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1U9Z
Asym. Unit
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Asym.Unit (184 KB)
Biol.Unit 1 (178 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PHOSPHORIBOSYL DIPHOSPHATE SYNTHASE COMPLEXED WITH AMP AND RIBOSE 5-PHOSPHATE
Authors
:
A. Kadziola, E. Johansson, C. H. Jepsen, J. Mcguire, S. Larsen, B. Hove- Jensen
Date
:
11 Aug 04 (Deposition) - 23 Aug 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Prpp Synthase; Ribose 5-Phosphate; Adenosine 5'- Monophosphate, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Kadziola, C. H. Jepsen, E. Johansson, J. Mcguire, S. Larsen, B. Hove-Jensen
Novel Class Iii Phosphoribosyl Diphosphate Synthase: Structure And Properties Of The Tetrameric, Phosphate-Activated, Non-Allosterically Inhibited Enzyme From Methanocaldococcus Jannaschii
J. Mol. Biol. V. 354 815 2005
(for further references see the
PDB file header
)
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: ADENOSINE MONOPHOSPHATE (AMPa)
1b: ADENOSINE MONOPHOSPHATE (AMPb)
1c: ADENOSINE MONOPHOSPHATE (AMPc)
1d: ADENOSINE MONOPHOSPHATE (AMPd)
2a: RIBOSE-5-PHOSPHATE (R5Pa)
2b: RIBOSE-5-PHOSPHATE (R5Pb)
2c: RIBOSE-5-PHOSPHATE (R5Pc)
2d: RIBOSE-5-PHOSPHATE (R5Pd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
AMP
4
Ligand/Ion
ADENOSINE MONOPHOSPHATE
2
R5P
4
Ligand/Ion
RIBOSE-5-PHOSPHATE
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:163 , ASP A:212 , ILE A:214 , ILE A:215 , SER A:216 , THR A:217 , GLY A:218 , GLY A:219 , THR A:220 , HOH A:5445
BINDING SITE FOR RESIDUE R5P A 5301
2
AC2
SOFTWARE
ASP B:163 , ASP B:212 , ILE B:214 , ILE B:215 , SER B:216 , THR B:217 , GLY B:218 , GLY B:219 , THR B:220 , HOH B:6445
BINDING SITE FOR RESIDUE R5P B 6301
3
AC3
SOFTWARE
ASP C:163 , ASP C:212 , ILE C:214 , ILE C:215 , SER C:216 , THR C:217 , GLY C:218 , GLY C:219 , THR C:220 , HOH C:7445
BINDING SITE FOR RESIDUE R5P C 7301
4
AC4
SOFTWARE
ASP D:163 , ASP D:212 , ILE D:214 , SER D:216 , THR D:217 , GLY D:218 , GLY D:219 , THR D:220 , HOH D:8445
BINDING SITE FOR RESIDUE R5P D 8301
5
AC5
SOFTWARE
ARG A:92 , GLN A:93 , ASP A:94 , PHE A:97 , HIS A:125 , PHE B:32 , ASP B:34 , GLU B:36 , HOH B:5424 , HOH B:5437
BINDING SITE FOR RESIDUE AMP B 5302
6
AC6
SOFTWARE
PHE A:32 , ASP A:34 , GLU A:36 , ARG B:92 , GLN B:93 , ASP B:94 , PHE B:97 , HIS B:125 , HOH B:6424 , HOH B:6437
BINDING SITE FOR RESIDUE AMP B 6302
7
AC7
SOFTWARE
ARG C:92 , GLN C:93 , PHE C:97 , HIS C:125 , PHE D:32 , ASP D:34 , GLU D:36 , HOH D:7424 , HOH D:7437
BINDING SITE FOR RESIDUE AMP D 7302
8
AC8
SOFTWARE
PHE C:32 , ASP C:34 , GLU C:36 , HOH C:8424 , HOH C:8437 , ARG D:92 , GLN D:93 , PHE D:97 , HIS D:125
BINDING SITE FOR RESIDUE AMP C 8302
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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
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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, 8)
Info
All SCOP Domains
1a: SCOP_d1u9za1 (A:1-155)
1b: SCOP_d1u9zb1 (B:1-155)
1c: SCOP_d1u9zb2 (B:156-284)
1d: SCOP_d1u9zc1 (C:1-155)
1e: SCOP_d1u9zc2 (C:156-284)
1f: SCOP_d1u9zd1 (D:1-155)
1g: SCOP_d1u9zd2 (D:156-284)
1h: SCOP_d1u9za2 (A:156-284)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PRTase-like
(145)
Superfamily
:
PRTase-like
(145)
Family
:
Phosphoribosylpyrophosphate synthetase-like
(6)
Protein domain
:
Phosphoribosylpyrophosphate synthetase
(5)
Methanocaldococcus jannaschii [TaxId: 2190]
(2)
1a
d1u9za1
A:1-155
1b
d1u9zb1
B:1-155
1c
d1u9zb2
B:156-284
1d
d1u9zc1
C:1-155
1e
d1u9zc2
C:156-284
1f
d1u9zd1
D:1-155
1g
d1u9zd2
D:156-284
1h
d1u9za2
A:156-284
[
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1u9zA01 (A:1-141,A:276-284)
1b: CATH_1u9zA02 (A:142-275)
1c: CATH_1u9zB02 (B:142-275)
1d: CATH_1u9zC02 (C:142-275)
1e: CATH_1u9zD02 (D:142-275)
1f: CATH_1u9zB01 (B:1-141,B:276-284)
1g: CATH_1u9zC01 (C:1-141,C:276-284)
1h: CATH_1u9zD01 (D:1-141,D:276-284)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.2020, no name defined]
(117)
Methanocaldococcus jannaschii. Organism_taxid: 2190.
(2)
1a
1u9zA01
A:1-141,A:276-284
1b
1u9zA02
A:142-275
1c
1u9zB02
B:142-275
1d
1u9zC02
C:142-275
1e
1u9zD02
D:142-275
1f
1u9zB01
B:1-141,B:276-284
1g
1u9zC01
C:1-141,C:276-284
1h
1u9zD01
D:1-141,D:276-284
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Pribosyltran_1u9zD01 (D:133-242)
1b: PFAM_Pribosyltran_1u9zD02 (D:133-242)
1c: PFAM_Pribosyltran_1u9zD03 (D:133-242)
1d: PFAM_Pribosyltran_1u9zD04 (D:133-242)
2a: PFAM_Pribosyltran_N_1u9zD05 (D:1-115)
2b: PFAM_Pribosyltran_N_1u9zD06 (D:1-115)
2c: PFAM_Pribosyltran_N_1u9zD07 (D:1-115)
2d: PFAM_Pribosyltran_N_1u9zD08 (D:1-115)
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(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PRTase-like
(59)
Family
:
Pribosyltran
(59)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth
(2)
1a
Pribosyltran-1u9zD01
D:133-242
1b
Pribosyltran-1u9zD02
D:133-242
1c
Pribosyltran-1u9zD03
D:133-242
1d
Pribosyltran-1u9zD04
D:133-242
Clan
:
no clan defined [family: Pribosyltran_N]
(7)
Family
:
Pribosyltran_N
(7)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth
(2)
2a
Pribosyltran_N-1u9zD05
D:1-115
2b
Pribosyltran_N-1u9zD06
D:1-115
2c
Pribosyltran_N-1u9zD07
D:1-115
2d
Pribosyltran_N-1u9zD08
D:1-115
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