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1PYD
Asym. Unit
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Asym.Unit (173 KB)
Biol.Unit 1 (167 KB)
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(1)
Title
:
CATALYTIC CENTERS IN THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE AT 2.4 ANGSTROMS RESOLUTION
Authors
:
W. Furey, F. Dyda
Date
:
23 Mar 93 (Deposition) - 30 Apr 94 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Lyase(Carbon-Carbon)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Dyda, W. Furey, S. Swaminathan, M. Sax, B. Farrenkopf, F. Jordan
Catalytic Centers In The Thiamin Diphosphate Dependent Enzyme Pyruvate Decarboxylase At 2. 4-A Resolution.
Biochemistry V. 32 6165 1993
(for further references see the
PDB file header
)
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
2a: THIAMIN DIPHOSPHATE (TDPa)
2b: THIAMIN DIPHOSPHATE (TDPb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MG
2
Ligand/Ion
MAGNESIUM ION
2
TDP
2
Ligand/Ion
THIAMIN DIPHOSPHATE
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: TD1 (UNKNOWN)
6: TD2 (UNKNOWN)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:444 , ASN A:471 , GLY A:473 , TDP A:557 , HOH A:560
BINDING SITE FOR RESIDUE MG A 559
2
AC2
SOFTWARE
ASP B:444 , ASN B:471 , GLY B:473 , TDP B:557 , HOH B:560
BINDING SITE FOR RESIDUE MG B 559
3
AC3
SOFTWARE
THR A:390 , GLY A:413 , ILE A:415 , GLY A:443 , ASP A:444 , GLY A:445 , SER A:446 , ASN A:471 , GLY A:473 , TYR A:474 , THR A:475 , ILE A:476 , GLU A:477 , MG A:559 , HOH A:560 , PRO B:26 , GLY B:27 , GLU B:51 , VAL B:76
BINDING SITE FOR RESIDUE TDP A 557
4
AC4
SOFTWARE
PRO A:26 , GLY A:27 , GLU A:51 , VAL A:76 , GLY B:389 , THR B:390 , GLY B:413 , ILE B:415 , GLY B:443 , ASP B:444 , GLY B:445 , SER B:446 , ASN B:471 , GLY B:473 , TYR B:474 , THR B:475 , ILE B:476 , GLU B:477 , MG B:559 , HOH B:560
BINDING SITE FOR RESIDUE TDP B 557
5
TD1
UNKNOWN
THR A:388 , THR A:390 , GLY A:413 , ILE A:415 , ASP A:444 , SER A:446 , LEU A:449 , LEU A:469 , ASN A:471 , ILE A:476 , GLY A:473 , GLU A:477 , LEU B:25 , ASP B:28 , GLU B:51 , THR B:73 , VAL B:76 , ASN B:83 , HIS B:114 , HIS B:115
NULL
6
TD2
UNKNOWN
THR B:388 , THR B:390 , GLY B:413 , ILE B:415 , ASP B:444 , SER B:446 , LEU B:449 , LEU B:469 , ASN B:471 , ILE B:476 , GLY B:473 , GLU B:477 , LEU A:25 , ASP A:28 , GLU A:51 , THR A:73 , VAL A:76 , ASN A:83 , HIS A:114 , HIS A:115
NULL
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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: TPP_ENZYMES (A:427-446,B:427-446)
;
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TPP_ENZYMES
PS00187
Thiamine pyrophosphate enzymes signature.
PDC1_YEAST
427-446
2
A:427-446
B:427-446
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Exons
(1, 2)
Info
All Exons
Exon 1.1 (A:2-556 (gaps) | B:2-556 (gaps))
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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
YLR044C
1
YLR044C.1
XII:234082-232391
1692
PDC1_YEAST
1-563
563
2
A:2-556 (gaps)
B:2-556 (gaps)
555
555
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SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1pyda1 (A:182-360)
1b: SCOP_d1pydb1 (B:182-360)
2a: SCOP_d1pyda3 (A:361-556)
2b: SCOP_d1pydb3 (B:361-556)
3a: SCOP_d1pyda2 (A:2-181)
3b: SCOP_d1pydb2 (B:2-181)
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)
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)
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
DHS-like NAD/FAD-binding domain
(176)
Superfamily
:
DHS-like NAD/FAD-binding domain
(176)
Family
:
Pyruvate oxidase and decarboxylase, middle domain
(74)
Protein domain
:
Pyruvate decarboxylase
(4)
Brewer's yeast (Saccharomyces uvarum) [TaxId: 230603]
(1)
1a
d1pyda1
A:182-360
1b
d1pydb1
B:182-360
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
Pyruvate oxidase and decarboxylase PP module
(43)
Protein domain
:
Pyruvate decarboxylase
(4)
Brewer's yeast (Saccharomyces uvarum) [TaxId: 230603]
(1)
2a
d1pyda3
A:361-556
2b
d1pydb3
B:361-556
Family
:
Pyruvate oxidase and decarboxylase Pyr module
(43)
Protein domain
:
Pyruvate decarboxylase
(4)
Brewer's yeast (Saccharomyces uvarum) [TaxId: 230603]
(1)
3a
d1pyda2
A:2-181
3b
d1pydb2
B:2-181
[
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1pydA03 (A:353-554)
1b: CATH_1pydB03 (B:353-554)
1c: CATH_1pydA01 (A:2-188)
1d: CATH_1pydB01 (B:2-188)
2a: CATH_1pydA02 (A:189-352)
2b: CATH_1pydB02 (B:189-352)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Baker's yeast (Saccharomyces cerevisiae)
(17)
1a
1pydA03
A:353-554
1b
1pydB03
B:353-554
1c
1pydA01
A:2-188
1d
1pydB01
B:2-188
Homologous Superfamily
:
TPP-binding domain
(120)
Baker's yeast (Saccharomyces cerevisiae)
(20)
2a
1pydA02
A:189-352
2b
1pydB02
B:189-352
[
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_TPP_enzyme_M_1pydB01 (B:201-339)
1b: PFAM_TPP_enzyme_M_1pydB02 (B:201-339)
2a: PFAM_TPP_enzyme_C_1pydB03 (B:387-526)
2b: PFAM_TPP_enzyme_C_1pydB04 (B:387-526)
3a: PFAM_TPP_enzyme_N_1pydB05 (B:4-180)
3b: PFAM_TPP_enzyme_N_1pydB06 (B:4-180)
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)
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)
Clan
:
FAD_DHS
(82)
Family
:
TPP_enzyme_M
(50)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(12)
1a
TPP_enzyme_M-1pydB01
B:201-339
1b
TPP_enzyme_M-1pydB02
B:201-339
Clan
:
THDP-binding
(106)
Family
:
TPP_enzyme_C
(54)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(12)
2a
TPP_enzyme_C-1pydB03
B:387-526
2b
TPP_enzyme_C-1pydB04
B:387-526
Family
:
TPP_enzyme_N
(54)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(12)
3a
TPP_enzyme_N-1pydB05
B:4-180
3b
TPP_enzyme_N-1pydB06
B:4-180
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