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.
3MBI
Biol. Unit 1
Info
Asym.Unit (217 KB)
Biol.Unit 1 (107 KB)
Biol.Unit 2 (108 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 PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) SYNTHETASE FROM THERMOPLASMA VOLCANIUM IN COMPLEX WITH ADP-MG2+ AND RIBOSE 5-PHOSPHATE
Authors
:
L. T. Cherney, M. M. Cherney, C. R. Garen, M. N. G. James
Date
:
25 Mar 10 (Deposition) - 20 Apr 11 (Release) - 25 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Phosphoribosyl Transferase, Atp Analog Binding, Ribose 5-Phosphate Binding, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. M. Cherney, L. T. Cherney, C. R. Garen, M. N. James
The Structures Of Thermoplasma Volcanium Phosphoribosyl Pyrophosphate Synthetase Bound To Ribose-5-Phosphate And At Analogs.
J. Mol. Biol. V. 413 844 2011
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
2a: 5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE (HSXa)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
4c: PHOSPHATE ION (PO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
2
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
HSX
-1
Ligand/Ion
5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
PO4
2
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC4 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC8 (SOFTWARE)
6: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:91 , ARG A:186 , SER A:214 , THR A:215 , GLY A:216 , GLY A:217 , THR A:218 , HOH A:307 , HOH A:322 , HOH A:331 , HOH A:369
BINDING SITE FOR RESIDUE PO4 A 286
2
AC2
SOFTWARE
HIS A:93 , HIS A:124 , HOH A:294
BINDING SITE FOR RESIDUE MG A 287
3
AC4
SOFTWARE
ARG A:91 , GLN A:92 , TYR A:96 , HIS A:124 , LYS A:184 , ARG A:186 , MG A:287 , HOH A:309 , HOH A:353 , HOH A:380 , PHE C:32 , ASP C:34 , GLU C:36 , HOH C:301 , HOH C:451
BINDING SITE FOR RESIDUE ADP A 288
4
AC6
SOFTWARE
PHE A:32 , ASP A:34 , GLU A:36 , HOH A:349 , ARG C:91 , GLN C:92 , TYR C:96 , HIS C:124 , ASP C:161 , LYS C:184 , ARG C:186 , MG C:289 , HOH C:290 , HOH C:291 , HOH C:321 , HOH C:335 , HOH C:343 , HOH C:417 , HOH C:580 , HOH C:604 , HOH C:853 , HOH C:1253
BINDING SITE FOR RESIDUE ADP C 286
5
AC8
SOFTWARE
ARG C:91 , ARG C:186 , SER C:214 , THR C:215 , GLY C:216 , THR C:218 , HOH C:302 , HOH C:328 , HOH C:371 , HOH C:529 , HOH C:853
BINDING SITE FOR RESIDUE PO4 C 287
6
AC9
SOFTWARE
HIS C:124 , ADP C:286 , HOH C:343 , HOH C:1252 , HOH C:1253
BINDING SITE FOR RESIDUE MG C 289
[
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
(1, 8)
Info
All SCOP Domains
1a: SCOP_d3mbia1 (A:-1-155)
1b: SCOP_d3mbid1 (D:1-155)
1c: SCOP_d3mbid2 (D:156-285)
1d: SCOP_d3mbia2 (A:156-285)
1e: SCOP_d3mbib1 (B:-1-155)
1f: SCOP_d3mbib2 (B:156-285)
1g: SCOP_d3mbic1 (C:1-155)
1h: SCOP_d3mbic2 (C:156-285)
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
:
automated matches
(39)
Protein domain
:
automated matches
(39)
Thermoplasma volcanium [TaxId: 50339]
(3)
1a
d3mbia1
A:-1-155
1b
d3mbid1
D:1-155
1c
d3mbid2
D:156-285
1d
d3mbia2
A:156-285
1e
d3mbib1
B:-1-155
1f
d3mbib2
B:156-285
1g
d3mbic1
C:1-155
1h
d3mbic2
C:156-285
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Pribosyltran_3mbiD01 (D:135-240)
1b: PFAM_Pribosyltran_3mbiD02 (D:135-240)
1c: PFAM_Pribosyltran_3mbiD03 (D:135-240)
1d: PFAM_Pribosyltran_3mbiD04 (D:135-240)
2a: PFAM_Pribosyltran_N_3mbiD05 (D:1-114)
2b: PFAM_Pribosyltran_N_3mbiD06 (D:1-114)
2c: PFAM_Pribosyltran_N_3mbiD07 (D:1-114)
2d: PFAM_Pribosyltran_N_3mbiD08 (D:1-114)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PRTase-like
(59)
Family
:
Pribosyltran
(59)
Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1)
(4)
1a
Pribosyltran-3mbiD01
D:135-240
1b
Pribosyltran-3mbiD02
D:135-240
1c
Pribosyltran-3mbiD03
D:135-240
1d
Pribosyltran-3mbiD04
D:135-240
Clan
:
no clan defined [family: Pribosyltran_N]
(7)
Family
:
Pribosyltran_N
(7)
Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1)
(4)
2a
Pribosyltran_N-3mbiD05
D:1-114
2b
Pribosyltran_N-3mbiD06
D:1-114
2c
Pribosyltran_N-3mbiD07
D:1-114
2d
Pribosyltran_N-3mbiD08
D:1-114
[
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 C
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 (217 KB)
Header - Asym.Unit
Biol.Unit 1 (107 KB)
Header - Biol.Unit 1
Biol.Unit 2 (108 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
3MBI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help