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1E6A
Asym. Unit
Info
Asym.Unit (113 KB)
Biol.Unit 1 (107 KB)
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(1)
Title
:
FLUORIDE-INHIBITED SUBSTRATE COMPLEX OF SACCHAROMYCES CEREVISIAE INORGANIC PYROPHOSPHATASE
Authors
:
P. Heikinheimo, V. Tuominen, A. -K. Ahonen, A. Teplyakov, B. S. Cooperman, A. A. Baykov, R. Lahti, A. Goldman
Date
:
09 Aug 00 (Deposition) - 19 Mar 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Phosphoryl Transfer, Hydrolysis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Heikinheimo, V. Tuominen, A. -K. Ahonen, A. Teplyakov, B. S. Cooperman, A. A. Baykov, R. Lahti, A. Goldman
Toward A Quantum-Mechanical Description Of Metal- Assisted Phosphoryl Transfer In Pyrophosphatase
Proc. Natl. Acad. Sci. Usa V. 98 3121 2001
[
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Hetero Components
(5, 15)
Info
All Hetero Components
1a: FLUORIDE ION (Fa)
1b: FLUORIDE ION (Fb)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
2e: MANGANESE (II) ION (MNe)
2f: MANGANESE (II) ION (MNf)
2g: MANGANESE (II) ION (MNg)
2h: MANGANESE (II) ION (MNh)
3a: SODIUM ION (NAa)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
5a: PYROPHOSPHATE 2- (POPa)
5b: PYROPHOSPHATE 2- (POPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
F
2
Ligand/Ion
FLUORIDE ION
2
MN
8
Ligand/Ion
MANGANESE (II) ION
3
NA
1
Ligand/Ion
SODIUM ION
4
PO4
2
Ligand/Ion
PHOSPHATE ION
5
POP
2
Ligand/Ion
PYROPHOSPHATE 2-
[
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Sites
(15, 15)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:115 , ASP A:120 , ASP A:152 , MN A:2002 , MN A:2004 , HOH A:2334 , POP A:3001 , F A:4001 , NA A:4740
BINDING SITE FOR RESIDUE MN A2001
02
AC2
SOFTWARE
ASP A:120 , MN A:2001 , HOH A:2335 , HOH A:2336 , HOH A:2337 , POP A:3001 , F A:4001
BINDING SITE FOR RESIDUE MN A2002
03
AC3
SOFTWARE
GLU A:58 , HOH A:2338 , HOH A:2339 , HOH A:2340 , POP A:3001 , NA A:4740
BINDING SITE FOR RESIDUE MN A2003
04
AC4
SOFTWARE
ASP A:147 , ASP A:152 , MN A:2001 , HOH A:2341 , HOH A:2342 , POP A:3001
BINDING SITE FOR RESIDUE MN A2004
05
AC5
SOFTWARE
ASP A:115 , ASP A:117 , ASP A:120 , MN A:2001 , MN A:2002 , HOH A:2336 , POP A:3001 , NA A:4740
BINDING SITE FOR RESIDUE F A4001
06
AC6
SOFTWARE
ASP A:115 , ASP A:117 , MN A:2001 , MN A:2003 , HOH A:2165 , HOH A:2339 , POP A:3001 , F A:4001
BINDING SITE FOR RESIDUE NA A4740
07
AC7
SOFTWARE
ASP B:1115 , ASP B:1120 , ASP B:1152 , MN B:2006 , MN B:2008 , HOH B:2294 , POP B:3002 , PO4 B:3004 , F B:4010
BINDING SITE FOR RESIDUE MN B2005
08
AC8
SOFTWARE
ASP B:1120 , MN B:2005 , HOH B:2295 , HOH B:2296 , HOH B:2297 , POP B:3002 , PO4 B:3004 , F B:4010
BINDING SITE FOR RESIDUE MN B2006
09
AC9
SOFTWARE
GLU B:1058 , HOH B:2298 , HOH B:2299 , HOH B:2300 , POP B:3002 , PO4 B:3003 , PO4 B:3004
BINDING SITE FOR RESIDUE MN B2007
10
BC1
SOFTWARE
ASP B:1147 , ASP B:1152 , MN B:2005 , HOH B:2301 , HOH B:2302 , POP B:3002 , PO4 B:3003 , PO4 B:3004
BINDING SITE FOR RESIDUE MN B2008
11
BC2
SOFTWARE
LYS B:1056 , GLU B:1058 , TYR B:1093 , ASP B:1115 , ASP B:1117 , ASP B:1120 , ASP B:1152 , MN B:2005 , MN B:2006 , MN B:2007 , MN B:2008 , HOH B:2096 , HOH B:2297 , HOH B:2301 , HOH B:2302 , POP B:3002 , PO4 B:3003 , F B:4010
BINDING SITE FOR RESIDUE PO4 B3004
12
BC3
SOFTWARE
ASP B:1115 , ASP B:1117 , ASP B:1120 , MN B:2005 , MN B:2006 , HOH B:2294 , HOH B:2295 , HOH B:2297 , POP B:3002 , PO4 B:3004
BINDING SITE FOR RESIDUE F B4010
13
BC4
SOFTWARE
LYS A:56 , GLU A:58 , ARG A:78 , TYR A:93 , ASP A:115 , ASP A:117 , ASP A:120 , ASP A:147 , ASP A:152 , TYR A:192 , LYS A:193 , MN A:2001 , MN A:2002 , MN A:2003 , MN A:2004 , HOH A:2145 , HOH A:2335 , HOH A:2339 , HOH A:2340 , HOH A:2341 , F A:4001 , NA A:4740
BINDING SITE FOR RESIDUE POP A3001
14
BC5
SOFTWARE
LYS B:1056 , GLU B:1058 , ARG B:1078 , TYR B:1093 , ASP B:1115 , ASP B:1117 , ASP B:1120 , ASP B:1147 , ASP B:1152 , TYR B:1192 , LYS B:1193 , MN B:2005 , MN B:2006 , MN B:2007 , MN B:2008 , HOH B:2096 , HOH B:2297 , HOH B:2300 , HOH B:2301 , HOH B:2303 , PO4 B:3003 , PO4 B:3004 , F B:4010
BINDING SITE FOR RESIDUE POP B3002
15
BC6
SOFTWARE
LYS B:1056 , GLU B:1058 , ARG B:1078 , ASP B:1147 , TYR B:1192 , LYS B:1193 , MN B:2007 , MN B:2008 , HOH B:2300 , HOH B:2301 , HOH B:2303 , POP B:3002 , PO4 B:3004
BINDING SITE FOR RESIDUE PO4 B3003
[
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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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PPASE (A:115-121,B:1115-1121)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PPASE
PS00387
Inorganic pyrophosphatase signature.
IPYR_YEAST
116-122
2
A:115-121
B:1115-1121
[
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Exons
(1, 2)
Info
All Exons
Exon 1.1 (A:1-284 | B:1001-1282)
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
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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
1.1
YBR011C
1
YBR011C.1
II:257973-257110
864
IPYR_YEAST
1-287
287
2
A:1-284
B:1001-1282
284
282
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1e6aa_ (A:)
1b: SCOP_d1e6ab_ (B:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
OB-fold
(1179)
Superfamily
:
Inorganic pyrophosphatase
(69)
Family
:
Inorganic pyrophosphatase
(56)
Protein domain
:
Inorganic pyrophosphatase
(41)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(19)
1a
d1e6aa_
A:
1b
d1e6ab_
B:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1e6aB00 (B:1001-1282)
1b: CATH_1e6aA00 (A:1-284)
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Inorganic Pyrophosphatase
(59)
Homologous Superfamily
:
Inorganic Pyrophosphatase
(59)
Saccharomyces cerevisiae. Organism_taxid: 4932.
(2)
1a
1e6aB00
B:1001-1282
1b
1e6aA00
A:1-284
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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