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.
4EG2
Biol. Unit 3
Info
Asym.Unit (830 KB)
Biol.Unit 1 (211 KB)
Biol.Unit 2 (210 KB)
Biol.Unit 3 (207 KB)
Biol.Unit 4 (206 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
2.2 ANGSTROM CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE FROM VIBRIO CHOLERAE IN COMPLEX WITH ZINC AND URIDINE
Authors
:
G. Minasov, Z. Wawrzak, T. Skarina, Y. Wang, S. Grimshaw, L. Papazisi, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date
:
30 Mar 12 (Deposition) - 02 May 12 (Release) - 02 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Keywords
:
Cytidine Deaminase, Ump Synthesis, Zn Binding, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Minasov, Z. Wawrzak, T. Skarina, Y. Wang, S. Grimshaw, L. Papazisi, A. Savchenko, W. F. Anderson
2. 2 Angstrom Crystal Structure Of Cytidine Deaminase From Vibrio Cholerae In Complex With Zinc And Uridine.
To Be Published
[
close entry info
]
Hetero Components
(3, 28)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
1h: ACETATE ION (ACTh)
1i: ACETATE ION (ACTi)
2a: MAGNESIUM ION (MGa)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
3ab: SELENOMETHIONINE (MSEab)
3ac: SELENOMETHIONINE (MSEac)
3ad: SELENOMETHIONINE (MSEad)
3ae: SELENOMETHIONINE (MSEae)
3af: SELENOMETHIONINE (MSEaf)
3ag: SELENOMETHIONINE (MSEag)
3ah: SELENOMETHIONINE (MSEah)
3ai: SELENOMETHIONINE (MSEai)
3aj: SELENOMETHIONINE (MSEaj)
3ak: SELENOMETHIONINE (MSEak)
3al: SELENOMETHIONINE (MSEal)
3am: SELENOMETHIONINE (MSEam)
3an: SELENOMETHIONINE (MSEan)
3ao: SELENOMETHIONINE (MSEao)
3ap: SELENOMETHIONINE (MSEap)
3aq: SELENOMETHIONINE (MSEaq)
3ar: SELENOMETHIONINE (MSEar)
3as: SELENOMETHIONINE (MSEas)
3at: SELENOMETHIONINE (MSEat)
3au: SELENOMETHIONINE (MSEau)
3av: SELENOMETHIONINE (MSEav)
3aw: SELENOMETHIONINE (MSEaw)
3ax: SELENOMETHIONINE (MSEax)
3ay: SELENOMETHIONINE (MSEay)
3az: SELENOMETHIONINE (MSEaz)
3b: SELENOMETHIONINE (MSEb)
3ba: SELENOMETHIONINE (MSEba)
3bb: SELENOMETHIONINE (MSEbb)
3bc: SELENOMETHIONINE (MSEbc)
3bd: SELENOMETHIONINE (MSEbd)
3be: SELENOMETHIONINE (MSEbe)
3bf: SELENOMETHIONINE (MSEbf)
3bg: SELENOMETHIONINE (MSEbg)
3bh: SELENOMETHIONINE (MSEbh)
3bi: SELENOMETHIONINE (MSEbi)
3bj: SELENOMETHIONINE (MSEbj)
3bk: SELENOMETHIONINE (MSEbk)
3bl: SELENOMETHIONINE (MSEbl)
3bm: SELENOMETHIONINE (MSEbm)
3bn: SELENOMETHIONINE (MSEbn)
3bo: SELENOMETHIONINE (MSEbo)
3bp: SELENOMETHIONINE (MSEbp)
3bq: SELENOMETHIONINE (MSEbq)
3br: SELENOMETHIONINE (MSEbr)
3bs: SELENOMETHIONINE (MSEbs)
3bt: SELENOMETHIONINE (MSEbt)
3bu: SELENOMETHIONINE (MSEbu)
3bv: SELENOMETHIONINE (MSEbv)
3bw: SELENOMETHIONINE (MSEbw)
3bx: SELENOMETHIONINE (MSEbx)
3by: SELENOMETHIONINE (MSEby)
3bz: SELENOMETHIONINE (MSEbz)
3c: SELENOMETHIONINE (MSEc)
3ca: SELENOMETHIONINE (MSEca)
3cb: SELENOMETHIONINE (MSEcb)
3cc: SELENOMETHIONINE (MSEcc)
3cd: SELENOMETHIONINE (MSEcd)
3ce: SELENOMETHIONINE (MSEce)
3cf: SELENOMETHIONINE (MSEcf)
3cg: SELENOMETHIONINE (MSEcg)
3ch: SELENOMETHIONINE (MSEch)
3ci: SELENOMETHIONINE (MSEci)
3cj: SELENOMETHIONINE (MSEcj)
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)
4a: URIDINE (URIa)
4b: URIDINE (URIb)
4c: URIDINE (URIc)
4d: URIDINE (URId)
4e: URIDINE (URIe)
4f: URIDINE (URIf)
4g: URIDINE (URIg)
4h: URIDINE (URIh)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
5e: ZINC ION (ZNe)
5f: ZINC ION (ZNf)
5g: ZINC ION (ZNg)
5h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
4
Ligand/Ion
ACETATE ION
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
MSE
22
Mod. Amino Acid
SELENOMETHIONINE
4
URI
2
Ligand/Ion
URIDINE
5
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC4 (SOFTWARE)
2: BC5 (SOFTWARE)
3: BC6 (SOFTWARE)
4: BC7 (SOFTWARE)
5: BC8 (SOFTWARE)
6: BC9 (SOFTWARE)
7: CC1 (SOFTWARE)
8: CC2 (SOFTWARE)
9: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
HOH B:499 , HOH B:604 , HOH B:605 , HOH E:551 , HOH E:552 , HOH F:559
BINDING SITE FOR RESIDUE MG B 301
2
BC5
SOFTWARE
HIS E:102 , CYS E:129 , CYS E:132 , URI E:302
BINDING SITE FOR RESIDUE ZN E 301
3
BC6
SOFTWARE
PHE E:71 , VAL E:73 , ASN E:89 , GLU E:91 , THR E:100 , HIS E:102 , ALA E:103 , GLU E:104 , PRO E:128 , CYS E:129 , ZN E:301 , ALA F:232 , ALA F:233 , PHE F:234
BINDING SITE FOR RESIDUE URI E 302
4
BC7
SOFTWARE
GLU E:253 , PHE E:255
BINDING SITE FOR RESIDUE ACT E 303
5
BC8
SOFTWARE
ARG E:4 , ALA E:66 , GLU E:70 , TYR E:72
BINDING SITE FOR RESIDUE ACT E 304
6
BC9
SOFTWARE
ASP E:51 , LYS E:151 , ARG E:152
BINDING SITE FOR RESIDUE ACT E 305
7
CC1
SOFTWARE
HIS F:102 , CYS F:129 , CYS F:132 , URI F:302
BINDING SITE FOR RESIDUE ZN F 301
8
CC2
SOFTWARE
ALA E:232 , ALA E:233 , PHE F:71 , VAL F:73 , ASN F:89 , GLU F:91 , THR F:100 , VAL F:101 , HIS F:102 , ALA F:103 , GLU F:104 , PRO F:128 , CYS F:129 , ZN F:301
BINDING SITE FOR RESIDUE URI F 302
9
CC3
SOFTWARE
TYR F:65 , GLU F:253 , PHE F:255
BINDING SITE FOR RESIDUE ACT F 303
[
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
(1, 16)
Info
All SCOP Domains
1a: SCOP_d4eg2a1 (A:-1-150)
1b: SCOP_d4eg2a2 (A:151-295)
1c: SCOP_d4eg2f1 (F:0-150)
1d: SCOP_d4eg2f2 (F:151-295)
1e: SCOP_d4eg2g1 (G:-1-150)
1f: SCOP_d4eg2g2 (G:151-295)
1g: SCOP_d4eg2h1 (H:-1-150)
1h: SCOP_d4eg2h2 (H:151-295)
1i: SCOP_d4eg2b1 (B:-1-150)
1j: SCOP_d4eg2b2 (B:151-295)
1k: SCOP_d4eg2c1 (C:0-150)
1l: SCOP_d4eg2c2 (C:151-295)
1m: SCOP_d4eg2d1 (D:-1-150)
1n: SCOP_d4eg2d2 (D:151-295)
1o: SCOP_d4eg2e1 (E:-1-150)
1p: SCOP_d4eg2e2 (E:151-295)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Cytidine deaminase-like
(78)
Superfamily
:
Cytidine deaminase-like
(76)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Vibrio cholerae [TaxId: 666]
(1)
1a
d4eg2a1
A:-1-150
1b
d4eg2a2
A:151-295
1c
d4eg2f1
F:0-150
1d
d4eg2f2
F:151-295
1e
d4eg2g1
G:-1-150
1f
d4eg2g2
G:151-295
1g
d4eg2h1
H:-1-150
1h
d4eg2h2
H:151-295
1i
d4eg2b1
B:-1-150
1j
d4eg2b2
B:151-295
1k
d4eg2c1
C:0-150
1l
d4eg2c2
C:151-295
1m
d4eg2d1
D:-1-150
1n
d4eg2d2
D:151-295
1o
d4eg2e1
E:-1-150
1p
d4eg2e2
E:151-295
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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 E
Chain F
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 (830 KB)
Header - Asym.Unit
Biol.Unit 1 (211 KB)
Header - Biol.Unit 1
Biol.Unit 2 (210 KB)
Header - Biol.Unit 2
Biol.Unit 3 (207 KB)
Header - Biol.Unit 3
Biol.Unit 4 (206 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
4EG2
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help