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1U1F
Asym. Unit
Info
Asym.Unit (241 KB)
Biol.Unit 1 (233 KB)
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(1)
Title
:
STRUCTURE OF E. COLI URIDINE PHOSPHORYLASE COMPLEXED TO 5-(M-(BENZYLOXY)BENZYL)ACYCLOURIDINE (BBAU)
Authors
:
W. Bu, E. C. Settembre, S. E. Ealick
Date
:
15 Jul 04 (Deposition) - 05 Jul 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Pyrimidine Nucleoside Phosphorylase; Uridine Salvage; Udp; 5-(M- (Benzyloxy)Benzyl)Acyclouridine; Bbau, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. Bu, E. C. Settembre, M. H. El Kouni, S. E. Ealick
Structural Basis For Inhibition Of Escherichia Coli Uridine Phosphorylase By 5-Substituted Acyclouridines.
Acta Crystallogr. , Sect. D V. 61 863 2005
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Hetero Components
(3, 15)
Info
All Hetero Components
1a: 1-((2-HYDROXYETHOXY)METHYL)-5-(3-(... (183a)
1b: 1-((2-HYDROXYETHOXY)METHYL)-5-(3-(... (183b)
1c: 1-((2-HYDROXYETHOXY)METHYL)-5-(3-(... (183c)
1d: 1-((2-HYDROXYETHOXY)METHYL)-5-(3-(... (183d)
1e: 1-((2-HYDROXYETHOXY)METHYL)-5-(3-(... (183e)
1f: 1-((2-HYDROXYETHOXY)METHYL)-5-(3-(... (183f)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
2c: POTASSIUM ION (Kc)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
3d: PHOSPHATE ION (PO4d)
3e: PHOSPHATE ION (PO4e)
3f: PHOSPHATE ION (PO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
183
6
Ligand/Ion
1-((2-HYDROXYETHOXY)METHYL)-5-(3-(BENZYLOXY)BENZYL)PYRIMIDINE-2,4(1H,3H)-DIONE
2
K
3
Ligand/Ion
POTASSIUM ION
3
PO4
6
Ligand/Ion
PHOSPHATE ION
[
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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: 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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:48 , GLY B:26 , ARG B:30 , ARG B:91 , ILE B:92 , GLY B:93 , THR B:94 , GLU B:198 , HOH B:4353
BINDING SITE FOR RESIDUE PO4 B 3301
02
AC2
SOFTWARE
GLY A:26 , ARG A:30 , ARG A:91 , ILE A:92 , GLY A:93 , THR A:94 , GLU A:198 , HOH A:4356 , HOH A:4404 , ARG B:48
BINDING SITE FOR RESIDUE PO4 A 4301
03
AC3
SOFTWARE
ARG C:48 , GLY D:26 , ARG D:30 , ARG D:91 , ILE D:92 , GLY D:93 , THR D:94 , GLU D:198 , HOH D:6335 , HOH D:6358 , HOH D:6392
BINDING SITE FOR RESIDUE PO4 D 5301
04
AC4
SOFTWARE
GLY C:26 , ARG C:30 , ARG C:91 , ILE C:92 , GLY C:93 , THR C:94 , GLU C:198 , 183 C:5300 , HOH C:6375 , HOH C:6420 , ARG D:48
BINDING SITE FOR RESIDUE PO4 C 6301
05
AC5
SOFTWARE
ARG E:48 , GLY F:26 , ARG F:30 , ARG F:91 , ILE F:92 , GLY F:93 , THR F:94 , GLU F:198 , HOH F:8337 , HOH F:8347
BINDING SITE FOR RESIDUE PO4 F 7301
06
AC6
SOFTWARE
GLY E:26 , ARG E:30 , ARG E:91 , ILE E:92 , GLY E:93 , THR E:94 , GLU E:198 , 183 E:7300 , HOH E:8356 , ARG F:48
BINDING SITE FOR RESIDUE PO4 E 8301
07
AC7
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 1001
08
AC8
SOFTWARE
GLU A:49 , ILE A:69 , SER A:73 , HOH A:4338 , GLU B:49 , ILE B:69 , SER B:73
BINDING SITE FOR RESIDUE K A 1002
09
AC9
SOFTWARE
GLU E:49 , ILE E:69 , SER E:73 , GLU F:49 , ILE F:69 , SER F:73
BINDING SITE FOR RESIDUE K E 1003
10
BC1
SOFTWARE
THR A:94 , THR A:95 , GLY A:96 , PHE A:162 , GLN A:166 , ARG A:168 , TYR A:195 , GLU A:196 , MET A:197 , ILE A:220 , MET A:234 , HOH A:4324 , HOH A:4372 , PHE B:7 , HIS B:8
BINDING SITE FOR RESIDUE 183 A 3300
11
BC2
SOFTWARE
PHE A:7 , HIS A:8 , ARG A:48 , THR B:94 , GLY B:96 , PHE B:162 , GLN B:166 , ARG B:168 , TYR B:195 , GLU B:196 , MET B:197 , ILE B:220 , GLU B:227 , HOH B:4356 , HOH B:4381
BINDING SITE FOR RESIDUE 183 B 4300
12
BC3
SOFTWARE
THR C:94 , THR C:95 , GLY C:96 , PHE C:162 , GLN C:166 , ARG C:168 , TYR C:195 , GLU C:196 , MET C:197 , ILE C:220 , PRO C:229 , MET C:234 , PO4 C:6301 , HOH C:6308 , HOH C:6375 , HOH C:6377 , PHE D:7 , HIS D:8
BINDING SITE FOR RESIDUE 183 C 5300
13
BC4
SOFTWARE
PHE C:7 , HIS C:8 , 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 , GLU D:227 , HOH D:6327
BINDING SITE FOR RESIDUE 183 D 6300
14
BC5
SOFTWARE
THR E:94 , 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 , MET E:234 , PO4 E:8301 , HOH E:8329 , HOH E:8344 , PHE F:7 , HIS F:8
BINDING SITE FOR RESIDUE 183 E 7300
15
BC6
SOFTWARE
PHE E:7 , HIS E:8 , THR F:94 , GLY F:96 , PHE F:162 , GLN F:166 , ARG F:168 , TYR F:195 , GLU F:196 , MET F:197 , VAL F:221 , HOH F:8310
BINDING SITE FOR RESIDUE 183 F 8300
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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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:
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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
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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_d1u1fa_ (A:)
1b: SCOP_d1u1fb_ (B:)
1c: SCOP_d1u1fc_ (C:)
1d: SCOP_d1u1fd_ (D:)
1e: SCOP_d1u1fe_ (E:)
1f: SCOP_d1u1ff_ (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
:
Uridine phosphorylase
(42)
Escherichia coli [TaxId: 562]
(15)
1a
d1u1fa_
A:
1b
d1u1fb_
B:
1c
d1u1fc_
C:
1d
d1u1fd_
D:
1e
d1u1fe_
E:
1f
d1u1ff_
F:
[
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1u1fB00 (B:3-253)
1b: CATH_1u1fC00 (C:4-253)
1c: CATH_1u1fD00 (D:4-253)
1d: CATH_1u1fF00 (F:4-253)
1e: CATH_1u1fE00 (E:3-253)
1f: CATH_1u1fA00 (A:4-253)
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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)
Escherichia coli. Organism_taxid: 562.
(30)
1a
1u1fB00
B:3-253
1b
1u1fC00
C:4-253
1c
1u1fD00
D:4-253
1d
1u1fF00
F:4-253
1e
1u1fE00
E:3-253
1f
1u1fA00
A:4-253
[
close CATH info
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_PNP_UDP_1_1u1fF01 (F:20-252)
1b: PFAM_PNP_UDP_1_1u1fF02 (F:20-252)
1c: PFAM_PNP_UDP_1_1u1fF03 (F:20-252)
1d: PFAM_PNP_UDP_1_1u1fF04 (F:20-252)
1e: PFAM_PNP_UDP_1_1u1fF05 (F:20-252)
1f: PFAM_PNP_UDP_1_1u1fF06 (F:20-252)
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Clan
:
PUP
(121)
Family
:
PNP_UDP_1
(121)
Escherichia coli (strain K12)
(27)
1a
PNP_UDP_1-1u1fF01
F:20-252
1b
PNP_UDP_1-1u1fF02
F:20-252
1c
PNP_UDP_1-1u1fF03
F:20-252
1d
PNP_UDP_1-1u1fF04
F:20-252
1e
PNP_UDP_1-1u1fF05
F:20-252
1f
PNP_UDP_1-1u1fF06
F:20-252
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