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.
1ZN7
Asym. Unit
Info
Asym.Unit (74 KB)
Biol.Unit 1 (68 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN ADENINE PHOSPHORIBOSYLTRANSFERASE COMPLEXED WITH PRPP, ADE AND R5P
Authors
:
J. Iulek, M. Silva, C. H. T. P. Tomich, O. H. Thiemann
Date
:
11 May 05 (Deposition) - 25 Apr 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.83
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Transferase, Glycosyltransferase, Purine Salvage
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. H. Silva, M. Silva, J. Iulek, O. H. Thiemann
Structural Complexes Of Human Adenine Phosphoribosyltransferase Reveal Novel Features Of The Aprt Catalytic Mechanism
J. Biomol. Struct. Dyn. V. 25 589 2008
[
close entry info
]
Hetero Components
(5, 10)
Info
All Hetero Components
1a: ADENINE (ADEa)
1b: ADENINE (ADEb)
2a: 5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE (HSXa)
2b: 5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE (HSXb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
5a: ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC... (PRPa)
5b: ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC... (PRPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADE
2
Ligand/Ion
ADENINE
2
HSX
2
Ligand/Ion
5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE
3
MG
2
Ligand/Ion
MAGNESIUM ION
4
PO4
2
Ligand/Ion
PHOSPHATE ION
5
PRP
2
Ligand/Ion
ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID
[
close Hetero Component info
]
Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRP A:502 , PO4 A:504 , HSX A:506 , HOH A:662 , HOH A:663
BINDING SITE FOR RESIDUE MG A 500
02
AC2
SOFTWARE
SER A:66 , ARG A:67 , LYS A:88 , MG A:500 , HSX A:506 , HOH A:663 , ARG B:87 , LYS B:91
BINDING SITE FOR RESIDUE PO4 A 504
03
AC3
SOFTWARE
ARG A:87 , LYS A:91 , SER B:66 , ARG B:67 , LYS B:88 , MG B:501 , HSX B:507 , HOH B:663 , HOH B:664
BINDING SITE FOR RESIDUE PO4 A 505
04
AC4
SOFTWARE
SER A:66 , ARG A:67 , LYS A:88 , ASP A:127 , ASP A:128 , LEU A:129 , ALA A:131 , THR A:132 , GLY A:133 , GLY A:134 , THR A:135 , MG A:500 , ADE A:655 , HOH A:658 , HOH A:662 , HOH A:663 , HOH A:687 , HOH A:729 , HOH A:745 , HOH A:819 , HOH A:829 , ARG B:87 , LYS B:91
BINDING SITE FOR RESIDUE PRP A 502
05
AC5
SOFTWARE
ARG A:67 , ASP A:127 , ASP A:128 , LEU A:129 , ALA A:131 , THR A:132 , GLY A:133 , GLY A:134 , THR A:135 , MG A:500 , PO4 A:504 , HOH A:658 , HOH A:659 , HOH A:687 , HOH A:745 , HOH A:819 , HOH A:829
BINDING SITE FOR RESIDUE HSX A 506
06
AC6
SOFTWARE
VAL A:25 , PHE A:26 , ARG A:27 , ARG A:67 , LEU A:129 , ALA A:131 , LEU A:159 , PRP A:502 , HOH A:656 , HOH A:657 , HOH A:658 , HOH A:659 , HOH A:660 , HOH A:661 , HOH A:809
BINDING SITE FOR RESIDUE ADE A 655
07
AC7
SOFTWARE
PO4 A:505 , PRP B:503 , HSX B:507 , HOH B:663 , HOH B:664
BINDING SITE FOR RESIDUE MG B 501
08
AC8
SOFTWARE
ARG A:87 , LYS A:91 , SER B:66 , ARG B:67 , LYS B:88 , ASP B:127 , ASP B:128 , LEU B:129 , ALA B:131 , THR B:132 , GLY B:133 , GLY B:134 , THR B:135 , MG B:501 , ADE B:656 , HOH B:657 , HOH B:663 , HOH B:664 , HOH B:701 , HOH B:717 , HOH B:794 , HOH B:796 , HOH B:836 , HOH B:846
BINDING SITE FOR RESIDUE PRP B 503
09
AC9
SOFTWARE
PO4 A:505 , ARG B:67 , ASP B:127 , ASP B:128 , LEU B:129 , ALA B:131 , THR B:132 , GLY B:133 , GLY B:134 , THR B:135 , MG B:501 , HOH B:657 , HOH B:701 , HOH B:717 , HOH B:796 , HOH B:836
BINDING SITE FOR RESIDUE HSX B 507
10
BC1
SOFTWARE
VAL B:25 , PHE B:26 , ARG B:27 , ARG B:67 , LEU B:129 , ALA B:131 , LEU B:159 , PRP B:503 , HOH B:657 , HOH B:659 , HOH B:660 , HOH B:661 , HOH B:662 , HOH B:819 , HOH B:838
BINDING SITE FOR RESIDUE ADE B 656
[
close Site info
]
SAPs(SNPs)/Variants
(9, 18)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_069049 (L33P, chain A/B, )
2: VAR_006747 (D65V, chain A/B, )
3: VAR_069050 (V84M, chain A/B, )
4: VAR_006748 (L110P, chain A/B, )
5: VAR_019055 (Q121R, chain A/B, )
6: VAR_069051 (G133D, chain A/B, )
7: VAR_006749 (M136T, chain A/B, )
8: VAR_022608 (V150F, chain A/B, )
9: VAR_022609 (C153R, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_069049
L
33
P
APT_HUMAN
Disease (APRTD)
---
A/B
L
33
P
2
UniProt
VAR_006747
D
65
V
APT_HUMAN
Disease (APRTD)
---
A/B
D
65
V
3
UniProt
VAR_069050
V
84
M
APT_HUMAN
Disease (APRTD)
200392753
A/B
V
84
M
4
UniProt
VAR_006748
L
110
P
APT_HUMAN
Disease (APRTD)
---
A/B
L
110
P
5
UniProt
VAR_019055
Q
121
R
APT_HUMAN
Polymorphism
8191494
A/B
Q
121
R
6
UniProt
VAR_069051
G
133
D
APT_HUMAN
Disease (APRTD)
---
A/B
G
133
D
7
UniProt
VAR_006749
M
136
T
APT_HUMAN
Disease (APRTD)
28999113
A/B
M
136
T
8
UniProt
VAR_022608
V
150
F
APT_HUMAN
Disease (APRTD)
---
A/B
V
150
F
9
UniProt
VAR_022609
C
153
R
APT_HUMAN
Disease (APRTD)
---
A/B
C
153
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PUR_PYR_PR_TRANSFER (A:123-135,B:123-135)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PUR_PYR_PR_TRANSFER
PS00103
Purine/pyrimidine phosphoribosyl transferases signature.
APT_HUMAN
123-135
2
A:123-135
B:123-135
[
close PROSITE info
]
Exons
(5, 10)
Info
All Exons
Exon 1.1 (A:3-27 | B:3-27)
Exon 1.2 (A:27-63 | B:27-63)
Exon 1.3 (A:63-107 | B:63-107)
Exon 1.4 (A:108-134 | B:108-134)
Exon 1.5a (A:134-180 | B:134-180)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5a
6: 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
1.1
ENST00000378364
1
ENSE00001436135
chr16:
88878342-88878228
115
APT_HUMAN
1-27
27
2
A:3-27
B:3-27
25
25
1.2
ENST00000378364
2
ENSE00001503918
chr16:
88878064-88877958
107
APT_HUMAN
27-63
37
2
A:27-63
B:27-63
37
37
1.3
ENST00000378364
3
ENSE00001503917
chr16:
88876964-88876831
134
APT_HUMAN
63-107
45
2
A:63-107
B:63-107
45
45
1.4
ENST00000378364
4
ENSE00001436356
chr16:
88876556-88876478
79
APT_HUMAN
108-134
27
2
A:108-134
B:108-134
27
27
1.5a
ENST00000378364
5a
ENSE00001436502
chr16:
88876248-88875877
372
APT_HUMAN
134-180
47
2
A:134-180
B:134-180
47
47
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1zn7a_ (A:)
1b: SCOP_d1zn7b_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PRTase-like
(145)
Superfamily
:
PRTase-like
(145)
Family
:
Phosphoribosyltransferases (PRTases)
(100)
Protein domain
:
Adenine PRTase
(13)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d1zn7a_
A:
1b
d1zn7b_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1zn7A00 (A:3-180)
1b: CATH_1zn7B00 (B:3-180)
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=3.40.50.2020, no name defined]
(117)
Human (Homo sapiens)
(19)
1a
1zn7A00
A:3-180
1b
1zn7B00
B:3-180
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Pribosyltran_1zn7B01 (B:30-157)
1b: PFAM_Pribosyltran_1zn7B02 (B:30-157)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PRTase-like
(59)
Family
:
Pribosyltran
(59)
Homo sapiens (Human)
(7)
1a
Pribosyltran-1zn7B01
B:30-157
1b
Pribosyltran-1zn7B02
B:30-157
[
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 (74 KB)
Header - Asym.Unit
Biol.Unit 1 (68 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
1ZN7
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
