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.
1NW4
Biol. Unit 3
Info
Asym.Unit (245 KB)
Biol.Unit 1 (237 KB)
Biol.Unit 2 (83 KB)
Biol.Unit 3 (83 KB)
Biol.Unit 4 (82 KB)
Biol.Unit 5 (83 KB)
Biol.Unit 6 (83 KB)
Biol.Unit 7 (83 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 PLASMODIUM FALCIPARUM PURINE NUCLEOSIDE PHOSPHORYLASE IN COMPLEX WITH IMMH AND SULFATE
Authors
:
W. Shi, L. M. Ting, G. A. Kicska, A. Lewandowicz, P. C. Tyler, G. B. Evans, R. H. Furneaux, K. Kim, S. C. Almo, V. L. Schramm
Date
:
05 Feb 03 (Deposition) - 16 Mar 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: D,E (1x)
Biol. Unit 3: A,F (1x)
Biol. Unit 4: B,C (1x)
Biol. Unit 5: E,F (1x)
Biol. Unit 6: C,D (1x)
Biol. Unit 7: A,B (1x)
Keywords
:
Transition State Complex, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. Shi, L. M. Ting, G. A. Kicska, A. Lewandowicz, P. C. Tyler, G. B. Evans R. H. Furneaux, K. Kim, S. C. Almo, V. L. Schramm
Plasmodium Falciparum Purine Nucleoside Phosphorylase: Crystal Structures, Immucillin Inhibitors, And Dual Catalytic Function.
J. Biol. Chem. V. 279 18103 2004
[
close entry info
]
Hetero Components
(3, 16)
Info
All Hetero Components
1a: 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHY... (IMHa)
1b: 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHY... (IMHb)
1c: 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHY... (IMHc)
1d: 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHY... (IMHd)
1e: 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHY... (IMHe)
1f: 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHY... (IMHf)
2a: ISOPROPYL ALCOHOL (IPAa)
2b: ISOPROPYL ALCOHOL (IPAb)
2c: ISOPROPYL ALCOHOL (IPAc)
2d: ISOPROPYL ALCOHOL (IPAd)
2e: ISOPROPYL ALCOHOL (IPAe)
2f: ISOPROPYL ALCOHOL (IPAf)
2g: ISOPROPYL ALCOHOL (IPAg)
2h: ISOPROPYL ALCOHOL (IPAh)
2i: ISOPROPYL ALCOHOL (IPAi)
2j: ISOPROPYL ALCOHOL (IPAj)
2k: ISOPROPYL ALCOHOL (IPAk)
2l: ISOPROPYL ALCOHOL (IPAl)
2m: ISOPROPYL ALCOHOL (IPAm)
2n: ISOPROPYL ALCOHOL (IPAn)
2o: ISOPROPYL ALCOHOL (IPAo)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
3s: SULFATE ION (SO4s)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IMH
2
Ligand/Ion
1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL
2
IPA
6
Ligand/Ion
ISOPROPYL ALCOHOL
3
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(24, 24)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC8 (SOFTWARE)
12: CC2 (SOFTWARE)
13: CC3 (SOFTWARE)
14: CC6 (SOFTWARE)
15: CC7 (SOFTWARE)
16: CC8 (SOFTWARE)
17: CC9 (SOFTWARE)
18: DC3 (SOFTWARE)
19: DC4 (SOFTWARE)
20: DC5 (SOFTWARE)
21: DC7 (SOFTWARE)
22: DC8 (SOFTWARE)
23: DC9 (SOFTWARE)
24: EC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:23 , ARG A:88 , GLY A:90 , SER A:91 , IMH A:301 , ARG B:45
BINDING SITE FOR RESIDUE SO4 A 401
02
AC2
SOFTWARE
ARG A:45 , GLY B:23 , ARG B:88 , GLY B:90 , SER B:91 , IMH B:302
BINDING SITE FOR RESIDUE SO4 B 402
03
AC5
SOFTWARE
GLY E:23 , ARG E:88 , GLY E:90 , SER E:91 , IMH E:305 , HOH E:833 , ARG F:45
BINDING SITE FOR RESIDUE SO4 E 405
04
AC6
SOFTWARE
ARG E:45 , GLY F:23 , ARG F:88 , GLY F:90 , SER F:91 , IMH F:306
BINDING SITE FOR RESIDUE SO4 F 406
05
AC9
SOFTWARE
ARG A:169 , HIS F:123 , GLY F:124 , ASP F:125 , IPA F:512 , HOH F:643
BINDING SITE FOR RESIDUE SO4 F 409
06
BC2
SOFTWARE
ASP A:218 , ASN A:219 , ASN A:220
BINDING SITE FOR RESIDUE SO4 A 411
07
BC3
SOFTWARE
LYS A:101 , ARG A:102 , ASP A:216 , PRO D:223
BINDING SITE FOR RESIDUE SO4 A 412
08
BC4
SOFTWARE
HIS A:123 , GLY A:124 , ASP A:125 , IPA A:510 , HOH A:601 , ARG F:169
BINDING SITE FOR RESIDUE SO4 A 413
09
BC5
SOFTWARE
LYS F:101 , ARG F:102 , ASP F:216 , HOH F:739 , HOH F:803 , HOH F:816
BINDING SITE FOR RESIDUE SO4 F 414
10
BC6
SOFTWARE
ARG F:27 , ASN F:220 , LEU F:221
BINDING SITE FOR RESIDUE SO4 F 415
11
BC8
SOFTWARE
HIS A:224 , LYS D:101 , ARG D:102 , ASP D:216
BINDING SITE FOR RESIDUE SO4 D 417
12
CC2
SOFTWARE
ARG A:88 , SER A:91 , CYS A:92 , GLY A:93 , TYR A:160 , GLU A:182 , MET A:183 , GLU A:184 , ASP A:206 , TRP A:212 , SO4 A:401 , HOH A:613 , HOH A:637 , HOH A:647 , HIS B:7 , IPA B:501
BINDING SITE FOR RESIDUE IMH A 301
13
CC3
SOFTWARE
HIS A:7 , IPA A:502 , ARG B:88 , SER B:91 , CYS B:92 , GLY B:93 , TYR B:160 , GLU B:182 , MET B:183 , GLU B:184 , ASP B:206 , TRP B:212 , SO4 B:402 , HOH B:764
BINDING SITE FOR RESIDUE IMH B 302
14
CC6
SOFTWARE
ARG E:88 , SER E:91 , CYS E:92 , GLY E:93 , TYR E:160 , GLU E:182 , MET E:183 , GLU E:184 , ASP E:206 , TRP E:212 , SO4 E:405 , HOH E:728 , HOH E:772 , HOH E:788 , HIS F:7
BINDING SITE FOR RESIDUE IMH E 305
15
CC7
SOFTWARE
HIS E:7 , ARG F:88 , SER F:91 , CYS F:92 , GLY F:93 , GLU F:182 , MET F:183 , GLU F:184 , ASP F:206 , TRP F:212 , SO4 F:406 , HOH F:605 , HOH F:693 , HOH F:767 , HOH F:832
BINDING SITE FOR RESIDUE IMH F 306
16
CC8
SOFTWARE
IMH A:301 , ASN B:44 , ARG B:45 , HOH B:839 , HOH B:840
BINDING SITE FOR RESIDUE IPA B 501
17
CC9
SOFTWARE
ARG A:6 , ASN A:44 , ARG A:45 , IMH B:302
BINDING SITE FOR RESIDUE IPA A 502
18
DC3
SOFTWARE
HOH E:772 , ASN F:44 , ARG F:45
BINDING SITE FOR RESIDUE IPA F 505
19
DC4
SOFTWARE
ASN E:44 , ARG E:45 , HOH F:767
BINDING SITE FOR RESIDUE IPA E 506
20
DC5
SOFTWARE
ARG A:169 , ARG B:116 , HIS B:119
BINDING SITE FOR RESIDUE IPA B 507
21
DC7
SOFTWARE
ARG A:116 , HIS A:119 , HOH A:822 , ARG B:169
BINDING SITE FOR RESIDUE IPA A 509
22
DC8
SOFTWARE
HIS A:119 , HIS A:123 , SO4 A:413 , ARG F:169
BINDING SITE FOR RESIDUE IPA A 510
23
DC9
SOFTWARE
ARG E:169 , ARG F:116 , HIS F:119 , LEU F:120 , HOH F:618
BINDING SITE FOR RESIDUE IPA F 511
24
EC1
SOFTWARE
ARG A:169 , HIS F:119 , HIS F:123 , SO4 F:409
BINDING SITE FOR RESIDUE IPA F 512
[
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, 6)
Info
All SCOP Domains
1a: SCOP_d1nw4a_ (A:)
1b: SCOP_d1nw4e_ (E:)
1c: SCOP_d1nw4f_ (F:)
1d: SCOP_d1nw4b_ (B:)
1e: SCOP_d1nw4c_ (C:)
1f: SCOP_d1nw4d_ (D:)
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
:
Putative uridine phosphorylase
(3)
Malaria parasite (Plasmodium falciparum) [TaxId: 5833]
(3)
1a
d1nw4a_
A:
1b
d1nw4e_
E:
1c
d1nw4f_
F:
1d
d1nw4b_
B:
1e
d1nw4c_
C:
1f
d1nw4d_
D:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1nw4A00 (A:3-245)
1b: CATH_1nw4E00 (E:3-245)
1c: CATH_1nw4F00 (F:3-245)
1d: CATH_1nw4B00 (B:3-245)
1e: CATH_1nw4C00 (C:3-245)
1f: CATH_1nw4D00 (D:3-245)
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)
Plasmodium falciparum 3d7. Organism_taxid: 36329. Strain: 3d7.
(2)
1a
1nw4A00
A:3-245
1b
1nw4E00
E:3-245
1c
1nw4F00
F:3-245
1d
1nw4B00
B:3-245
1e
1nw4C00
C:3-245
1f
1nw4D00
D:3-245
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_PNP_UDP_1_1nw4F01 (F:17-244)
1b: PFAM_PNP_UDP_1_1nw4F02 (F:17-244)
1c: PFAM_PNP_UDP_1_1nw4F03 (F:17-244)
1d: PFAM_PNP_UDP_1_1nw4F04 (F:17-244)
1e: PFAM_PNP_UDP_1_1nw4F05 (F:17-244)
1f: PFAM_PNP_UDP_1_1nw4F06 (F:17-244)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PUP
(121)
Family
:
PNP_UDP_1
(121)
Plasmodium falciparum (isolate 3D7)
(2)
1a
PNP_UDP_1-1nw4F01
F:17-244
1b
PNP_UDP_1-1nw4F02
F:17-244
1c
PNP_UDP_1-1nw4F03
F:17-244
1d
PNP_UDP_1-1nw4F04
F:17-244
1e
PNP_UDP_1-1nw4F05
F:17-244
1f
PNP_UDP_1-1nw4F06
F:17-244
[
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 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 (245 KB)
Header - Asym.Unit
Biol.Unit 1 (237 KB)
Header - Biol.Unit 1
Biol.Unit 2 (83 KB)
Header - Biol.Unit 2
Biol.Unit 3 (83 KB)
Header - Biol.Unit 3
Biol.Unit 4 (82 KB)
Header - Biol.Unit 4
Biol.Unit 5 (83 KB)
Header - Biol.Unit 5
Biol.Unit 6 (83 KB)
Header - Biol.Unit 6
Biol.Unit 7 (83 KB)
Header - Biol.Unit 7
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
1NW4
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
