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1RQI
Asym. Unit
Info
Asym.Unit (106 KB)
Biol.Unit 1 (99 KB)
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(1)
Title
:
ACTIVE CONFORMATION OF FARNESYL PYROPHOSPHATE SYNTHASE BOUND TO ISOPENTYL PYROPHOSPHATE AND DIMETHYLALLYL S-THIOLODIPHOSPHATE
Authors
:
D. J. Hosfield, Y. Zhang, D. R. Dougan, A. Brooun, L. W. Tari, R. V. Swanson, J. Finn
Date
:
05 Dec 03 (Deposition) - 02 Mar 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.42
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Isoprenyl Synthase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. J. Hosfield, Y. Zhang, D. R. Dougan, A. Brooun, L. W. Tari, R. V. Swanson, J. Finn
Structural Basis For Bisphosphonate-Mediated Inhibition Of Isoprenoid Biosynthesis
J. Biol. Chem. V. 279 8526 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 11)
Info
All Hetero Components
1a: DIPHOSPHATE (DPOa)
2a: DIMETHYLALLYL S-THIOLODIPHOSPHATE (DSTa)
2b: DIMETHYLALLYL S-THIOLODIPHOSPHATE (DSTb)
3a: ISOPENTYL PYROPHOSPHATE (IPRa)
3b: ISOPENTYL PYROPHOSPHATE (IPRb)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DPO
1
Ligand/Ion
DIPHOSPHATE
2
DST
2
Ligand/Ion
DIMETHYLALLYL S-THIOLODIPHOSPHATE
3
IPR
2
Ligand/Ion
ISOPENTYL PYROPHOSPHATE
4
MG
6
Ligand/Ion
MAGNESIUM ION
[
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Sites
(11, 11)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP B:244 , ASP B:248 , DST B:400 , HOH B:700 , HOH B:701 , HOH B:741
BINDING SITE FOR RESIDUE MG B 600
02
AC2
SOFTWARE
ASP B:105 , ASP B:111 , DST B:400 , MG B:602 , HOH B:704 , HOH B:705 , HOH B:862
BINDING SITE FOR RESIDUE MG B 601
03
AC3
SOFTWARE
ASP B:105 , ASP B:111 , DST B:400 , MG B:601 , HOH B:702 , HOH B:703
BINDING SITE FOR RESIDUE MG B 602
04
AC4
SOFTWARE
ASP A:244 , DST A:401 , HOH A:717 , HOH A:718 , HOH A:734
BINDING SITE FOR RESIDUE MG A 603
05
AC5
SOFTWARE
ASP A:105 , ASP A:111 , DST A:401 , MG A:605 , HOH A:721 , HOH A:722 , HOH A:738
BINDING SITE FOR RESIDUE MG A 604
06
AC6
SOFTWARE
ASP A:105 , ASP A:111 , ASP A:113 , DST A:401 , MG A:604 , HOH A:719 , HOH A:720
BINDING SITE FOR RESIDUE MG A 605
07
AC7
SOFTWARE
SER B:101 , ASP B:105 , ASP B:111 , ARG B:116 , MET B:175 , GLN B:179 , LYS B:202 , ASP B:244 , LYS B:258 , IPR B:500 , MG B:600 , MG B:601 , MG B:602 , HOH B:700 , HOH B:701 , HOH B:702 , HOH B:704
BINDING SITE FOR RESIDUE DST B 400
08
AC8
SOFTWARE
SER A:101 , LEU A:102 , ASP A:105 , ASP A:111 , ARG A:116 , MET A:175 , GLN A:179 , LYS A:202 , ASP A:244 , LYS A:258 , IPR A:501 , MG A:603 , MG A:604 , MG A:605 , HOH A:717 , HOH A:718 , HOH A:719 , HOH A:720 , HOH A:721 , HOH A:734 , HOH A:738 , HOH A:835
BINDING SITE FOR RESIDUE DST A 401
09
AC9
SOFTWARE
GLY B:65 , LYS B:66 , ARG B:69 , HIS B:98 , LEU B:102 , ARG B:117 , PHE B:240 , GLN B:241 , ASP B:244 , DST B:400 , HOH B:706 , HOH B:707 , HOH B:710 , HOH B:711 , HOH B:712 , HOH B:713
BINDING SITE FOR RESIDUE IPR B 500
10
BC1
SOFTWARE
GLY A:65 , LYS A:66 , ARG A:69 , HIS A:98 , ARG A:117 , THR A:203 , PHE A:240 , GLN A:241 , ASP A:244 , DST A:401 , HOH A:723 , HOH A:724 , HOH A:727 , HOH A:728 , HOH A:729 , HOH A:730
BINDING SITE FOR RESIDUE IPR A 501
11
BC2
SOFTWARE
GLN A:27 , ALA A:30 , CYS A:31 , GLN A:34 , PHE A:71 , TYR A:74 , ALA A:75 , HIS A:78 , HOH A:844 , HOH A:872 , HIS B:189
BINDING SITE FOR RESIDUE DPO A 606
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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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: POLYPRENYL_SYNTHASE_1 (A:102-118,B:102-118)
2: POLYPRENYL_SYNTHASE_2 (A:236-248,B:236-248)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
POLYPRENYL_SYNTHASE_1
PS00723
Polyprenyl synthases signature 1.
ISPA_ECOLI
81-97
2
A:102-118
B:102-118
2
POLYPRENYL_SYNTHASE_2
PS00444
Polyprenyl synthases signature 2.
ISPA_ECOLI
215-227
2
A:236-248
B:236-248
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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, 2)
Info
All SCOP Domains
1a: SCOP_d1rqia_ (A:)
1b: SCOP_d1rqib_ (B:)
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Class
:
All alpha proteins
(14657)
Fold
:
Terpenoid synthases
(196)
Superfamily
:
Terpenoid synthases
(196)
Family
:
Isoprenyl diphosphate synthases
(57)
Protein domain
:
Farnesyl diphosphate synthase (geranyltranstransferase)
(8)
Escherichia coli [TaxId: 562]
(2)
1a
d1rqia_
A:
1b
d1rqib_
B:
[
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]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1rqiA00 (A:21-320)
1b: CATH_1rqiB00 (B:23-320)
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Organisms
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Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Farnesyl Diphosphate Synthase
(109)
Homologous Superfamily
:
Farnesyl Diphosphate Synthase
(109)
Escherichia coli. Organism_taxid: 562.
(2)
1a
1rqiA00
A:21-320
1b
1rqiB00
B:23-320
[
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]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_polyprenyl_synt_1rqiB01 (B:53-316)
1b: PFAM_polyprenyl_synt_1rqiB02 (B:53-316)
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Clan
:
no clan defined [family: polyprenyl_synt]
(86)
Family
:
polyprenyl_synt
(86)
Escherichia coli (strain K12)
(2)
1a
polyprenyl_synt-1rqiB01
B:53-316
1b
polyprenyl_synt-1rqiB02
B:53-316
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Asymmetric Unit 1
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