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.
2WHS
Asym. Unit
Info
Asym.Unit (167 KB)
Biol.Unit 1 (41 KB)
Biol.Unit 2 (44 KB)
Biol.Unit 3 (42 KB)
Biol.Unit 4 (44 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
FLUORESCENT PROTEIN MKEIMA AT PH 3.8
Authors
:
S. Violot, P. Carpentier, L. Blanchoin, D. Bourgeois
Date
:
06 May 09 (Deposition) - 11 Aug 09 (Release) - 04 Jul 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Fluorescent Protein, Stokes Shift, Mkeima
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Violot, P. Carpentier, L. Blanchoin, D. Bourgeois
Reverse Ph-Dependence Of Chromophore Protonation Explains The Large Stokes Shift Of The Red Fluorescent Protein Mkeima.
J. Am. Chem. Soc. V. 131 10356 2009
[
close entry info
]
Hetero Components
(2, 15)
Info
All Hetero Components
1a: [2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-... (CRQa)
1b: [2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-... (CRQb)
1c: [2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-... (CRQc)
1d: [2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-... (CRQd)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CRQ
4
Mod. Amino Acid
[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETIC ACID
2
SO4
11
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG D:216 , HIS D:217 , HOH D:2209 , HOH D:2210 , HOH D:2211
BINDING SITE FOR RESIDUE SO4 D1222
02
AC2
SOFTWARE
ARG B:216 , HIS B:217 , HOH B:2221
BINDING SITE FOR RESIDUE SO4 B1222
03
AC3
SOFTWARE
THR D:102 , VAL D:103 , SER D:104 , LYS D:119 , ILE D:120 , SER D:121
BINDING SITE FOR RESIDUE SO4 D1223
04
AC4
SOFTWARE
ASN C:94 , PHE C:95 , GLU D:96 , HIS D:168 , LEU D:170 , HOH D:2213 , HOH D:2214
BINDING SITE FOR RESIDUE SO4 D1224
05
AC5
SOFTWARE
ASN A:94 , PHE A:95 , GLU A:96 , GLU A:172 , GLU B:96 , HIS B:168 , LEU B:170
BINDING SITE FOR RESIDUE SO4 A1220
06
AC6
SOFTWARE
GLU B:90 , ARG B:91 , SER B:92 , LYS B:174 , THR B:176
BINDING SITE FOR RESIDUE SO4 B1223
07
AC7
SOFTWARE
THR B:102 , SER B:104 , LYS B:119 , ILE B:120 , SER B:121
BINDING SITE FOR RESIDUE SO4 B1224
08
AC8
SOFTWARE
THR A:102 , VAL A:103 , SER A:104 , LYS A:119 , ILE A:120 , SER A:121
BINDING SITE FOR RESIDUE SO4 A1221
09
AC9
SOFTWARE
THR C:102 , VAL C:103 , SER C:104 , LYS C:119 , SER C:121
BINDING SITE FOR RESIDUE SO4 C1220
10
BC1
SOFTWARE
GLU A:96 , HIS A:168 , LEU A:170 , ASN B:94 , PHE B:95 , GLU B:96 , HOH B:2120
BINDING SITE FOR RESIDUE SO4 A1222
11
BC2
SOFTWARE
VAL C:18 , ASN C:19 , HIS C:21 , PRO C:51
BINDING SITE FOR RESIDUE SO4 C1221
[
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
(0, 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.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2whsa_ (A:)
1b: SCOP_d2whsb_ (B:)
1c: SCOP_d2whsc_ (C:)
1d: SCOP_d2whsd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
GFP-like
(339)
Superfamily
:
GFP-like
(339)
Family
:
Fluorescent proteins
(271)
Protein domain
:
automated matches
(102)
Montipora sp. [TaxId: 321802]
(4)
1a
d2whsa_
A:
1b
d2whsb_
B:
1c
d2whsc_
C:
1d
d2whsd_
D:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_GFP_2whsD01 (D:1-218)
1b: PFAM_GFP_2whsD02 (D:1-218)
1c: PFAM_GFP_2whsD03 (D:1-218)
1d: PFAM_GFP_2whsD04 (D:1-218)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GFP
(101)
Family
:
GFP
(101)
Montipora sp. 20
(3)
1a
GFP-2whsD01
D:1-218
1b
GFP-2whsD02
D:1-218
1c
GFP-2whsD03
D:1-218
1d
GFP-2whsD04
D:1-218
[
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
Chain C
Chain D
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 (167 KB)
Header - Asym.Unit
Biol.Unit 1 (41 KB)
Header - Biol.Unit 1
Biol.Unit 2 (44 KB)
Header - Biol.Unit 2
Biol.Unit 3 (42 KB)
Header - Biol.Unit 3
Biol.Unit 4 (44 KB)
Header - Biol.Unit 4
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
2WHS
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
