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.
3KVV
Asym. Unit
Info
Asym.Unit (242 KB)
Biol.Unit 1 (236 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
TRAPPING OF AN OXOCARBENIUM ION INTERMEDIATE IN UP CRYSTALS
Authors
:
D. Paul, S. O'Leary, K. Rajashankar, W. Bu, A. Toms, E. Settembre, J. San T. P. Begley, S. E. Ealick
Date
:
30 Nov 09 (Deposition) - 28 Apr 10 (Release) - 05 May 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Oxocarbenium Ion, Glycal, Pyrimidine Salvage, Uridine Phosphorylase, Cytoplasm, Glycosyltransferase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Paul, S. E. O'Leary, K. Rajashankar, W. Bu, A. Toms, E. C. Settembre, J. M. Sanders, T. P. Begley, S. E. Ealick
Glycal Formation In Crystals Of Uridine Phosphorylase.
Biochemistry V. 49 3499 2010
[
close entry info
]
Hetero Components
(3, 18)
Info
All Hetero Components
1a: 1,4-ANHYDRO-D-ERYTHRO-PENT-1-ENITO... (R2Ba)
1b: 1,4-ANHYDRO-D-ERYTHRO-PENT-1-ENITO... (R2Bb)
1c: 1,4-ANHYDRO-D-ERYTHRO-PENT-1-ENITO... (R2Bc)
1d: 1,4-ANHYDRO-D-ERYTHRO-PENT-1-ENITO... (R2Bd)
1e: 1,4-ANHYDRO-D-ERYTHRO-PENT-1-ENITO... (R2Be)
1f: 1,4-ANHYDRO-D-ERYTHRO-PENT-1-ENITO... (R2Bf)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
3a: 5-FLUOROURACIL (URFa)
3b: 5-FLUOROURACIL (URFb)
3c: 5-FLUOROURACIL (URFc)
3d: 5-FLUOROURACIL (URFd)
3e: 5-FLUOROURACIL (URFe)
3f: 5-FLUOROURACIL (URFf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
R2B
6
Ligand/Ion
1,4-ANHYDRO-D-ERYTHRO-PENT-1-ENITOL
2
SO4
6
Ligand/Ion
SULFATE ION
3
URF
6
Ligand/Ion
5-FLUOROURACIL
[
close Hetero Component info
]
Sites
(18, 18)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:94 , THR A:95 , GLY A:96 , PHE A:162 , GLN A:166 , ARG A:168 , GLU A:196 , MET A:197 , ILE A:220 , VAL A:221 , R2B A:256 , HOH A:263
BINDING SITE FOR RESIDUE URF A 254
02
AC2
SOFTWARE
GLY A:26 , ARG A:30 , ARG A:91 , ILE A:92 , GLY A:93 , THR A:94 , R2B A:256 , ARG B:48
BINDING SITE FOR RESIDUE SO4 A 255
03
AC3
SOFTWARE
ILE A:69 , ARG A:91 , THR A:94 , PHE A:162 , GLU A:196 , MET A:197 , GLU A:198 , URF A:254 , SO4 A:255 , HOH A:317 , HIS B:8
BINDING SITE FOR RESIDUE R2B A 256
04
AC4
SOFTWARE
THR B:94 , THR B:95 , GLY B:96 , PHE B:162 , GLN B:166 , ARG B:168 , TYR B:195 , GLU B:196 , MET B:197 , ILE B:220 , VAL B:221 , R2B B:256 , HOH B:284
BINDING SITE FOR RESIDUE URF B 254
05
AC5
SOFTWARE
ARG A:48 , GLY B:26 , ARG B:30 , ARG B:91 , ILE B:92 , GLY B:93 , THR B:94 , R2B B:256
BINDING SITE FOR RESIDUE SO4 B 255
06
AC6
SOFTWARE
HIS A:8 , ILE B:69 , ARG B:91 , THR B:94 , GLU B:196 , MET B:197 , GLU B:198 , URF B:254 , SO4 B:255 , HOH B:324
BINDING SITE FOR RESIDUE R2B B 256
07
AC7
SOFTWARE
THR C:94 , THR C:95 , GLY C:96 , PHE C:162 , GLN C:166 , ARG C:168 , GLU C:196 , MET C:197 , ILE C:220 , VAL C:221 , R2B C:256 , HOH C:283
BINDING SITE FOR RESIDUE URF C 254
08
AC8
SOFTWARE
GLY C:26 , ARG C:30 , ARG C:91 , ILE C:92 , GLY C:93 , THR C:94 , R2B C:256 , ARG D:48
BINDING SITE FOR RESIDUE SO4 C 255
09
AC9
SOFTWARE
ILE C:69 , ARG C:91 , THR C:94 , GLU C:196 , MET C:197 , GLU C:198 , URF C:254 , SO4 C:255 , HOH C:462 , HIS D:8
BINDING SITE FOR RESIDUE R2B C 256
10
BC1
SOFTWARE
THR D:94 , THR D:95 , GLY D:96 , PHE D:162 , GLN D:166 , ARG D:168 , TYR D:195 , GLU D:196 , MET D:197 , ILE D:220 , VAL D:221 , R2B D:256 , HOH D:378
BINDING SITE FOR RESIDUE URF D 254
11
BC2
SOFTWARE
ARG C:48 , GLY D:26 , ARG D:30 , ARG D:91 , ILE D:92 , GLY D:93 , THR D:94 , R2B D:256
BINDING SITE FOR RESIDUE SO4 D 255
12
BC3
SOFTWARE
HIS C:8 , ILE D:69 , ARG D:91 , THR D:94 , PHE D:162 , GLU D:196 , MET D:197 , GLU D:198 , URF D:254 , SO4 D:255
BINDING SITE FOR RESIDUE R2B D 256
13
BC4
SOFTWARE
THR E:95 , GLY E:96 , PHE E:162 , GLN E:166 , ARG E:168 , TYR E:195 , GLU E:196 , MET E:197 , ILE E:220 , VAL E:221 , R2B E:256 , HOH E:271
BINDING SITE FOR RESIDUE URF E 254
14
BC5
SOFTWARE
GLY E:26 , ARG E:30 , ARG E:91 , ILE E:92 , GLY E:93 , THR E:94 , R2B E:256 , ARG F:48
BINDING SITE FOR RESIDUE SO4 E 255
15
BC6
SOFTWARE
ILE E:69 , ARG E:91 , THR E:94 , GLU E:196 , MET E:197 , GLU E:198 , URF E:254 , SO4 E:255 , HIS F:8
BINDING SITE FOR RESIDUE R2B E 256
16
BC7
SOFTWARE
THR F:94 , THR F:95 , GLY F:96 , PHE F:162 , GLN F:166 , ARG F:168 , GLU F:196 , MET F:197 , ILE F:220 , VAL F:221 , R2B F:256 , HOH F:278
BINDING SITE FOR RESIDUE URF F 254
17
BC8
SOFTWARE
ARG E:48 , GLY F:26 , ARG F:30 , ARG F:91 , ILE F:92 , GLY F:93 , THR F:94 , R2B F:256
BINDING SITE FOR RESIDUE SO4 F 255
18
BC9
SOFTWARE
HIS E:8 , ILE F:69 , ARG F:91 , THR F:94 , PHE F:162 , GLU F:196 , MET F:197 , GLU F:198 , URF F:254 , SO4 F:255 , HOH F:563
BINDING SITE FOR RESIDUE R2B F 256
[
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
(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.
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d3kvva_ (A:)
1b: SCOP_d3kvvb_ (B:)
1c: SCOP_d3kvvc_ (C:)
1d: SCOP_d3kvvd_ (D:)
1e: SCOP_d3kvve_ (E:)
1f: SCOP_d3kvvf_ (F:)
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
d3kvva_
A:
1b
d3kvvb_
B:
1c
d3kvvc_
C:
1d
d3kvvd_
D:
1e
d3kvve_
E:
1f
d3kvvf_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_3kvvE00 (E:3-253)
1b: CATH_3kvvA00 (A:4-253)
1c: CATH_3kvvB00 (B:3-253)
1d: CATH_3kvvC00 (C:4-253)
1e: CATH_3kvvD00 (D:4-253)
1f: CATH_3kvvF00 (F: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: 83333. Strain: k-12.
(1)
1a
3kvvE00
E:3-253
1b
3kvvA00
A:4-253
1c
3kvvB00
B:3-253
1d
3kvvC00
C:4-253
1e
3kvvD00
D:4-253
1f
3kvvF00
F:4-253
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_PNP_UDP_1_3kvvF01 (F:20-253)
1b: PFAM_PNP_UDP_1_3kvvF02 (F:20-253)
1c: PFAM_PNP_UDP_1_3kvvF03 (F:20-253)
1d: PFAM_PNP_UDP_1_3kvvF04 (F:20-253)
1e: PFAM_PNP_UDP_1_3kvvF05 (F:20-253)
1f: PFAM_PNP_UDP_1_3kvvF06 (F:20-253)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PUP
(121)
Family
:
PNP_UDP_1
(121)
Escherichia coli (strain K12)
(27)
1a
PNP_UDP_1-3kvvF01
F:20-253
1b
PNP_UDP_1-3kvvF02
F:20-253
1c
PNP_UDP_1-3kvvF03
F:20-253
1d
PNP_UDP_1-3kvvF04
F:20-253
1e
PNP_UDP_1-3kvvF05
F:20-253
1f
PNP_UDP_1-3kvvF06
F: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 (242 KB)
Header - Asym.Unit
Biol.Unit 1 (236 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
3KVV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
