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1PVD
Asym. Unit
Info
Asym.Unit (183 KB)
Biol.Unit 1 (177 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE FROM THE YEAST SACCHAROMYCES CEREVISIAE AT 2.3 ANGSTROMS RESOLUTION
Authors
:
W. Furey, P. Arjunan
Date
:
20 Apr 95 (Deposition) - 31 Jul 95 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Lyase (Carbon-Carbon)
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Arjunan, T. Umland, F. Dyda, S. Swaminathan, W. Furey, M. Sax, B. Farrenkopf, Y. Gao, D. Zhang, F. Jordan
Crystal Structure Of The Thiamin Diphosphate-Dependent Enzyme Pyruvate Decarboxylase From The Yeast Saccharomyces Cerevisiae At 2. 3 A Resolution.
J. Mol. Biol. V. 256 590 1996
(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: THIAMINE DIPHOSPHATE (TPPa)
2b: THIAMINE DIPHOSPHATE (TPPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
2
Ligand/Ion
MAGNESIUM ION
2
TPP
2
Ligand/Ion
THIAMINE DIPHOSPHATE
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: TPA (UNKNOWN)
6: TPB (UNKNOWN)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:444 , ASN A:471 , GLY A:473 , TPP A:557 , HOH A:559
BINDING SITE FOR RESIDUE MG A 558
2
AC2
SOFTWARE
ASP B:444 , ASN B:471 , GLY B:473 , TPP B:557 , HOH B:559
BINDING SITE FOR RESIDUE MG B 558
3
AC3
SOFTWARE
GLY A:389 , THR A:390 , GLY A:413 , SER A:414 , 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:558 , HOH A:559 , HOH A:583 , HOH A:647 , PRO B:26 , GLY B:27 , GLU B:51 , VAL B:76
BINDING SITE FOR RESIDUE TPP A 557
4
AC4
SOFTWARE
PRO A:26 , GLU A:51 , VAL A:76 , GLY B:389 , THR B:390 , GLY B:413 , SER B:414 , 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:558 , HOH B:559 , HOH B:612 , HOH B:791 , HOH B:861
BINDING SITE FOR RESIDUE TPP B 557
5
TPA
UNKNOWN
GLY A:413 , ILE A:415 , THR A:388 , THR A:390 , SER A:446 , ILE A:476 , LEU A:469 , ASN A:471 , ASP A:444 , GLY A:473 , GLU A:477 , LEU A:449 , GLU B:51 , ASP B:28 , THR B:73 , VAL B:76 , ASN B:83 , LEU B:25 , HIS B:114 , HIS B:115
NULL
6
TPB
UNKNOWN
GLY B:413 , ILE B:415 , THR B:388 , THR B:390 , SER B:446 , ILE B:476 , LEU B:469 , ASN B:471 , ASP B:444 , GLY B:473 , GLU B:477 , LEU B:449 , GLU A:51 , ASP A:28 , THR A:73 , VAL A:76 , ASN A:83 , LEU A:25 , 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)
;
View:
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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_d1pvda1 (A:182-360)
1b: SCOP_d1pvdb1 (B:182-360)
2a: SCOP_d1pvda3 (A:361-556)
2b: SCOP_d1pvdb3 (B:361-556)
3a: SCOP_d1pvda2 (A:2-181)
3b: SCOP_d1pvdb2 (B:2-181)
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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)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
1a
d1pvda1
A:182-360
1b
d1pvdb1
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)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
2a
d1pvda3
A:361-556
2b
d1pvdb3
B:361-556
Family
:
Pyruvate oxidase and decarboxylase Pyr module
(43)
Protein domain
:
Pyruvate decarboxylase
(4)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
3a
d1pvda2
A:2-181
3b
d1pvdb2
B:2-181
[
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1pvdA03 (A:353-556)
1b: CATH_1pvdB03 (B:353-554)
1c: CATH_1pvdA01 (A:2-188)
1d: CATH_1pvdB01 (B:2-188)
2a: CATH_1pvdA02 (A:189-352)
2b: CATH_1pvdB02 (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
1pvdA03
A:353-556
1b
1pvdB03
B:353-554
1c
1pvdA01
A:2-188
1d
1pvdB01
B:2-188
Homologous Superfamily
:
TPP-binding domain
(120)
Baker's yeast (Saccharomyces cerevisiae)
(20)
2a
1pvdA02
A:189-352
2b
1pvdB02
B:189-352
[
close CATH info
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_TPP_enzyme_M_1pvdB01 (B:201-339)
1b: PFAM_TPP_enzyme_M_1pvdB02 (B:201-339)
2a: PFAM_TPP_enzyme_C_1pvdB03 (B:387-526)
2b: PFAM_TPP_enzyme_C_1pvdB04 (B:387-526)
3a: PFAM_TPP_enzyme_N_1pvdB05 (B:4-180)
3b: PFAM_TPP_enzyme_N_1pvdB06 (B:4-180)
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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-1pvdB01
B:201-339
1b
TPP_enzyme_M-1pvdB02
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-1pvdB03
B:387-526
2b
TPP_enzyme_C-1pvdB04
B:387-526
Family
:
TPP_enzyme_N
(54)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(12)
3a
TPP_enzyme_N-1pvdB05
B:4-180
3b
TPP_enzyme_N-1pvdB06
B:4-180
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