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1NW4
Biol. Unit 1
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)
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(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
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Hetero Components
(3, 40)
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
6
Ligand/Ion
1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL
2
IPA
15
Ligand/Ion
ISOPROPYL ALCOHOL
3
SO4
19
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(40, 40)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (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
AC3
SOFTWARE
GLY C:23 , ARG C:88 , GLY C:90 , SER C:91 , IMH C:303 , ARG D:45
BINDING SITE FOR RESIDUE SO4 C 403
04
AC4
SOFTWARE
ARG C:45 , GLY D:23 , ARG D:88 , ALA D:89 , GLY D:90 , SER D:91 , IMH D:304
BINDING SITE FOR RESIDUE SO4 D 404
05
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
06
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
07
AC7
SOFTWARE
GLY B:124 , ASP B:125 , IPA B:508 , HOH B:813 , ARG C:169
BINDING SITE FOR RESIDUE SO4 B 407
08
AC8
SOFTWARE
HIS D:123 , GLY D:124 , ASP D:125 , IPA D:514 , HOH D:686 , HOH D:787 , ARG E:169
BINDING SITE FOR RESIDUE SO4 D 408
09
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
10
BC1
SOFTWARE
LYS B:101 , ARG B:102 , ASP B:216
BINDING SITE FOR RESIDUE SO4 B 410
11
BC2
SOFTWARE
ASP A:218 , ASN A:219 , ASN A:220
BINDING SITE FOR RESIDUE SO4 A 411
12
BC3
SOFTWARE
LYS A:101 , ARG A:102 , ASP A:216 , PRO D:223
BINDING SITE FOR RESIDUE SO4 A 412
13
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
14
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
15
BC6
SOFTWARE
ARG F:27 , ASN F:220 , LEU F:221
BINDING SITE FOR RESIDUE SO4 F 415
16
BC7
SOFTWARE
ARG D:169 , HIS E:123 , GLY E:124 , ASP E:125 , IPA E:513 , HOH E:806
BINDING SITE FOR RESIDUE SO4 E 416
17
BC8
SOFTWARE
HIS A:224 , LYS D:101 , ARG D:102 , ASP D:216
BINDING SITE FOR RESIDUE SO4 D 417
18
BC9
SOFTWARE
ARG B:169 , IPA B:515 , HIS C:123 , GLY C:124 , ASP C:125 , HOH C:694
BINDING SITE FOR RESIDUE SO4 C 418
19
CC1
SOFTWARE
LYS E:101 , ARG E:102 , ASP E:216
BINDING SITE FOR RESIDUE SO4 E 419
20
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
21
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
22
CC4
SOFTWARE
ARG C:88 , SER C:91 , CYS C:92 , GLY C:93 , TYR C:160 , GLU C:182 , MET C:183 , GLU C:184 , ASP C:206 , TRP C:212 , SO4 C:403 , HOH C:720 , HOH C:838 , HIS D:7 , IPA D:503
BINDING SITE FOR RESIDUE IMH C 303
23
CC5
SOFTWARE
HIS C:7 , ARG D:88 , SER D:91 , CYS D:92 , GLY D:93 , TYR D:160 , VAL D:181 , GLU D:182 , MET D:183 , GLU D:184 , ASP D:206 , TRP D:212 , SO4 D:404 , HOH D:662 , HOH D:675 , HOH D:676
BINDING SITE FOR RESIDUE IMH D 304
24
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
25
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
26
CC8
SOFTWARE
IMH A:301 , ASN B:44 , ARG B:45 , HOH B:839 , HOH B:840
BINDING SITE FOR RESIDUE IPA B 501
27
CC9
SOFTWARE
ARG A:6 , ASN A:44 , ARG A:45 , IMH B:302
BINDING SITE FOR RESIDUE IPA A 502
28
DC1
SOFTWARE
IMH C:303 , ARG D:6 , ARG D:45
BINDING SITE FOR RESIDUE IPA D 503
29
DC2
SOFTWARE
ARG C:6 , ASN C:44 , ARG C:45 , HOH D:675
BINDING SITE FOR RESIDUE IPA C 504
30
DC3
SOFTWARE
HOH E:772 , ASN F:44 , ARG F:45
BINDING SITE FOR RESIDUE IPA F 505
31
DC4
SOFTWARE
ASN E:44 , ARG E:45 , HOH F:767
BINDING SITE FOR RESIDUE IPA E 506
32
DC5
SOFTWARE
ARG A:169 , ARG B:116 , HIS B:119
BINDING SITE FOR RESIDUE IPA B 507
33
DC6
SOFTWARE
HIS B:119 , HIS B:123 , SO4 B:407 , ARG C:169
BINDING SITE FOR RESIDUE IPA B 508
34
DC7
SOFTWARE
ARG A:116 , HIS A:119 , HOH A:822 , ARG B:169
BINDING SITE FOR RESIDUE IPA A 509
35
DC8
SOFTWARE
HIS A:119 , HIS A:123 , SO4 A:413 , ARG F:169
BINDING SITE FOR RESIDUE IPA A 510
36
DC9
SOFTWARE
ARG E:169 , ARG F:116 , HIS F:119 , LEU F:120 , HOH F:618
BINDING SITE FOR RESIDUE IPA F 511
37
EC1
SOFTWARE
ARG A:169 , HIS F:119 , HIS F:123 , SO4 F:409
BINDING SITE FOR RESIDUE IPA F 512
38
EC2
SOFTWARE
ARG D:169 , HIS E:119 , HIS E:123 , SO4 E:416
BINDING SITE FOR RESIDUE IPA E 513
39
EC3
SOFTWARE
HIS D:119 , HIS D:123 , SO4 D:408 , ARG E:169
BINDING SITE FOR RESIDUE IPA D 514
40
EC4
SOFTWARE
ARG B:169 , HIS C:119 , HIS C:123 , SO4 C:418
BINDING SITE FOR RESIDUE IPA B 515
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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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:
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(
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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)
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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)
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Organisms
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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
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