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.
4P9C
Biol. Unit 1
Info
Asym.Unit (279 KB)
Biol.Unit 1 (139 KB)
Biol.Unit 2 (139 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 DCMP DEAMINASE FROM THE CYANOPHAGE S-TIM5 IN COMPLEX WITH DCMP AND DUMP
Authors
:
A. Marx, A. Alian
Date
:
03 Apr 14 (Deposition) - 26 Nov 14 (Release) - 14 Jan 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,E,F,J,K,L (1x)
Biol. Unit 2: B,C,D,G,H,I (1x)
Keywords
:
Dcmp Deaminase, Cytidine Deaminase, Deoxycytidylate Deaminase, S- Tim5, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Marx, A. Alian
The First Crystal Structure Of A Dttp-Bound Deoxycytidylate Deaminase Validates And Details The Allosteric-Inhibitor Binding Site.
J. Biol. Chem. V. 290 682 2015
[
close entry info
]
Hetero Components
(1, 6)
Info
All Hetero Components
1a: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE (DCMa)
1b: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE (DCMb)
1c: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE (DCMc)
1d: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE (DCMd)
1e: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE (DCMe)
1f: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE (DCMf)
1g: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE (DCMg)
1h: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE (DCMh)
1i: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE (DCMi)
1j: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE (DCMj)
1k: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE (DCMk)
1l: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE (DCMl)
2a: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE (DUa)
2b: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE (DUb)
2c: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE (DUc)
2d: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE (DUd)
2e: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE (DUe)
2f: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE (DUf)
2g: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE (DUg)
2h: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE (DUh)
2i: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE (DUi)
2j: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE (DUj)
2k: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE (DUk)
2l: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE (DUl)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
3i: ZINC ION (ZNi)
3j: ZINC ION (ZNj)
3k: ZINC ION (ZNk)
3l: ZINC ION (ZNl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DCM
6
Ligand/Ion
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
2
DU
-1
Ligand/Ion
2'-DEOXYURIDINE-5'-MONOPHOSPHATE
3
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AD4 (SOFTWARE)
05: AD5 (SOFTWARE)
06: AD6 (SOFTWARE)
07: AD7 (SOFTWARE)
08: AD8 (SOFTWARE)
09: AD9 (SOFTWARE)
10: AF1 (SOFTWARE)
11: AF2 (SOFTWARE)
12: AF3 (SOFTWARE)
13: AF4 (SOFTWARE)
14: AF5 (SOFTWARE)
15: AF6 (SOFTWARE)
16: AF7 (SOFTWARE)
17: AF8 (SOFTWARE)
18: AF9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:67 , GLU A:69 , CYS A:95 , CYS A:98 , DU A:203
binding site for residue ZN A 201
02
AC2
SOFTWARE
HIS A:40 , GLY A:41 , TRP A:42 , GLY A:44 , THR A:45 , SER A:47 , ASN A:71 , LYS A:75 , HOH A:325 , GLN L:104
binding site for residue DCM A 202
03
AC3
SOFTWARE
CYS A:22 , ARG A:24 , VAL A:27 , ASN A:43 , THR A:61 , HIS A:67 , ALA A:68 , GLU A:69 , CYS A:95 , TYR A:116 , ARG A:117 , ZN A:201 , HOH A:301 , HOH A:317
binding site for residue DU A 203
04
AD4
SOFTWARE
HIS E:67 , GLU E:69 , CYS E:95 , CYS E:98 , DU E:203
binding site for residue ZN E 201
05
AD5
SOFTWARE
HIS E:40 , GLY E:41 , TRP E:42 , GLY E:44 , THR E:45 , SER E:47 , ASN E:71 , LYS E:75 , GLN K:104
binding site for residue DCM E 202
06
AD6
SOFTWARE
CYS E:22 , ARG E:24 , VAL E:27 , ASN E:43 , THR E:61 , HIS E:67 , ALA E:68 , GLU E:69 , CYS E:95 , TYR E:116 , ARG E:117 , ZN E:201 , HOH E:304 , HOH E:320 , HOH E:329
binding site for residue DU E 203
07
AD7
SOFTWARE
HIS F:67 , GLU F:69 , CYS F:95 , CYS F:98 , DU F:203
binding site for residue ZN F 201
08
AD8
SOFTWARE
HIS F:40 , GLY F:41 , TRP F:42 , GLY F:44 , THR F:45 , SER F:47 , ASN F:71 , HOH F:321 , GLN J:104 , HOH L:305
binding site for residue DCM F 202
09
AD9
SOFTWARE
CYS F:22 , ARG F:24 , VAL F:27 , ASN F:43 , THR F:61 , HIS F:67 , ALA F:68 , GLU F:69 , CYS F:95 , TYR F:116 , ARG F:117 , ZN F:201 , HOH F:301 , HOH F:325
binding site for residue DU F 203
10
AF1
SOFTWARE
HIS J:67 , GLU J:69 , CYS J:95 , CYS J:98 , DU J:203 , HOH J:322
binding site for residue ZN J 201
11
AF2
SOFTWARE
GLN F:104 , HIS J:40 , GLY J:41 , TRP J:42 , GLY J:44 , THR J:45 , SER J:47 , ASN J:71 , HOH J:313 , HOH J:320
binding site for residue DCM J 202
12
AF3
SOFTWARE
CYS J:22 , ARG J:24 , VAL J:27 , ASN J:43 , THR J:61 , HIS J:67 , ALA J:68 , GLU J:69 , CYS J:95 , TYR J:116 , ARG J:117 , ZN J:201 , HOH J:321 , HOH J:322
binding site for residue DU J 203
13
AF4
SOFTWARE
HIS K:67 , GLU K:69 , CYS K:95 , CYS K:98 , DU K:203
binding site for residue ZN K 201
14
AF5
SOFTWARE
GLN E:104 , HIS K:40 , GLY K:41 , TRP K:42 , GLY K:44 , THR K:45 , SER K:47 , ASN K:71
binding site for residue DCM K 202
15
AF6
SOFTWARE
CYS K:22 , ARG K:24 , VAL K:27 , ASN K:43 , THR K:61 , HIS K:67 , ALA K:68 , GLU K:69 , CYS K:95 , TYR K:116 , ZN K:201
binding site for residue DU K 203
16
AF7
SOFTWARE
HIS L:67 , GLU L:69 , CYS L:95 , CYS L:98 , DU L:203 , HOH L:312
binding site for residue ZN L 201
17
AF8
SOFTWARE
GLN A:104 , HOH F:317 , HIS L:40 , GLY L:41 , TRP L:42 , GLY L:44 , THR L:45 , SER L:47 , ASN L:71
binding site for residue DCM L 202
18
AF9
SOFTWARE
CYS L:22 , ARG L:24 , ASN L:43 , THR L:61 , HIS L:67 , ALA L:68 , GLU L:69 , CYS L:95 , TYR L:116 , ARG L:117 , ZN L:201 , HOH L:312 , HOH L:313
binding site for residue DU L 203
[
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
(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
(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 A
Chain E
Chain F
Chain J
Chain K
Chain L
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 (279 KB)
Header - Asym.Unit
Biol.Unit 1 (139 KB)
Header - Biol.Unit 1
Biol.Unit 2 (139 KB)
Header - Biol.Unit 2
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
4P9C
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help