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.
1Z4Q
Asym. Unit
Info
Asym.Unit (42 KB)
Biol.Unit 1 (72 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE D41N VARIANT OF THE HUMAN MITOCHONDRIAL DEOXYRIBONUCLEOTIDASE IN COMPLEX WITH 2',3'-DIDEOXY-2',3-DIDEHYDROTHYMIDINE 5'-MONOPHOSPHATE (D4T-MP)
Authors
:
K. Wallden, B. Ruzzenente, A. Rinaldo-Matthis, V. Bianchi, P. Nordlund
Date
:
16 Mar 05 (Deposition) - 26 Jul 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Alfa Beta Fold, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Wallden, B. Ruzzenente, A. Rinaldo-Matthis, V. Bianchi, P. Nordlund
Structural Basis For Substrate Specificity Of The Human Mitochondrial Deoxyribonucleotidase
Structure V. 13 1081 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: [(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DI... (D4Ma)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
D4M
1
Ligand/Ion
[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL DIHYDROGENPHOSPHATE
2
MG
2
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:119 , LEU A:121 , THR A:124 , HOH A:2330 , HOH A:2349 , HOH A:2376
BINDING SITE FOR RESIDUE MG A 2229
2
AC2
SOFTWARE
ASN A:41 , ASP A:43 , ASP A:176 , D4M A:1489 , HOH A:2264 , HOH A:2309
BINDING SITE FOR RESIDUE MG A 2001
3
AC3
SOFTWARE
ASN A:41 , ASP A:43 , PHE A:49 , PHE A:75 , TRP A:76 , VAL A:77 , SER A:78 , TRP A:96 , SER A:131 , ILE A:133 , LYS A:165 , MG A:2001 , HOH A:2264 , HOH A:2309 , HOH A:2372 , HOH A:2378 , HOH A:2379 , HOH A:2383 , HOH A:2387
BINDING SITE FOR RESIDUE D4M A 1489
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(5, 5)
Info
All Exons
Exon 1.1b (A:34-89)
Exon 1.3 (A:90-123)
Exon 1.4 (A:123-143)
Exon 1.5a (A:144-182)
Exon 1.7c (A:182-227)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1b
2: Boundary 1.1b/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5a
5: Boundary 1.5a/1.7c
6: Boundary 1.7c/-
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
1.1b
ENST00000389022
1b
ENSE00001547211
chr17:
17206680-17207131
452
NT5M_HUMAN
1-89
89
1
A:34-89
56
1.3
ENST00000389022
3
ENSE00001481533
chr17:
17209857-17209957
101
NT5M_HUMAN
90-123
34
1
A:90-123
34
1.4
ENST00000389022
4
ENSE00001481531
chr17:
17226499-17226559
61
NT5M_HUMAN
123-143
21
1
A:123-143
21
1.5a
ENST00000389022
5a
ENSE00001504694
chr17:
17248108-17248222
115
NT5M_HUMAN
144-182
39
1
A:144-182
39
1.7c
ENST00000389022
7c
ENSE00001504693
chr17:
17250119-17250975
857
NT5M_HUMAN
182-228
47
1
A:182-227
46
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1z4qa_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
HAD-like
(349)
Superfamily
:
HAD-like
(349)
Family
:
5'(3')-deoxyribonucleotidase (dNT-2)
(18)
Protein domain
:
automated matches
(14)
Human (Homo sapiens) [TaxId: 9606]
(12)
1a
d1z4qa_
A:
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1z4qA01 (A:34-48,A:104-227)
2a: CATH_1z4qA02 (A:49-103)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1000, no name defined]
(211)
Human (Homo sapiens)
(42)
1a
1z4qA01
A:34-48,A:104-227
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Ribonucleotide Reductase Protein R1; domain 1
(62)
Homologous Superfamily
:
Deoxyribonucleotidase; domain 2
(16)
Human (Homo sapiens)
(13)
2a
1z4qA02
A:49-103
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_NT5C_1z4qA01 (A:34-227)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HAD
(186)
Family
:
NT5C
(10)
Homo sapiens (Human)
(10)
1a
NT5C-1z4qA01
A:34-227
[
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 (42 KB)
Header - Asym.Unit
Biol.Unit 1 (72 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
1Z4Q
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
