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2IK6
Asym. Unit
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Asym.Unit (105 KB)
Biol.Unit 1 (100 KB)
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(1)
Title
:
YEAST INORGANIC PYROPHOSPHATASE VARIANT D120E WITH MAGNESIUM AND PHOSPHATE
Authors
:
E. Oksanen, A. K. Ahonen, H. Tuominen, V. Tuominen, R. Lahti, A. Goldman, P. Heikinheimo
Date
:
02 Oct 06 (Deposition) - 13 Feb 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Inorganic Pyrophosphatase, Mechanism, X-Ray Crystallography, Structure-Function, Mutagenesis, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Oksanen, A. K. Ahonen, H. Tuominen, V. Tuominen, R. Lahti, A. Goldman, P. Heikinheimo
A Complete Structural Description Of The Catalytic Cycle Of Yeast Pyrophosphatase.
Biochemistry V. 46 1228 2007
(for further references see the
PDB file header
)
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Hetero Components
(3, 8)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
5
Ligand/Ion
MAGNESIUM ION
2
MPD
1
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
PO4
2
Ligand/Ion
PHOSPHATE ION
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:115 , GLU A:120 , ASP A:152 , HOH A:339 , HOH A:481 , HOH A:503
BINDING SITE FOR RESIDUE MG A 287
2
AC2
SOFTWARE
PO4 A:289 , HOH A:465 , HOH A:490 , HOH A:498
BINDING SITE FOR RESIDUE MG A 288
3
AC3
SOFTWARE
ASP B:115 , GLU B:120 , ASP B:152 , HOH B:294 , HOH B:578 , HOH B:579
BINDING SITE FOR RESIDUE MG B 287
4
AC4
SOFTWARE
MG B:289 , PO4 B:290 , HOH B:451 , HOH B:452 , HOH B:487 , HOH B:564 , HOH B:588
BINDING SITE FOR RESIDUE MG B 288
5
AC5
SOFTWARE
MG B:288 , HOH B:355 , HOH B:452 , HOH B:487 , HOH B:505 , HOH B:582 , HOH B:588
BINDING SITE FOR RESIDUE MG B 289
6
AC6
SOFTWARE
ARG B:78 , ASP B:147 , TYR B:192 , LYS B:193 , MG B:288 , HOH B:334 , HOH B:336 , HOH B:451 , HOH B:452 , HOH B:564 , HOH B:579 , HOH B:588
BINDING SITE FOR RESIDUE PO4 B 290
7
AC7
SOFTWARE
ARG A:78 , ASP A:147 , TYR A:192 , LYS A:193 , MG A:288 , HOH A:358 , HOH A:414 , HOH A:461 , HOH A:490 , HOH A:498 , HOH A:503
BINDING SITE FOR RESIDUE PO4 A 289
8
AC8
SOFTWARE
ASN B:186 , SER B:206 , GLY B:207 , HOH B:396 , HOH B:429 , HOH B:462
BINDING SITE FOR RESIDUE MPD B 291
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PPASE (A:115-121,B:115-121)
;
View:
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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:115-121
[
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Exons
(1, 2)
Info
All Exons
Exon 1.1 (A:1-282 (gaps) | B:1-282)
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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:1-282 (gaps)
B:1-282
282
282
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2ik6a_ (A:)
1b: SCOP_d2ik6b_ (B:)
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Protein Domains
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)
(
)
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
d2ik6a_
A:
1b
d2ik6b_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2ik6A00 (A:1-282)
1b: CATH_2ik6B00 (B:1-282)
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Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Inorganic Pyrophosphatase
(59)
Homologous Superfamily
:
Inorganic Pyrophosphatase
(59)
Baker's yeast (Saccharomyces cerevisiae)
(17)
1a
2ik6A00
A:1-282
1b
2ik6B00
B:1-282
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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