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1YHM
Asym. Unit
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
(5, 63)
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
3
Ligand/Ion
4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE
2
IPE
3
Ligand/Ion
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
3
MG
9
Ligand/Ion
MAGNESIUM ION
4
MSE
45
Mod. Amino Acid
SELENOMETHIONINE
5
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(18, 18)
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)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
View:
Select:
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
AC6
SOFTWARE
GLN C:21 , HIS C:141
BINDING SITE FOR RESIDUE SO4 C 2370
07
AC7
SOFTWARE
ASP B:250 , AHD B:1901 , HOH B:1906 , HOH B:1907 , HOH B:1909
BINDING SITE FOR RESIDUE MG B 1401
08
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
09
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
10
BC1
SOFTWARE
ASP C:250 , AHD C:2901 , HOH C:2906 , HOH C:2907 , HOH C:2909
BINDING SITE FOR RESIDUE MG C 2401
11
BC2
SOFTWARE
ASP C:98 , ASP C:102 , MG C:2403 , AHD C:2901 , HOH C:2903 , HOH C:2904
BINDING SITE FOR RESIDUE MG C 2402
12
BC3
SOFTWARE
ASP C:98 , ASP C:102 , MG C:2402 , AHD C:2901 , HOH C:2902 , HOH C:2905 , HOH C:2908
BINDING SITE FOR RESIDUE MG C 2403
13
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
14
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
15
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
16
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
17
BC8
SOFTWARE
ASP C:98 , ASP C:102 , ARG C:107 , GLN C:167 , LYS C:207 , GLN C:247 , ASP C:250 , LYS C:264 , MG C:2401 , MG C:2402 , MG C:2403 , IPE C:2900 , HOH C:2902 , HOH C:2904 , HOH C:2905 , HOH C:2906 , HOH C:2907 , HOH C:2909
BINDING SITE FOR RESIDUE AHD C 2901
18
BC9
SOFTWARE
GLY C:47 , LYS C:48 , ARG C:51 , GLN C:91 , ARG C:108 , THR C:208 , PHE C:246 , GLN C:247 , ASP C:250 , LYS C:362 , AHD C:2901
BINDING SITE FOR RESIDUE IPE C 2900
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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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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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, 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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Organisms
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(
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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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(
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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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