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1BRW
Asym. Unit
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Asym.Unit (140 KB)
Biol.Unit 1 (134 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A CLOSED CONFORMATION
Authors
:
M. J. Pugmire, S. E. Ealick
Date
:
25 Aug 98 (Deposition) - 13 Jan 99 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Nucleoside Phosphorylase, Domain Movement, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. J. Pugmire, S. E. Ealick
The Crystal Structure Of Pyrimidine Nucleoside Phosphorylase In A Closed Conformation.
Structure V. 6 1467 1998
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 7)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
2b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
4a: URACIL (URAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
MES
2
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3
PO4
2
Ligand/Ion
PHOSPHATE ION
4
URA
1
Ligand/Ion
URACIL
[
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]
Sites
(9, 9)
Info
All Sites
1: AC1 (AUTHOR)
2: AC2 (AUTHOR)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
AUTHOR
LYS A:187 , ARG A:168 , TYR A:165 , SER A:183 , SER A:182 , SER A:110 , LYS A:108 , THR A:120 , LYS A:81 , SER A:83
ACTIVE SITE
2
AC2
AUTHOR
LYS B:1187 , ARG B:1168 , TYR B:1165 , SER B:1183 , SER B:1182 , SER B:1110 , LYS B:1108 , THR B:1120 , LYS B:1081 , SER B:1083
ACTIVE SITE
3
AC3
SOFTWARE
LYS A:81 , HIS A:82 , SER A:83 , THR A:92 , LYS A:108 , SER A:110 , THR A:120 , HOH A:4003 , HOH A:4012 , HOH A:4105
BINDING SITE FOR RESIDUE PO4 A 2001
4
AC4
SOFTWARE
LYS B:1081 , HIS B:1082 , SER B:1083 , THR B:1092 , LYS B:1108 , SER B:1110 , THR B:1120 , HOH B:4066
BINDING SITE FOR RESIDUE PO4 B 2002
5
AC5
SOFTWARE
GLY A:88 , THR A:90 , LEU A:243 , ALA A:246 , GLU A:255
BINDING SITE FOR RESIDUE CA A 3001
6
AC6
SOFTWARE
GLY B:1088 , THR B:1090 , LEU B:1243 , ALA B:1246 , GLU B:1255
BINDING SITE FOR RESIDUE CA B 3002
7
AC7
SOFTWARE
HIS B:1082 , SER B:1083 , THR B:1084 , LEU B:1114 , TYR B:1165 , ARG B:1168 , ILE B:1180 , SER B:1183 , ILE B:1184 , LYS B:1187
BINDING SITE FOR RESIDUE URA B 5001
8
AC8
SOFTWARE
LYS B:1018 , GLU B:1022 , ARG B:1026 , GLN B:1064 , HOH B:4019
BINDING SITE FOR RESIDUE MES B 6001
9
AC9
SOFTWARE
TYR A:46 , ARG A:48 , GLY A:49 , ARG A:216 , HOH A:4021 , HOH A:4071
BINDING SITE FOR RESIDUE MES A 6002
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: THYMID_PHOSPHORYLASE (A:110-125,B:1110-1125)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THYMID_PHOSPHORYLASE
PS00647
Thymidine and pyrimidine-nucleoside phosphorylases signature.
PDP_GEOSE
110-125
2
A:110-125
B:1110-1125
[
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Exons
(0, 0)
Info
All Exons
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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1brwa1 (A:1-70)
1b: SCOP_d1brwb1 (B:1001-1070)
2a: SCOP_d1brwa3 (A:331-433)
2b: SCOP_d1brwb3 (B:1331-1433)
3a: SCOP_d1brwa2 (A:71-330)
3b: SCOP_d1brwb2 (B:1071-1330)
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)
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)
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(
)
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)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Methionine synthase domain-like
(29)
Superfamily
:
Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
(22)
Family
:
Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
(19)
Protein domain
:
Pyrimidine nucleoside phosphorylase
(1)
Bacillus stearothermophilus [TaxId: 1422]
(1)
1a
d1brwa1
A:1-70
1b
d1brwb1
B:1001-1070
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
alpha/beta-Hammerhead
(191)
Superfamily
:
Pyrimidine nucleoside phosphorylase C-terminal domain
(12)
Family
:
Pyrimidine nucleoside phosphorylase C-terminal domain
(9)
Protein domain
:
Pyrimidine nucleoside phosphorylase
(1)
Bacillus stearothermophilus [TaxId: 1422]
(1)
2a
d1brwa3
A:331-433
2b
d1brwb3
B:1331-1433
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
(22)
Superfamily
:
Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
(22)
Family
:
Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
(21)
Protein domain
:
Pyrimidine nucleoside phosphorylase
(1)
Bacillus stearothermophilus [TaxId: 1422]
(1)
3a
d1brwa2
A:71-330
3b
d1brwb2
B:1071-1330
[
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]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1brwA02 (A:68-330,A:425-433)
1b: CATH_1brwB02 (B:1068-1330,B:1425-1433)
2a: CATH_1brwA01 (A:331-424)
2b: CATH_1brwB01 (B:1331-1424)
3a: CATH_1brwA03 (A:1-67)
3b: CATH_1brwB03 (B:1001-1067)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
(23)
Homologous Superfamily
:
Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
(23)
Geobacillus stearothermophilus. Organism_taxid: 1422
(1)
1a
1brwA02
A:68-330,A:425-433
1b
1brwB02
B:1068-1330,B:1425-1433
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aldehyde Oxidoreductase; domain 3
(111)
Homologous Superfamily
:
[code=3.90.1170.30, no name defined]
(10)
Geobacillus stearothermophilus. Organism_taxid: 1422
(1)
2a
1brwA01
A:331-424
2b
1brwB01
B:1331-1424
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
(19)
Homologous Superfamily
:
Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C
(18)
Geobacillus stearothermophilus. Organism_taxid: 1422
(1)
3a
1brwA03
A:1-67
3b
1brwB03
B:1001-1067
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Pfam Domains
(0, 0)
Info
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Asymmetric Unit 1
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