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1YHM
Biol. Unit 1
Info
Asym.Unit (193 KB)
Biol.Unit 1 (122 KB)
Biol.Unit 2 (123 KB)
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(1)
Title
:
STRUCTURE OF THE COMPLEX OF TRYPANOSOMA CRUZI FARNESYL DISPHOSPHATE SYNTHASE WITH ALENDRONATE, ISOPENTENYL DIPHOSPHATE AND MG+2
Authors
:
S. B. Gabelli, J. S. Mclellan, A. Montalvetti, E. Oldfield, R. Docampo,
Date
:
09 Jan 05 (Deposition) - 20 Dec 05 (Release) - 17 Apr 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C (2x)
Keywords
:
Farnesyl Diphosphate Synthase, Alendronate, Isopentenyl Diphosphate, Mevalonate Patway, Geranyl Transferase, Dimethylallyl Transferase, Fpps, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. B. Gabelli, J. S. Mclellan, A. Montalvetti, E. Oldfield, R. Docampo L. M. Amzel
Structure And Mechanism Of The Farnesyl Diphosphate Synthas From Trypanosoma Cruzi: Implications For Drug Design.
Proteins V. 62 80 2005
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Hetero Components
(4, 36)
Info
All Hetero Components
1a: 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDI... (AHDa)
1b: 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDI... (AHDb)
1c: 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDI... (AHDc)
2a: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIP... (IPEa)
2b: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIP... (IPEb)
2c: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIP... (IPEc)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
4a: SELENOMETHIONINE (MSEa)
4aa: SELENOMETHIONINE (MSEaa)
4ab: SELENOMETHIONINE (MSEab)
4ac: SELENOMETHIONINE (MSEac)
4ad: SELENOMETHIONINE (MSEad)
4ae: SELENOMETHIONINE (MSEae)
4af: SELENOMETHIONINE (MSEaf)
4ag: SELENOMETHIONINE (MSEag)
4ah: SELENOMETHIONINE (MSEah)
4ai: SELENOMETHIONINE (MSEai)
4aj: SELENOMETHIONINE (MSEaj)
4ak: SELENOMETHIONINE (MSEak)
4al: SELENOMETHIONINE (MSEal)
4am: SELENOMETHIONINE (MSEam)
4an: SELENOMETHIONINE (MSEan)
4ao: SELENOMETHIONINE (MSEao)
4ap: SELENOMETHIONINE (MSEap)
4aq: SELENOMETHIONINE (MSEaq)
4ar: SELENOMETHIONINE (MSEar)
4as: SELENOMETHIONINE (MSEas)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
4m: SELENOMETHIONINE (MSEm)
4n: SELENOMETHIONINE (MSEn)
4o: SELENOMETHIONINE (MSEo)
4p: SELENOMETHIONINE (MSEp)
4q: SELENOMETHIONINE (MSEq)
4r: SELENOMETHIONINE (MSEr)
4s: SELENOMETHIONINE (MSEs)
4t: SELENOMETHIONINE (MSEt)
4u: SELENOMETHIONINE (MSEu)
4v: SELENOMETHIONINE (MSEv)
4w: SELENOMETHIONINE (MSEw)
4x: SELENOMETHIONINE (MSEx)
4y: SELENOMETHIONINE (MSEy)
4z: SELENOMETHIONINE (MSEz)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AHD
2
Ligand/Ion
4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE
2
IPE
2
Ligand/Ion
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
MSE
30
Mod. Amino Acid
SELENOMETHIONINE
5
SO4
2
Ligand/Ion
SULFATE ION
[
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Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC7 (SOFTWARE)
07: AC8 (SOFTWARE)
08: AC9 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC5 (SOFTWARE)
11: BC6 (SOFTWARE)
12: BC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:250 , AHD A:901 , HOH A:905 , HOH A:906
BINDING SITE FOR RESIDUE MG A 401
02
AC2
SOFTWARE
ASP A:98 , ASP A:102 , MG A:403 , AHD A:901 , HOH A:902 , HOH A:903
BINDING SITE FOR RESIDUE MG A 402
03
AC3
SOFTWARE
ASP A:98 , ASP A:102 , ASP A:170 , MG A:402 , AHD A:901 , HOH A:904 , HOH A:907
BINDING SITE FOR RESIDUE MG A 403
04
AC4
SOFTWARE
HIS A:141 , LYS B:158
BINDING SITE FOR RESIDUE SO4 A 370
05
AC5
SOFTWARE
GLN B:21 , HIS B:141
BINDING SITE FOR RESIDUE SO4 B 1370
06
AC7
SOFTWARE
ASP B:250 , AHD B:1901 , HOH B:1906 , HOH B:1907 , HOH B:1909
BINDING SITE FOR RESIDUE MG B 1401
07
AC8
SOFTWARE
ASP B:98 , ASP B:102 , MG B:1403 , AHD B:1901 , HOH B:1903 , HOH B:1904
BINDING SITE FOR RESIDUE MG B 1402
08
AC9
SOFTWARE
ASP B:98 , ASP B:102 , ASP B:170 , MG B:1402 , AHD B:1901 , HOH B:1902 , HOH B:1905 , HOH B:1908
BINDING SITE FOR RESIDUE MG B 1403
09
BC4
SOFTWARE
ASP A:98 , ASP A:102 , ARG A:107 , LYS A:207 , TYR A:211 , GLN A:247 , ASP A:250 , LYS A:264 , MG A:401 , MG A:402 , MG A:403 , IPE A:900 , HOH A:902 , HOH A:903 , HOH A:904 , HOH A:905 , HOH A:906
BINDING SITE FOR RESIDUE AHD A 901
10
BC5
SOFTWARE
GLY A:47 , LYS A:48 , ARG A:51 , GLN A:91 , ARG A:108 , THR A:208 , TYR A:211 , PHE A:246 , LYS A:362 , AHD A:901
BINDING SITE FOR RESIDUE IPE A 900
11
BC6
SOFTWARE
ASP B:98 , ASP B:102 , ARG B:107 , LYS B:207 , TYR B:211 , GLN B:247 , ASP B:250 , LYS B:264 , MG B:1401 , MG B:1402 , MG B:1403 , IPE B:1900 , HOH B:1902 , HOH B:1904 , HOH B:1905 , HOH B:1906 , HOH B:1907 , HOH B:1909
BINDING SITE FOR RESIDUE AHD B 1901
12
BC7
SOFTWARE
GLY B:47 , LYS B:48 , ARG B:51 , GLN B:91 , ARG B:108 , THR B:208 , TYR B:211 , PHE B:246 , ASP B:250 , LYS B:362 , AHD B:1901 , HOH B:1924 , HOH B:1932 , HOH B:1943
BINDING SITE FOR RESIDUE IPE B 1900
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d1yhma_ (A:)
1b: SCOP_d1yhmb_ (B:)
1c: SCOP_d1yhmc_ (C:)
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Protein Domains
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(
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Organisms
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)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Terpenoid synthases
(196)
Superfamily
:
Terpenoid synthases
(196)
Family
:
automated matches
(68)
Protein domain
:
automated matches
(68)
Trypanosoma cruzi [TaxId: 5693]
(14)
1a
d1yhma_
A:
1b
d1yhmb_
B:
1c
d1yhmc_
C:
[
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_1yhmA00 (A:2-362)
1b: CATH_1yhmB00 (B:2-362)
1c: CATH_1yhmC00 (C:2-362)
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)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Farnesyl Diphosphate Synthase
(109)
Homologous Superfamily
:
Farnesyl Diphosphate Synthase
(109)
Trypanosoma cruzi. Organism_taxid: 5693.
(7)
1a
1yhmA00
A:2-362
1b
1yhmB00
B:2-362
1c
1yhmC00
C:2-362
[
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Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_polyprenyl_synt_1yhmC01 (C:35-323)
1b: PFAM_polyprenyl_synt_1yhmC02 (C:35-323)
1c: PFAM_polyprenyl_synt_1yhmC03 (C:35-323)
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Clan
:
no clan defined [family: polyprenyl_synt]
(86)
Family
:
polyprenyl_synt
(86)
Trypanosoma cruzi
(3)
1a
polyprenyl_synt-1yhmC01
C:35-323
1b
polyprenyl_synt-1yhmC02
C:35-323
1c
polyprenyl_synt-1yhmC03
C:35-323
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