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.
1P6O
Asym. Unit
Info
Asym.Unit (126 KB)
Biol.Unit 1 (122 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE CRYSTAL STRUCTURE OF YEAST CYTOSINE DEAMINASE BOUND TO 4(R)-HYDROXYL-3,4-DIHYDROPYRIMIDINE AT 1.14 ANGSTROMS.
Authors
:
G. C. Ireton, M. E. Black, B. L. Stoddard
Date
:
29 Apr 03 (Deposition) - 19 Aug 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.14
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Cytosine Deaminase, Hydrolase, Dimer, Inhibitor Bound
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. C. Ireton, M. E. Black, B. L. Stoddard
The 1. 14 A Crystal Structure Of Yeast Cytosine Deaminase. Evolution Of Nucleotide Salvage Enzymes And Implications For Genetic Chemotherapy.
Structure V. 11 961 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 9)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
1c: ACETIC ACID (ACYc)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: 4-HYDROXY-3,4-DIHYDRO-1H-PYRIMIDIN... (HPYa)
3b: 4-HYDROXY-3,4-DIHYDRO-1H-PYRIMIDIN... (HPYb)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
3
Ligand/Ion
ACETIC ACID
2
CA
2
Ligand/Ion
CALCIUM ION
3
HPY
2
Ligand/Ion
4-HYDROXY-3,4-DIHYDRO-1H-PYRIMIDIN-2-ONE
4
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS B:262 , CYS B:291 , CYS B:294 , HPY B:410
BINDING SITE FOR RESIDUE ZN B 400
2
AC2
SOFTWARE
HIS A:62 , CYS A:91 , CYS A:94 , HPY A:411
BINDING SITE FOR RESIDUE ZN A 401
3
AC3
SOFTWARE
GLU A:75 , GLU B:328 , GLN B:350 , HOH B:1016 , HOH B:1060 , HOH B:1237
BINDING SITE FOR RESIDUE CA B 402
4
AC4
SOFTWARE
GLN A:150 , HOH A:1231 , HOH A:1311 , GLU B:275 , HOH B:1312 , HOH B:1392
BINDING SITE FOR RESIDUE CA B 403
5
AC5
SOFTWARE
ILE B:233 , ASN B:251 , HIS B:262 , GLY B:263 , GLU B:264 , PRO B:290 , CYS B:291 , CYS B:294 , ASP B:355 , ZN B:400
BINDING SITE FOR RESIDUE HPY B 410
6
AC6
SOFTWARE
ILE A:33 , ASN A:51 , HIS A:62 , GLY A:63 , GLU A:64 , PRO A:90 , CYS A:91 , CYS A:94 , ASP A:155 , ZN A:401
BINDING SITE FOR RESIDUE HPY A 411
7
AC7
SOFTWARE
ASP A:42 , HOH A:1214 , HOH A:1222 , HOH A:1228 , ARG B:273
BINDING SITE FOR RESIDUE ACY A 420
8
AC8
SOFTWARE
GLY B:302 , GLY B:326 , HIS B:327 , PHE B:353 , HOH B:1093 , HOH B:1188
BINDING SITE FOR RESIDUE ACY B 421
9
AC9
SOFTWARE
LYS A:77 , ASN B:240 , ASP B:281 , PRO B:304 , PHE B:353 , HOH B:1105 , HOH B:1162
BINDING SITE FOR RESIDUE ACY B 422
[
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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: CYT_DCMP_DEAMINASES_2 (A:9-129,B:209-329)
2: CYT_DCMP_DEAMINASES_1 (A:62-98,B:262-298)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYT_DCMP_DEAMINASES_2
PS51747
Cytidine and deoxycytidylate deaminases domain profile.
FCY1_YEAST
9-129
2
A:9-129
B:209-329
2
CYT_DCMP_DEAMINASES_1
PS00903
Cytidine and deoxycytidylate deaminases zinc-binding region signature.
FCY1_YEAST
62-98
2
A:62-98
B:262-298
[
close PROSITE info
]
Exons
(1, 2)
Info
All Exons
Exon 1.1 (A:3-158 | B:201-358)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
YPR062W
1
YPR062W.1
XVI:677162-677638
477
FCY1_YEAST
1-158
158
2
A:3-158
B:201-358
156
158
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1p6oa_ (A:)
1b: SCOP_d1p6ob_ (B:)
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
:
Deoxycytidylate deaminase-like
(29)
Protein domain
:
Cytosine deaminase
(7)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(7)
1a
d1p6oa_
A:
1b
d1p6ob_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1p6oA00 (A:3-158)
1b: CATH_1p6oB00 (B:198-358)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Cytidine Deaminase; domain 2
(44)
Homologous Superfamily
:
Cytidine Deaminase, domain 2
(32)
Baker's yeast (Saccharomyces cerevisiae)
(8)
1a
1p6oA00
A:3-158
1b
1p6oB00
B:198-358
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_dCMP_cyt_deam_1_1p6oB01 (B:208-310)
1b: PFAM_dCMP_cyt_deam_1_1p6oB02 (B:208-310)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CDA
(39)
Family
:
dCMP_cyt_deam_1
(28)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(8)
1a
dCMP_cyt_deam_1-1p6oB01
B:208-310
1b
dCMP_cyt_deam_1-1p6oB02
B:208-310
[
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 (126 KB)
Header - Asym.Unit
Biol.Unit 1 (122 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
1P6O
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help