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1Y1Q
Asym. Unit
Info
Asym.Unit (232 KB)
Biol.Unit 1 (227 KB)
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Title
:
CRYSTAL STRUCTURE OF THE URIDINE PHOSPHORYLASE FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH URIDINE-5P-MONOPHOSPHATE AND SULFATE ION AT 2.35A RESOLUTION
Authors
:
A. G. Gabdoulkhakov, M. V. Dontsova, G. S. Kachalova, C. Betzel, S. E. Ea A. M. Mikhailov
Date
:
19 Nov 04 (Deposition) - 22 Nov 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Nucleoside Phosphorylase, Transferase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
A. G. Gabdoulkhakov, M. V. Dontsova, G. S. Kachalova, C. Betzel, S. E. Ealick, A. M. Mikhailov
Crystal Structures Of Salmonella Typhimurium Uridine Phosphorylase In Native And Three Complexes Forms - With Uridine, Uracil And Sulfate.
To Be Published
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Hetero Components
(2, 5)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
2a: URIDINE-5'-MONOPHOSPHATE (Ua)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
4
Ligand/Ion
SULFATE ION
2
U
1
Ligand/Ion
URIDINE-5'-MONOPHOSPHATE
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:1048 , GLY E:5026 , ASP E:5027 , ARG E:5091 , GLY E:5093 , THR E:5094
BINDING SITE FOR RESIDUE SO4 E 7001
2
AC2
SOFTWARE
THR A:1111 , VAL A:1131 , PHE A:1134 , THR D:4111
BINDING SITE FOR RESIDUE SO4 A 7003
3
AC3
SOFTWARE
GLY A:1026 , ARG A:1091 , THR A:1094 , HOH A:9050 , ARG E:5048
BINDING SITE FOR RESIDUE SO4 A 7004
4
AC4
SOFTWARE
ARG C:3048 , GLY F:6026 , ARG F:6091 , GLY F:6093 , THR F:6094 , GLU F:6198
BINDING SITE FOR RESIDUE SO4 F 7005
5
AC5
SOFTWARE
GLY C:3026 , ARG C:3091 , ILE C:3092 , GLY C:3093 , THR C:3094 , THR C:3095 , GLY C:3096 , PHE C:3162 , GLN C:3166 , ARG C:3168 , TYR C:3195 , GLU C:3196 , MET C:3197 , GLU C:3198 , ARG F:6048 , HOH F:9094
BINDING SITE FOR RESIDUE U C 8003
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: PNP_UDP_1 (A:1066-1081,B:2066-2081,C:3066-308...)
;
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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_SALTY
66-81
6
A:1066-1081
B:2066-2081
C:3066-3081
D:4066-4081
E:5066-5081
F:6066-6081
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Exons
(0, 0)
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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_d1y1qa_ (A:)
1b: SCOP_d1y1qb_ (B:)
1c: SCOP_d1y1qc_ (C:)
1d: SCOP_d1y1qd_ (D:)
1e: SCOP_d1y1qe_ (E:)
1f: SCOP_d1y1qf_ (F:)
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Protein Domains
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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)
Salmonella typhimurium [TaxId: 90371]
(23)
1a
d1y1qa_
A:
1b
d1y1qb_
B:
1c
d1y1qc_
C:
1d
d1y1qd_
D:
1e
d1y1qe_
E:
1f
d1y1qf_
F:
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1y1qA00 (A:1004-1253)
1b: CATH_1y1qD00 (D:4004-4253)
1c: CATH_1y1qF00 (F:6004-6253)
1d: CATH_1y1qC00 (C:3004-3253)
1e: CATH_1y1qB00 (B:2004-2253)
1f: CATH_1y1qE00 (E:5004-5253)
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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)
Salmonella typhimurium lt2. Organism_taxid: 99287. Strain: lt2.
(16)
1a
1y1qA00
A:1004-1253
1b
1y1qD00
D:4004-4253
1c
1y1qF00
F:6004-6253
1d
1y1qC00
C:3004-3253
1e
1y1qB00
B:2004-2253
1f
1y1qE00
E:5004-5253
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_PNP_UDP_1_1y1qF01 (F:6020-6253)
1b: PFAM_PNP_UDP_1_1y1qF02 (F:6020-6253)
1c: PFAM_PNP_UDP_1_1y1qF03 (F:6020-6253)
1d: PFAM_PNP_UDP_1_1y1qF04 (F:6020-6253)
1e: PFAM_PNP_UDP_1_1y1qF05 (F:6020-6253)
1f: PFAM_PNP_UDP_1_1y1qF06 (F:6020-6253)
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Clan
:
PUP
(121)
Family
:
PNP_UDP_1
(121)
Salmonella typhimurium
(11)
1a
PNP_UDP_1-1y1qF01
F:6020-6253
1b
PNP_UDP_1-1y1qF02
F:6020-6253
1c
PNP_UDP_1-1y1qF03
F:6020-6253
1d
PNP_UDP_1-1y1qF04
F:6020-6253
1e
PNP_UDP_1-1y1qF05
F:6020-6253
1f
PNP_UDP_1-1y1qF06
F:6020-6253
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Asymmetric Unit 1
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Asym.Unit (232 KB)
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