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.
1T3N
Biol. Unit 1
Info
Asym.Unit (279 KB)
Biol.Unit 1 (137 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
Models
(2 )
Title
:
STRUCTURE OF THE CATALYTIC CORE OF DNA POLYMERASE IOTA IN COMPLEX WITH DNA AND DTTP
Authors
:
D. T. Nair, R. E. Johnson, S. Prakash, L. Prakash, A. K. Aggarwal
Date
:
27 Apr 04 (Deposition) - 20 Jul 04 (Release) - 09 Sep 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,P,T (2 x)
Biol. Unit 1: A,B,P,T (1x)
Keywords
:
Protein, Dna, Dttp, Replication-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. T. Nair, R. E. Johnson, S. Prakash, L. Prakash, A. K. Aggarwal
Replication By Human Dna Polymerase-Iota Occurs By Hoogstee Base-Pairing.
Nature V. 430 377 2004
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSP... (DOCa)
2a: MAGNESIUM ION (MGa)
3a: THYMIDINE-5'-TRIPHOSPHATE (TTPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DOC
1
Mod. Nucleotide
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
TTP
1
Ligand/Ion
THYMIDINE-5'-TRIPHOSPHATE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP B:454 , LEU B:455 , ASP B:546
BINDING SITE FOR RESIDUE MG B 869
2
AC2
SOFTWARE
ASP B:454 , LEU B:455 , ASP B:456 , CYS B:457 , PHE B:458 , TYR B:459 , VAL B:484 , THR B:485 , TYR B:488 , ARG B:491 , LEU B:498 , ASP B:546 , LYS B:634 , DOC P:13 , DA T:5 , DG T:6
BINDING SITE FOR RESIDUE TTP B 868
[
close Site info
]
SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_021239 (R491G, chain A/A/B, )
2: VAR_021240 (I656M, chain A/A/B, )
3: VAR_021241 (E671K, chain A/A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_021239
R
96
G
POLI_HUMAN
Polymorphism
3218778
A
A/B
R
71
491
G
2
UniProt
VAR_021240
I
261
M
POLI_HUMAN
Polymorphism
3218784
A
A/B
I
236
656
M
3
UniProt
VAR_021241
E
276
K
POLI_HUMAN
Polymorphism
3218783
A
A/B
E
251
671
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: UMUC (A:30-243,B:450-663)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UMUC
PS50173
UmuC domain profile.
POLI_HUMAN
55-268
2
A:30-243
B:450-663
[
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1t3na1 (A:300-414)
1b: SCOP_d1t3nb1 (B:720-834)
2a: SCOP_d1t3na2 (A:27-299)
2b: SCOP_d1t3nb2 (B:447-719)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Lesion bypass DNA polymerase (Y-family), little finger domain
(103)
Superfamily
:
Lesion bypass DNA polymerase (Y-family), little finger domain
(103)
Family
:
Lesion bypass DNA polymerase (Y-family), little finger domain
(62)
Protein domain
:
DNA polymerase iota
(19)
Human (Homo sapiens) [TaxId: 9606]
(19)
1a
d1t3na1
A:300-414
1b
d1t3nb1
B:720-834
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
Lesion bypass DNA polymerase (Y-family), catalytic domain
(104)
Protein domain
:
DNA polymerase iota
(19)
Human (Homo sapiens) [TaxId: 9606]
(19)
2a
d1t3na2
A:27-299
2b
d1t3nb2
B:447-719
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1t3nA01 (A:27-36,A:99-221)
1b: CATH_1t3nB01 (B:447-456,B:519-641)
2a: CATH_1t3nA04 (A:299-414)
2b: CATH_1t3nB04 (B:719-834)
3a: CATH_1t3nA03 (A:222-298)
3b: CATH_1t3nB03 (B:642-718)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.270, no name defined]
(278)
[unclassified]
(58)
1a
1t3nA01
A:27-36,A:99-221
1b
1t3nB01
B:447-456,B:519-641
Topology
:
Dna Ligase; domain 1
(375)
Homologous Superfamily
:
[code=3.30.1490.100, no name defined]
(80)
[unclassified]
(29)
2a
1t3nA04
A:299-414
2b
1t3nB04
B:719-834
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
[unclassified]
(230)
3a
1t3nA03
A:222-298
3b
1t3nB03
B:642-718
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_IMS_1t3nB01 (B:453-631)
1b: PFAM_IMS_1t3nB02 (B:453-631)
2a: PFAM_IMS_C_1t3nB03 (B:687-822)
2b: PFAM_IMS_C_1t3nB04 (B:687-822)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: IMS]
(76)
Family
:
IMS
(76)
Homo sapiens (Human)
(14)
1a
IMS-1t3nB01
B:453-631
1b
IMS-1t3nB02
B:453-631
Clan
:
no clan defined [family: IMS_C]
(74)
Family
:
IMS_C
(74)
Homo sapiens (Human)
(14)
2a
IMS_C-1t3nB03
B:687-822
2b
IMS_C-1t3nB04
B:687-822
[
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 P
Chain T
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 (137 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
1T3N
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
