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2Q80
Asym. Unit
Info
Asym.Unit (287 KB)
Biol.Unit 1 (275 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN GERANYLGERANYL PYROPHOSPHATE SYNTHASE BOUND TO GGPP
Authors
:
K. L. Kavanagh, J. E. Dunford, G. Bunkoczi, C. Smee, F. Von Delft, C. Arr J. Weigelt, A. Edwards, M. Sundstrom, U. Oppermann, Structural Geno Consortium (Sgc)
Date
:
08 Jun 07 (Deposition) - 19 Jun 07 (Release) - 05 Dec 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Isoprenoid Pathway, Isopentenyl Transferase, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. L. Kavanagh, J. E. Dunford, G. Bunkoczi, R. G. Russell, U. Oppermann
The Crystal Structure Of Human Geranylgeranyl Pyrophosphate Synthase Reveals A Novel Hexameric Arrangement And Inhibitory Product Binding
J. Biol. Chem. V. 281 22004 2006
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Hetero Components
(2, 18)
Info
All Hetero Components
1a: GERANYLGERANYL DIPHOSPHATE (GRGa)
1b: GERANYLGERANYL DIPHOSPHATE (GRGb)
1c: GERANYLGERANYL DIPHOSPHATE (GRGc)
1d: GERANYLGERANYL DIPHOSPHATE (GRGd)
1e: GERANYLGERANYL DIPHOSPHATE (GRGe)
1f: GERANYLGERANYL DIPHOSPHATE (GRGf)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
2i: MAGNESIUM ION (MGi)
2j: MAGNESIUM ION (MGj)
2k: MAGNESIUM ION (MGk)
2l: MAGNESIUM ION (MGl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GRG
6
Ligand/Ion
GERANYLGERANYL DIPHOSPHATE
2
MG
12
Ligand/Ion
MAGNESIUM ION
[
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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:64 , ASP A:68 , GLN A:126 , MG A:401 , GRG A:500
BINDING SITE FOR RESIDUE MG A 400
02
AC2
SOFTWARE
ASP A:64 , ASP A:68 , LYS A:202 , MG A:400 , GRG A:500
BINDING SITE FOR RESIDUE MG A 401
03
AC3
SOFTWARE
ASP B:64 , ASP B:68 , GLN B:126 , ASP B:129 , MG B:401 , GRG B:500
BINDING SITE FOR RESIDUE MG B 400
04
AC4
SOFTWARE
ASP B:64 , ASP B:68 , GLU B:210 , MG B:400 , GRG B:500
BINDING SITE FOR RESIDUE MG B 401
05
AC5
SOFTWARE
ASP C:64 , ASP C:68 , GLN C:126 , ASP C:129 , GRG C:500
BINDING SITE FOR RESIDUE MG C 400
06
AC6
SOFTWARE
ASP C:64 , ASP C:68 , GRG C:500
BINDING SITE FOR RESIDUE MG C 401
07
AC7
SOFTWARE
ASP D:64 , ASP D:68 , GLN D:126 , ASP D:129 , GRG D:500
BINDING SITE FOR RESIDUE MG D 400
08
AC8
SOFTWARE
ASP D:64 , ASP D:68 , GRG D:500
BINDING SITE FOR RESIDUE MG D 401
09
AC9
SOFTWARE
ASP E:64 , ASP E:68 , MG E:401 , GRG E:500
BINDING SITE FOR RESIDUE MG E 400
10
BC1
SOFTWARE
ASP E:64 , ASP E:68 , MG E:400 , GRG E:500
BINDING SITE FOR RESIDUE MG E 401
11
BC2
SOFTWARE
ASP F:64 , ASP F:68 , GLN F:126 , ASP F:129 , MG F:401 , GRG F:500
BINDING SITE FOR RESIDUE MG F 400
12
BC3
SOFTWARE
ASP F:64 , ASP F:68 , MG F:400 , GRG F:500
BINDING SITE FOR RESIDUE MG F 401
13
BC4
SOFTWARE
LEU A:31 , SER A:32 , THR A:53 , ASP A:64 , ASP A:68 , ARG A:73 , GLN A:126 , LYS A:151 , LEU A:155 , PHE A:156 , ALA A:159 , VAL A:160 , GLN A:185 , ASP A:188 , LYS A:202 , LYS A:212 , MG A:400 , MG A:401
BINDING SITE FOR RESIDUE GRG A 500
14
BC5
SOFTWARE
SER B:32 , THR B:53 , SER B:60 , ASP B:64 , ASP B:68 , ARG B:73 , GLN B:126 , LYS B:151 , ALA B:159 , GLN B:185 , LYS B:202 , LYS B:212 , MG B:400 , MG B:401
BINDING SITE FOR RESIDUE GRG B 500
15
BC6
SOFTWARE
ARG C:28 , SER C:32 , THR C:53 , HIS C:57 , ASP C:64 , ASP C:68 , ARG C:73 , GLN C:126 , LYS C:151 , PHE C:156 , ALA C:159 , MET C:163 , GLN C:185 , ASP C:188 , LYS C:212 , MG C:400 , MG C:401
BINDING SITE FOR RESIDUE GRG C 500
16
BC7
SOFTWARE
SER D:32 , THR D:53 , ASP D:64 , ASP D:68 , ARG D:73 , GLN D:126 , LYS D:151 , PHE D:156 , ALA D:159 , VAL D:160 , GLN D:185 , ASP D:188 , LYS D:202 , LYS D:212 , MG D:400 , MG D:401
BINDING SITE FOR RESIDUE GRG D 500
17
BC8
SOFTWARE
LEU E:31 , SER E:32 , PHE E:35 , THR E:53 , ASP E:64 , ASP E:68 , ARG E:73 , LYS E:151 , ALA E:159 , GLN E:185 , ASP E:188 , LYS E:202 , LYS E:212 , MG E:400 , MG E:401
BINDING SITE FOR RESIDUE GRG E 500
18
BC9
SOFTWARE
ASP F:64 , ASP F:68 , ARG F:73 , GLN F:126 , LYS F:151 , LEU F:155 , GLN F:185 , ASP F:188 , LYS F:202 , MG F:400 , MG F:401
BINDING SITE FOR RESIDUE GRG F 500
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: POLYPRENYL_SYNTHASE_1 (A:61-75,B:61-75,C:61-75,D:61-75,E:...)
2: POLYPRENYL_SYNTHASE_2 (A:180-192,B:180-192,C:180-192,D:18...)
;
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.
GGPPS_HUMAN
61-75
6
A:61-75
B:61-75
C:61-75
D:61-75
E:61-75
F:61-75
2
POLYPRENYL_SYNTHASE_2
PS00444
Polyprenyl synthases signature 2.
GGPPS_HUMAN
180-192
6
A:180-192
B:180-192
C:180-192
D:180-192
E:180-192
F:180-192
[
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Exons
(3, 18)
Info
All Exons
Exon 1.5a (A:6-24 | B:6-24 | C:6-24 | D:6-24 ...)
Exon 1.6 (A:24-47 | B:24-47 | C:24-47 | D:24...)
Exon 1.7f (A:48-296 (gaps) | B:48-295 (gaps) ...)
View:
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All Exon Boundaries
1: Boundary 1.2b/1.5a
2: Boundary 1.5a/1.6
3: Boundary 1.6/1.7f
4: Boundary 1.7f/-
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.2b
ENST00000358966
2b
ENSE00001509902
chr1:
235491753-235491813
61
GGPPS_HUMAN
-
0
0
-
-
1.5a
ENST00000358966
5a
ENSE00002187801
chr1:
235498557-235498649
93
GGPPS_HUMAN
1-24
24
6
A:6-24
B:6-24
C:6-24
D:6-24
E:6-24
F:6-24
19
19
19
19
19
19
1.6
ENST00000358966
6
ENSE00001738962
chr1:
235505023-235505093
71
GGPPS_HUMAN
24-47
24
6
A:24-47
B:24-47
C:24-47
D:24-47
E:24-47
F:24-47
24
24
24
24
24
24
1.7f
ENST00000358966
7f
ENSE00001758247
chr1:
235505326-235507840
2515
GGPPS_HUMAN
48-300
253
6
A:48-296 (gaps)
B:48-295 (gaps)
C:48-295 (gaps)
D:48-295 (gaps)
E:48-295 (gaps)
F:48-295 (gaps)
249
248
248
248
248
248
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SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d2q80a1 (A:6-296)
1b: SCOP_d2q80b_ (B:)
1c: SCOP_d2q80c_ (C:)
1d: SCOP_d2q80d_ (D:)
1e: SCOP_d2q80e_ (E:)
1f: SCOP_d2q80f_ (F:)
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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
:
Isoprenyl diphosphate synthases
(57)
Protein domain
:
Geranylgeranyl pyrophosphate synthetase
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d2q80a1
A:6-296
1b
d2q80b_
B:
1c
d2q80c_
C:
1d
d2q80d_
D:
1e
d2q80e_
E:
1f
d2q80f_
F:
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_polyprenyl_synt_2q80F01 (F:12-265)
1b: PFAM_polyprenyl_synt_2q80F02 (F:12-265)
1c: PFAM_polyprenyl_synt_2q80F03 (F:12-265)
1d: PFAM_polyprenyl_synt_2q80F04 (F:12-265)
1e: PFAM_polyprenyl_synt_2q80F05 (F:12-265)
1f: PFAM_polyprenyl_synt_2q80F06 (F:12-265)
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Clan
:
no clan defined [family: polyprenyl_synt]
(86)
Family
:
polyprenyl_synt
(86)
Homo sapiens (Human)
(19)
1a
polyprenyl_synt-2q80F01
F:12-265
1b
polyprenyl_synt-2q80F02
F:12-265
1c
polyprenyl_synt-2q80F03
F:12-265
1d
polyprenyl_synt-2q80F04
F:12-265
1e
polyprenyl_synt-2q80F05
F:12-265
1f
polyprenyl_synt-2q80F06
F:12-265
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Asym.Unit (287 KB)
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