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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2O3H
Asym. Unit
Info
Asym.Unit (56 KB)
Biol.Unit 1 (52 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 THE HUMAN C65A APE
Authors
:
M. M. Georgiadis, R. K. Gaur, S. Delaplane, J. Svenson
Date
:
01 Dec 06 (Deposition) - 11 Dec 07 (Release) - 16 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Ape, Endonuclease, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. M. Georgiadis, M. Luo, R. K. Gaur, S. Delaplane, X. Li, M. R. Kelley
Evolution Of The Redox Function In Mammalian Apurinic/Apyrimidinic Endonuclease
Mutat. Res. V. 643 54 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 6)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
2a: SAMARIUM (III) ION (SMa)
2b: SAMARIUM (III) ION (SMb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
4
Ligand/Ion
ACETATE ION
2
SM
2
Ligand/Ion
SAMARIUM (III) ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:216 , GLU A:217 , GLU A:242 , GLN A:245 , HOH A:506 , HOH A:589 , HOH A:646
BINDING SITE FOR RESIDUE SM A 400
2
AC2
SOFTWARE
ASP A:70 , GLU A:96 , HOH A:559 , HOH A:593 , HOH A:676 , HOH A:703 , HOH A:789
BINDING SITE FOR RESIDUE SM A 401
3
AC3
SOFTWARE
LYS A:78 , LEU A:104 , ALA A:106 , GLN A:109 , HOH A:652 , HOH A:697 , HOH A:784
BINDING SITE FOR RESIDUE ACT A 500
4
AC4
SOFTWARE
ASN A:272 , ARG A:274 , SER A:275
BINDING SITE FOR RESIDUE ACT A 501
5
AC5
SOFTWARE
MET A:37 , ALA A:38 , SER A:120 , TYR A:144 , ASP A:152 , HOH A:523 , HOH A:530
BINDING SITE FOR RESIDUE ACT A 502
6
AC6
SOFTWARE
SER A:56 , TYR A:128 , SER A:129 , TYR A:171
BINDING SITE FOR RESIDUE ACT A 503
[
close Site info
]
SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_013455 (Q51H, chain A, )
2: VAR_014823 (I64V, chain A, )
3: VAR_019790 (D148E, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_013455
Q
51
H
APEX1_HUMAN
Polymorphism
1048945
A
Q
51
H
2
UniProt
VAR_014823
I
64
V
APEX1_HUMAN
Polymorphism
2307486
A
I
64
V
3
UniProt
VAR_019790
D
148
E
APEX1_HUMAN
Polymorphism
1130409
A
D
148
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 4)
Info
All PROSITE Patterns/Profiles
1: AP_NUCLEASE_F1_4 (A:62-318)
2: AP_NUCLEASE_F1_1 (A:89-98)
3: AP_NUCLEASE_F1_2 (A:251-267)
4: AP_NUCLEASE_F1_3 (A:277-288)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AP_NUCLEASE_F1_4
PS51435
AP endonucleases family 1 profile.
APEX1_HUMAN
62-318
1
A:62-318
2
AP_NUCLEASE_F1_1
PS00726
AP endonucleases family 1 signature 1.
APEX1_HUMAN
89-98
1
A:89-98
3
AP_NUCLEASE_F1_2
PS00727
AP endonucleases family 1 signature 2.
APEX1_HUMAN
251-267
1
A:251-267
4
AP_NUCLEASE_F1_3
PS00728
AP endonucleases family 1 signature 3.
APEX1_HUMAN
277-288
1
A:277-288
[
close PROSITE info
]
Exons
(3, 3)
Info
All Exons
Exon 1.3a (A:37-82)
Exon 1.4 (A:83-147 (gaps))
Exon 1.5a (A:147-318)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2/1.3a
2: Boundary 1.3a/1.4
3: Boundary 1.4/1.5a
4: Boundary 1.5a/-
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
1.1c
ENST00000398030
1c
ENSE00001531237
chr14:
20923400-20923497
98
APEX1_HUMAN
-
0
0
-
-
1.2
ENST00000398030
2
ENSE00000889014
chr14:
20923737-20923862
126
APEX1_HUMAN
1-20
20
0
-
-
1.3a
ENST00000398030
3a
ENSE00000652723
chr14:
20924073-20924260
188
APEX1_HUMAN
20-82
63
1
A:37-82
46
1.4
ENST00000398030
4
ENSE00000652726
chr14:
20924827-20925019
193
APEX1_HUMAN
83-147
65
1
A:83-147 (gaps)
65
1.5a
ENST00000398030
5a
ENSE00001842242
chr14:
20925150-20925895
746
APEX1_HUMAN
147-318
172
1
A:147-318
172
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2o3ha_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
DNase I-like
(70)
Superfamily
:
DNase I-like
(70)
Family
:
DNase I-like
(31)
Protein domain
:
automated matches
(7)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d2o3ha_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2o3hA00 (A:37-318)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Deoxyribonuclease I; Chain A
(35)
Homologous Superfamily
:
[code=3.60.10.10, no name defined]
(35)
Human (Homo sapiens)
(8)
1a
2o3hA00
A:37-318
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Exo_endo_phos_2o3hA01 (A:65-309)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Exo_endo_phos]
(21)
Family
:
Exo_endo_phos
(21)
Homo sapiens (Human)
(9)
1a
Exo_endo_phos-2o3hA01
A:65-309
[
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 (56 KB)
Header - Asym.Unit
Biol.Unit 1 (52 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
2O3H
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help