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1ODJ
Asym. Unit
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Asym.Unit (232 KB)
Biol.Unit 1 (224 KB)
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(1)
Title
:
PURINE NUCLEOSIDE PHOSPHORYLASE FROM THERMUS THERMOPHILUS
Authors
:
T. H. Tahirov, E. Inagaki, M. Miyano
Date
:
19 Feb 03 (Deposition) - 04 Mar 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Transferase, Nucleoside Phosphorylase, Alpha-Beta Protein, Guanosine, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. H. Tahirov, E. Inagaki, N. Ohshima, T. Kitao, C. Kuroishi, Y. Ukita, K. Takio, M. Kobayashi, S. Kuramitsu, S. Yokoyama, M. Miyano
Crystal Structure Of Purine Nucleoside Phosphorylase From Thermus Thermophilus
J. Mol. Biol. V. 337 1149 2004
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: GUANOSINE (GMPa)
1b: GUANOSINE (GMPb)
1c: GUANOSINE (GMPc)
1d: GUANOSINE (GMPd)
1e: GUANOSINE (GMPe)
1f: GUANOSINE (GMPf)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GMP
6
Ligand/Ion
GUANOSINE
2
SO4
6
Ligand/Ion
SULFATE ION
[
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]
Sites
(12, 12)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:21 , ARG A:25 , ARG A:87 , GLY A:89 , THR A:90 , GMP A:1237 , ARG B:44
BINDING SITE FOR RESIDUE SO4 A1236
02
AC2
SOFTWARE
ARG A:44 , GLY B:21 , ARG B:25 , ARG B:87 , VAL B:88 , GLY B:89 , THR B:90 , GMP B:1237
BINDING SITE FOR RESIDUE SO4 B1236
03
AC3
SOFTWARE
GLY C:21 , ARG C:25 , ARG C:87 , VAL C:88 , GLY C:89 , THR C:90 , GMP C:1237 , ARG D:44
BINDING SITE FOR RESIDUE SO4 C1236
04
AC4
SOFTWARE
ARG C:44 , GLY D:21 , ARG D:25 , ARG D:87 , GLY D:89 , THR D:90 , GMP D:1237
BINDING SITE FOR RESIDUE SO4 D1236
05
AC5
SOFTWARE
GLY E:21 , ARG E:25 , ARG E:87 , GLY E:89 , THR E:90 , GMP E:1237 , ARG F:44
BINDING SITE FOR RESIDUE SO4 E1236
06
AC6
SOFTWARE
ARG E:44 , GLY F:21 , ARG F:25 , ARG F:87 , GLY F:89 , THR F:90 , GMP F:1237
BINDING SITE FOR RESIDUE SO4 F1236
07
AC7
SOFTWARE
MET A:65 , ARG A:87 , THR A:90 , ALA A:91 , GLY A:92 , GLU A:156 , PHE A:159 , PHE A:178 , GLU A:179 , MET A:180 , GLU A:181 , SER A:203 , ILE A:206 , SO4 A:1236 , HOH A:2047 , HIS B:5 , ARG B:44
BINDING SITE FOR RESIDUE GMP A1237
08
AC8
SOFTWARE
HIS A:5 , ARG A:44 , MET B:65 , ARG B:87 , THR B:90 , ALA B:91 , GLY B:92 , GLU B:156 , PHE B:159 , GLU B:179 , MET B:180 , GLU B:181 , ASN B:204 , ILE B:206 , SO4 B:1236 , HOH B:2050
BINDING SITE FOR RESIDUE GMP B1237
09
AC9
SOFTWARE
ARG C:87 , THR C:90 , ALA C:91 , GLY C:92 , GLU C:156 , PHE C:159 , PHE C:178 , GLU C:179 , MET C:180 , GLU C:181 , SO4 C:1236 , HIS D:5 , ARG D:44
BINDING SITE FOR RESIDUE GMP C1237
10
BC1
SOFTWARE
HIS C:5 , ARG D:87 , THR D:90 , ALA D:91 , GLY D:92 , GLU D:156 , PHE D:159 , PHE D:178 , MET D:180 , GLU D:181 , SER D:203 , ASN D:204 , SO4 D:1236 , HOH D:2023
BINDING SITE FOR RESIDUE GMP D1237
11
BC2
SOFTWARE
ARG E:87 , THR E:90 , ALA E:91 , GLY E:92 , GLU E:156 , PHE E:159 , PHE E:178 , GLU E:179 , MET E:180 , GLU E:181 , SER E:203 , SO4 E:1236 , HOH E:2040 , HIS F:5 , ARG F:44
BINDING SITE FOR RESIDUE GMP E1237
12
BC3
SOFTWARE
HIS E:5 , ARG E:44 , MET F:65 , ARG F:87 , THR F:90 , ALA F:91 , GLY F:92 , GLU F:156 , PHE F:159 , PHE F:178 , GLU F:179 , MET F:180 , GLU F:181 , SER F:203 , ASN F:204 , ILE F:206 , SO4 F:1236 , HOH F:2060
BINDING SITE FOR RESIDUE GMP F1237
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
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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_d1odja_ (A:)
1b: SCOP_d1odjb_ (B:)
1c: SCOP_d1odjc_ (C:)
1d: SCOP_d1odjd_ (D:)
1e: SCOP_d1odje_ (E:)
1f: SCOP_d1odjf_ (F:)
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Protein Domains
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)
(
)
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
:
Purine nucleoside phosphorylase, PNP
(93)
Thermus thermophilus [TaxId: 274]
(4)
1a
d1odja_
A:
1b
d1odjb_
B:
1c
d1odjc_
C:
1d
d1odjd_
D:
1e
d1odje_
E:
1f
d1odjf_
F:
[
close SCOP info
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1odjA00 (A:2-235)
1b: CATH_1odjB00 (B:2-235)
1c: CATH_1odjC00 (C:2-235)
1d: CATH_1odjD00 (D:2-235)
1e: CATH_1odjE00 (E:2-235)
1f: CATH_1odjF00 (F:2-235)
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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)
Thermus thermophilus. Organism_taxid: 300852. Strain: hb8.
(3)
1a
1odjA00
A:2-235
1b
1odjB00
B:2-235
1c
1odjC00
C:2-235
1d
1odjD00
D:2-235
1e
1odjE00
E:2-235
1f
1odjF00
F:2-235
[
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_PNP_UDP_1_1odjF01 (F:15-234)
1b: PFAM_PNP_UDP_1_1odjF02 (F:15-234)
1c: PFAM_PNP_UDP_1_1odjF03 (F:15-234)
1d: PFAM_PNP_UDP_1_1odjF04 (F:15-234)
1e: PFAM_PNP_UDP_1_1odjF05 (F:15-234)
1f: PFAM_PNP_UDP_1_1odjF06 (F:15-234)
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Clan
:
PUP
(121)
Family
:
PNP_UDP_1
(121)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(4)
1a
PNP_UDP_1-1odjF01
F:15-234
1b
PNP_UDP_1-1odjF02
F:15-234
1c
PNP_UDP_1-1odjF03
F:15-234
1d
PNP_UDP_1-1odjF04
F:15-234
1e
PNP_UDP_1-1odjF05
F:15-234
1f
PNP_UDP_1-1odjF06
F:15-234
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