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1WGJ
Asym. Unit
Info
Asym.Unit (103 KB)
Biol.Unit 1 (98 KB)
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(1)
Title
:
STRUCTURE OF INORGANIC PYROPHOSPHATASE
Authors
:
P. Heikinheimo, J. Lehtonen, A. Goldman
Date
:
24 Oct 96 (Deposition) - 19 Nov 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Pyrophosphate Phosphohydrolase, Hydrolase, Manganese
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Heikinheimo, J. Lehtonen, A. Baykov, R. Lahti, B. S. Cooperman, A. Goldman
The Structural Basis For Pyrophosphatase Catalysis.
Structure V. 4 1491 1996
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 12)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1b: MANGANESE (II) ION (MNb)
1c: MANGANESE (II) ION (MNc)
1d: MANGANESE (II) ION (MNd)
1e: MANGANESE (II) ION (MNe)
1f: MANGANESE (II) ION (MNf)
1g: MANGANESE (II) ION (MNg)
1h: MANGANESE (II) ION (MNh)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
2d: PHOSPHATE ION (PO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MN
8
Ligand/Ion
MANGANESE (II) ION
2
PO4
4
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(14, 14)
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: ASA (UNKNOWN)
11: ASB (UNKNOWN)
12: BC1 (SOFTWARE)
13: BC2 (SOFTWARE)
14: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:115 , ASP A:120 , ASP A:152 , MN A:288 , PO4 A:292 , HOH A:293 , HOH A:294
BINDING SITE FOR RESIDUE MN A 287
02
AC2
SOFTWARE
ASP A:120 , MN A:287 , PO4 A:292 , HOH A:293 , HOH A:295 , HOH A:296 , HOH A:297
BINDING SITE FOR RESIDUE MN A 288
03
AC3
SOFTWARE
GLU A:58 , PO4 A:291 , PO4 A:292 , HOH A:298 , HOH A:299 , HOH A:300
BINDING SITE FOR RESIDUE MN A 289
04
AC4
SOFTWARE
ASP A:147 , ASP A:152 , PO4 A:291 , PO4 A:292 , HOH A:301 , HOH A:302
BINDING SITE FOR RESIDUE MN A 290
05
AC5
SOFTWARE
LYS A:56 , GLU A:58 , ARG A:78 , ASP A:147 , TYR A:192 , LYS A:193 , MN A:289 , MN A:290 , PO4 A:292 , HOH A:298 , HOH A:301 , HOH A:351 , HOH A:388
BINDING SITE FOR RESIDUE PO4 A 291
06
AC6
SOFTWARE
LYS A:56 , GLU A:58 , TYR A:93 , ASP A:115 , ASP A:120 , ASP A:152 , MN A:287 , MN A:288 , MN A:289 , MN A:290 , PO4 A:291 , HOH A:293 , HOH A:295 , HOH A:302 , HOH A:309
BINDING SITE FOR RESIDUE PO4 A 292
07
AC7
SOFTWARE
ASP B:115 , ASP B:120 , ASP B:152 , MN B:288 , MN B:290 , PO4 B:292 , HOH B:293 , HOH B:294
BINDING SITE FOR RESIDUE MN B 287
08
AC8
SOFTWARE
ASP B:120 , MN B:287 , PO4 B:292 , HOH B:293 , HOH B:295 , HOH B:296 , HOH B:297
BINDING SITE FOR RESIDUE MN B 288
09
AC9
SOFTWARE
GLU B:58 , PO4 B:291 , PO4 B:292 , HOH B:298 , HOH B:299 , HOH B:300
BINDING SITE FOR RESIDUE MN B 289
10
ASA
UNKNOWN
GLU A:48 , LYS A:56 , GLU A:58 , ARG A:78 , TYR A:89 , TYR A:93 , ASP A:115 , ASP A:117 , ASP A:120 , ASP A:147 , ASP A:152 , LYS A:154 , TYR A:192 , LYS A:193
ACTIVE SITE A.
11
ASB
UNKNOWN
GLU B:48 , LYS B:56 , GLU B:58 , ARG B:78 , TYR B:89 , TYR B:93 , ASP B:115 , ASP B:117 , ASP B:120 , ASP B:147 , ASP B:152 , LYS B:154 , TYR B:192 , LYS B:193
ACTIVE SITE B.
12
BC1
SOFTWARE
ASP B:147 , ASP B:152 , MN B:287 , PO4 B:291 , PO4 B:292 , HOH B:301 , HOH B:302
BINDING SITE FOR RESIDUE MN B 290
13
BC2
SOFTWARE
LYS B:56 , GLU B:58 , ARG B:78 , ASP B:147 , TYR B:192 , LYS B:193 , MN B:289 , MN B:290 , PO4 B:292 , HOH B:299 , HOH B:396 , HOH B:417
BINDING SITE FOR RESIDUE PO4 B 291
14
BC3
SOFTWARE
LYS B:56 , GLU B:58 , TYR B:93 , ASP B:120 , ASP B:152 , MN B:287 , MN B:288 , MN B:289 , MN B:290 , PO4 B:291 , HOH B:293 , HOH B:297 , HOH B:302 , HOH B:310
BINDING SITE FOR RESIDUE PO4 B 292
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PPASE (A:115-121,B:115-121)
;
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:115-121
[
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]
Exons
(1, 2)
Info
All Exons
Exon 1.1 (A:1-282 | B:1-282)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
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
1.1
YBR011C
1
YBR011C.1
II:257973-257110
864
IPYR_YEAST
1-287
287
2
A:1-282
B:1-282
282
282
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1wgja_ (A:)
1b: SCOP_d1wgjb_ (B:)
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(
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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
d1wgja_
A:
1b
d1wgjb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1wgjA00 (A:1-282)
1b: CATH_1wgjB00 (B:1-282)
View:
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Classes
(
)
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Homologous Superfamilies
(
)
(
)
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
1wgjA00
A:1-282
1b
1wgjB00
B:1-282
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Pyrophosphatase_1wgjB01 (B:44-228)
1b: PFAM_Pyrophosphatase_1wgjB02 (B:44-228)
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Clans
(
)
(
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(
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(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Pyrophosphatase]
(19)
Family
:
Pyrophosphatase
(19)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(5)
1a
Pyrophosphatase-1wgjB01
B:44-228
1b
Pyrophosphatase-1wgjB02
B:44-228
[
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]
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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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