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.
1RXU
Biol. Unit 1
Info
Asym.Unit (725 KB)
Biol.Unit 1 (243 KB)
Biol.Unit 2 (245 KB)
Biol.Unit 3 (245 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
E. COLI URIDINE PHOSPHORYLASE: THYMIDINE PHOSPHATE COMPLEX
Authors
:
T. T. Caradoc-Davies, S. M. Cutfield, I. L. Lamont, J. F. Cutfield
Date
:
18 Dec 03 (Deposition) - 13 Apr 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Biol. Unit 3: M,N,O,P,Q,R (1x)
Keywords
:
Pentosyltransferase, Uridine Phosphorylase, Thymidine, Induced Fit, Specificity, Potassium, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. T. Caradoc-Davies, S. M. Cutfield, I. L. Lamont, J. F. Cutfield
Crystal Structures Of Escherichia Coli Uridine Phosphorylas In Two Native And Three Complexed Forms Reveal Basis Of Substrate Specificity, Induced Conformational Changes And Influence Of Potassium
J. Mol. Biol. V. 337 337 2004
[
close entry info
]
Hetero Components
(2, 12)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
1e: POTASSIUM ION (Ke)
1f: POTASSIUM ION (Kf)
1g: POTASSIUM ION (Kg)
1h: POTASSIUM ION (Kh)
1i: POTASSIUM ION (Ki)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
2d: PHOSPHATE ION (PO4d)
2e: PHOSPHATE ION (PO4e)
2f: PHOSPHATE ION (PO4f)
2g: PHOSPHATE ION (PO4g)
2h: PHOSPHATE ION (PO4h)
2i: PHOSPHATE ION (PO4i)
2j: PHOSPHATE ION (PO4j)
2k: PHOSPHATE ION (PO4k)
2l: PHOSPHATE ION (PO4l)
2m: PHOSPHATE ION (PO4m)
2n: PHOSPHATE ION (PO4n)
2o: PHOSPHATE ION (PO4o)
2p: PHOSPHATE ION (PO4p)
2q: PHOSPHATE ION (PO4q)
2r: PHOSPHATE ION (PO4r)
3a: THYMIDINE (THMa)
3b: THYMIDINE (THMb)
3c: THYMIDINE (THMc)
3d: THYMIDINE (THMd)
3e: THYMIDINE (THMe)
3f: THYMIDINE (THMf)
3g: THYMIDINE (THMg)
3h: THYMIDINE (THMh)
3i: THYMIDINE (THMi)
3j: THYMIDINE (THMj)
3k: THYMIDINE (THMk)
3l: THYMIDINE (THMl)
3m: THYMIDINE (THMm)
3n: THYMIDINE (THMn)
3o: THYMIDINE (THMo)
3p: THYMIDINE (THMp)
3q: THYMIDINE (THMq)
3r: THYMIDINE (THMr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
-1
Ligand/Ion
POTASSIUM ION
2
PO4
6
Ligand/Ion
PHOSPHATE ION
3
THM
6
Ligand/Ion
THYMIDINE
[
close Hetero Component info
]
Sites
(15, 15)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: CC1 (SOFTWARE)
08: CC2 (SOFTWARE)
09: CC3 (SOFTWARE)
10: DC1 (SOFTWARE)
11: DC2 (SOFTWARE)
12: DC3 (SOFTWARE)
13: DC4 (SOFTWARE)
14: DC5 (SOFTWARE)
15: DC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:26 , ASP A:27 , ARG A:30 , ARG A:91 , ILE A:92 , GLY A:93 , THR A:94 , THM A:2012 , ARG B:48
BINDING SITE FOR RESIDUE PO4 A 2011
02
AC2
SOFTWARE
ARG A:48 , GLY B:26 , ARG B:30 , ARG B:91 , ILE B:92 , GLY B:93 , THR B:94 , THM B:2022
BINDING SITE FOR RESIDUE PO4 B 2021
03
AC3
SOFTWARE
GLY C:26 , ARG C:30 , ARG C:91 , ILE C:92 , GLY C:93 , THR C:94 , THM C:2032 , ARG D:48
BINDING SITE FOR RESIDUE PO4 C 2031
04
AC4
SOFTWARE
ARG C:48 , GLY D:26 , ARG D:30 , ARG D:91 , ILE D:92 , GLY D:93 , THR D:94 , THM D:2042
BINDING SITE FOR RESIDUE PO4 D 2041
05
AC5
SOFTWARE
GLY E:26 , ARG E:30 , ARG E:91 , ILE E:92 , GLY E:93 , THR E:94 , THM E:2052 , ARG F:48
BINDING SITE FOR RESIDUE PO4 E 2051
06
AC6
SOFTWARE
ARG E:48 , GLY F:26 , ARG F:30 , ARG F:91 , ILE F:92 , GLY F:93 , THR F:94 , THM F:2062
BINDING SITE FOR RESIDUE PO4 F 2061
07
CC1
SOFTWARE
GLU A:49 , ILE A:69 , SER A:73 , GLU B:49 , ILE B:69 , SER B:73
BINDING SITE FOR RESIDUE K A 3001
08
CC2
SOFTWARE
GLU C:49 , ILE C:69 , SER C:73 , GLU D:49 , ILE D:69 , SER D:73
BINDING SITE FOR RESIDUE K C 3002
09
CC3
SOFTWARE
GLU E:49 , ILE E:69 , SER E:73 , GLU F:49 , ILE F:69 , SER F:73
BINDING SITE FOR RESIDUE K F 3003
10
DC1
SOFTWARE
ILE A:69 , THR A:94 , PHE A:162 , GLN A:166 , ARG A:168 , GLU A:196 , MET A:197 , GLU A:198 , ILE A:220 , PO4 A:2011 , HOH A:3009 , HIS B:8 , ARG B:48
BINDING SITE FOR RESIDUE THM A 2012
11
DC2
SOFTWARE
HIS A:8 , ILE B:69 , THR B:94 , GLY B:96 , PHE B:162 , GLN B:166 , ARG B:168 , GLU B:196 , MET B:197 , GLU B:198 , ILE B:220 , PO4 B:2021 , HOH B:2035
BINDING SITE FOR RESIDUE THM B 2022
12
DC3
SOFTWARE
ILE C:69 , THR C:94 , GLY C:96 , PHE C:162 , GLN C:166 , ARG C:168 , GLU C:196 , MET C:197 , GLU C:198 , ILE C:220 , PRO C:229 , PO4 C:2031 , HOH C:3017 , HIS D:8
BINDING SITE FOR RESIDUE THM C 2032
13
DC4
SOFTWARE
HIS C:8 , THR D:94 , THR D:95 , GLY D:96 , GLN D:166 , ARG D:168 , TYR D:195 , GLU D:196 , MET D:197 , GLU D:198 , ILE D:220 , VAL D:221 , PO4 D:2041 , HOH D:2052
BINDING SITE FOR RESIDUE THM D 2042
14
DC5
SOFTWARE
ILE E:69 , THR E:94 , GLY E:96 , GLN E:166 , ARG E:168 , GLU E:196 , MET E:197 , GLU E:198 , ILE E:220 , VAL E:221 , PRO E:229 , PO4 E:2051 , HOH E:2066 , HIS F:8
BINDING SITE FOR RESIDUE THM E 2052
15
DC6
SOFTWARE
HIS E:8 , ARG F:91 , THR F:94 , GLY F:96 , PHE F:162 , GLN F:166 , ARG F:168 , TYR F:195 , GLU F:196 , MET F:197 , GLU F:198 , ILE F:220 , VAL F:221 , PO4 F:2061 , HOH F:3022
BINDING SITE FOR RESIDUE THM F 2062
[
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
(1, 6)
Info
All PROSITE Patterns/Profiles
1: PNP_UDP_1 (A:66-81,B:66-81,C:66-81,D:66-81,E:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PNP_UDP_1
PS01232
Purine and other phosphorylases family 1 signature.
UDP_ECOLI
66-81
6
A:66-81
B:66-81
C:66-81
D:66-81
E:66-81
F:66-81
-
-
-
-
-
-
-
-
-
-
-
-
[
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, 18)
Info
All SCOP Domains
1a: SCOP_d1rxua_ (A:)
1b: SCOP_d1rxub_ (B:)
1c: SCOP_d1rxuc_ (C:)
1d: SCOP_d1rxud_ (D:)
1e: SCOP_d1rxue_ (E:)
1f: SCOP_d1rxuf_ (F:)
1g: SCOP_d1rxug_ (G:)
1h: SCOP_d1rxuh_ (H:)
1i: SCOP_d1rxui_ (I:)
1j: SCOP_d1rxuj_ (J:)
1k: SCOP_d1rxuk_ (K:)
1l: SCOP_d1rxul_ (L:)
1m: SCOP_d1rxum_ (M:)
1n: SCOP_d1rxun_ (N:)
1o: SCOP_d1rxuo_ (O:)
1p: SCOP_d1rxup_ (P:)
1q: SCOP_d1rxuq_ (Q:)
1r: SCOP_d1rxur_ (R:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Phosphorylase/hydrolase-like
(558)
Superfamily
:
Purine and uridine phosphorylases
(283)
Family
:
Purine and uridine phosphorylases
(224)
Protein domain
:
Uridine phosphorylase
(42)
Escherichia coli [TaxId: 562]
(15)
1a
d1rxua_
A:
1b
d1rxub_
B:
1c
d1rxuc_
C:
1d
d1rxud_
D:
1e
d1rxue_
E:
1f
d1rxuf_
F:
1g
d1rxug_
G:
1h
d1rxuh_
H:
1i
d1rxui_
I:
1j
d1rxuj_
J:
1k
d1rxuk_
K:
1l
d1rxul_
L:
1m
d1rxum_
M:
1n
d1rxun_
N:
1o
d1rxuo_
O:
1p
d1rxup_
P:
1q
d1rxuq_
Q:
1r
d1rxur_
R:
[
close SCOP info
]
CATH Domains
(1, 18)
Info
all CATH domains
1a: CATH_1rxuA00 (A:4-253)
1b: CATH_1rxuB00 (B:4-253)
1c: CATH_1rxuC00 (C:4-253)
1d: CATH_1rxuD00 (D:4-253)
1e: CATH_1rxuE00 (E:4-253)
1f: CATH_1rxuF00 (F:4-253)
1g: CATH_1rxuG00 (G:4-253)
1h: CATH_1rxuH00 (H:4-253)
1i: CATH_1rxuI00 (I:4-253)
1j: CATH_1rxuJ00 (J:4-253)
1k: CATH_1rxuK00 (K:4-253)
1l: CATH_1rxuL00 (L:4-253)
1m: CATH_1rxuM00 (M:4-253)
1n: CATH_1rxuN00 (N:4-253)
1o: CATH_1rxuO00 (O:4-253)
1p: CATH_1rxuP00 (P:4-253)
1q: CATH_1rxuQ00 (Q:4-253)
1r: CATH_1rxuR00 (R:4-253)
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=3.40.50.1580, no name defined]
(194)
Escherichia coli. Organism_taxid: 562.
(30)
1a
1rxuA00
A:4-253
1b
1rxuB00
B:4-253
1c
1rxuC00
C:4-253
1d
1rxuD00
D:4-253
1e
1rxuE00
E:4-253
1f
1rxuF00
F:4-253
1g
1rxuG00
G:4-253
1h
1rxuH00
H:4-253
1i
1rxuI00
I:4-253
1j
1rxuJ00
J:4-253
1k
1rxuK00
K:4-253
1l
1rxuL00
L:4-253
1m
1rxuM00
M:4-253
1n
1rxuN00
N:4-253
1o
1rxuO00
O:4-253
1p
1rxuP00
P:4-253
1q
1rxuQ00
Q:4-253
1r
1rxuR00
R:4-253
[
close CATH info
]
Pfam Domains
(1, 18)
Info
all PFAM domains
1a: PFAM_PNP_UDP_1_1rxuR01 (R:20-253)
1b: PFAM_PNP_UDP_1_1rxuR02 (R:20-253)
1c: PFAM_PNP_UDP_1_1rxuR03 (R:20-253)
1d: PFAM_PNP_UDP_1_1rxuR04 (R:20-253)
1e: PFAM_PNP_UDP_1_1rxuR05 (R:20-253)
1f: PFAM_PNP_UDP_1_1rxuR06 (R:20-253)
1g: PFAM_PNP_UDP_1_1rxuR07 (R:20-253)
1h: PFAM_PNP_UDP_1_1rxuR08 (R:20-253)
1i: PFAM_PNP_UDP_1_1rxuR09 (R:20-253)
1j: PFAM_PNP_UDP_1_1rxuR10 (R:20-253)
1k: PFAM_PNP_UDP_1_1rxuR11 (R:20-253)
1l: PFAM_PNP_UDP_1_1rxuR12 (R:20-253)
1m: PFAM_PNP_UDP_1_1rxuR13 (R:20-253)
1n: PFAM_PNP_UDP_1_1rxuR14 (R:20-253)
1o: PFAM_PNP_UDP_1_1rxuR15 (R:20-253)
1p: PFAM_PNP_UDP_1_1rxuR16 (R:20-253)
1q: PFAM_PNP_UDP_1_1rxuR17 (R:20-253)
1r: PFAM_PNP_UDP_1_1rxuR18 (R:20-253)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PUP
(121)
Family
:
PNP_UDP_1
(121)
Escherichia coli (strain K12)
(27)
1a
PNP_UDP_1-1rxuR01
R:20-253
1b
PNP_UDP_1-1rxuR02
R:20-253
1c
PNP_UDP_1-1rxuR03
R:20-253
1d
PNP_UDP_1-1rxuR04
R:20-253
1e
PNP_UDP_1-1rxuR05
R:20-253
1f
PNP_UDP_1-1rxuR06
R:20-253
1g
PNP_UDP_1-1rxuR07
R:20-253
1h
PNP_UDP_1-1rxuR08
R:20-253
1i
PNP_UDP_1-1rxuR09
R:20-253
1j
PNP_UDP_1-1rxuR10
R:20-253
1k
PNP_UDP_1-1rxuR11
R:20-253
1l
PNP_UDP_1-1rxuR12
R:20-253
1m
PNP_UDP_1-1rxuR13
R:20-253
1n
PNP_UDP_1-1rxuR14
R:20-253
1o
PNP_UDP_1-1rxuR15
R:20-253
1p
PNP_UDP_1-1rxuR16
R:20-253
1q
PNP_UDP_1-1rxuR17
R:20-253
1r
PNP_UDP_1-1rxuR18
R:20-253
[
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 C
Chain D
Chain E
Chain F
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 (725 KB)
Header - Asym.Unit
Biol.Unit 1 (243 KB)
Header - Biol.Unit 1
Biol.Unit 2 (245 KB)
Header - Biol.Unit 2
Biol.Unit 3 (245 KB)
Header - Biol.Unit 3
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
1RXU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
