family
:
NTP_transf_3
(13)
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
(7)
1a
NTP_transf_3-2vd4A01
A:8-258
Clan
:
no clan defined [family: Hexapep]
(52)
Family
:
Hexapep
(52)
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
(10)
2a
Hexapep-2vd4A02
A:394-429
2b
Hexapep-2vd4A03
A:394-429
2c
Hexapep-2vd4A04
A:394-429
2d
Hexapep-2vd4A05
A:394-429
[
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 (84 KB)
Header - Asym.Unit
Biol.Unit 1 (228 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
2VD4
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help