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1QPB
Biol. Unit 2
Info
Asym.Unit (184 KB)
Biol.Unit 1 (351 KB)
Biol.Unit 2 (178 KB)
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(1)
Title
:
PYRUVATE DECARBOYXLASE FROM YEAST (FORM B) COMPLEXED WITH PYRUVAMIDE
Authors
:
G. Lu, D. Dobritzsch, G. Schneider
Date
:
26 Nov 99 (Deposition) - 04 Feb 00 (Release) - 22 Dec 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Biol. Unit 2: A,B (1x)
Keywords
:
Thiamine Pyruvate, Pyruvamide, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Lu, D. Dobritzsch, S. Baumann, G. Schneider, S. Konig
The Structural Basis Of Substrate Activation In Yeast Pyruvate Decarboxylase A Crystallographic And Kinetic Study
Eur. J. Biochem. V. 267 861 2000
(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: PYRUVAMIDE (PYMa)
2b: PYRUVAMIDE (PYMb)
3a: THIAMINE DIPHOSPHATE (TPPa)
3b: THIAMINE DIPHOSPHATE (TPPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
PYM
2
Ligand/Ion
PYRUVAMIDE
3
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: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:444 , ASN A:471 , GLY A:473 , TPP A:600 , HOH A:2077
BINDING SITE FOR RESIDUE MG A 601
2
AC2
SOFTWARE
ASP B:444 , ASN B:471 , GLY B:473 , THR B:475 , TPP B:600 , HOH B:2043
BINDING SITE FOR RESIDUE MG B 601
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:601 , HOH A:2077 , HOH A:2084 , PRO B:26 , GLU B:51 , VAL B:76 , PYM B:602
BINDING SITE FOR RESIDUE TPP A 600
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 , MG B:601 , HOH B:2043
BINDING SITE FOR RESIDUE TPP B 600
5
AC5
SOFTWARE
GLU A:477 , TPP A:600 , HOH A:2085 , ASP B:28 , HIS B:114 , HIS B:115
BINDING SITE FOR RESIDUE PYM B 602
6
AC6
SOFTWARE
TYR A:157 , VAL A:158 , ARG A:224 , HIS A:225 , ASP A:226
BINDING SITE FOR RESIDUE PYM A 602
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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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
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1qpba1 (A:182-360)
1b: SCOP_d1qpbb1 (B:182-360)
2a: SCOP_d1qpba3 (A:361-556)
2b: SCOP_d1qpbb3 (B:361-556)
3a: SCOP_d1qpba2 (A:2-181)
3b: SCOP_d1qpbb2 (B:2-181)
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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)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
1a
d1qpba1
A:182-360
1b
d1qpbb1
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
d1qpba3
A:361-556
2b
d1qpbb3
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
d1qpba2
A:2-181
3b
d1qpbb2
B:2-181
[
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]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1qpbA03 (A:353-554)
1b: CATH_1qpbB03 (B:353-554)
1c: CATH_1qpbA01 (A:2-188)
1d: CATH_1qpbB01 (B:2-188)
2a: CATH_1qpbA02 (A:189-352)
2b: CATH_1qpbB02 (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)
Saccharomyces pastorianus. Organism_taxid: 520522. Strain: weihenstephan 34/70 (2124, bohemian lager)
(1)
1a
1qpbA03
A:353-554
1b
1qpbB03
B:353-554
1c
1qpbA01
A:2-188
1d
1qpbB01
B:2-188
Homologous Superfamily
:
TPP-binding domain
(120)
Saccharomyces pastorianus. Organism_taxid: 520522. Strain: weihenstephan 34/70 (2124, bohemian lager)
(1)
2a
1qpbA02
A:189-352
2b
1qpbB02
B:189-352
[
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_TPP_enzyme_M_1qpbB01 (B:201-339)
1b: PFAM_TPP_enzyme_M_1qpbB02 (B:201-339)
2a: PFAM_TPP_enzyme_C_1qpbB03 (B:387-526)
2b: PFAM_TPP_enzyme_C_1qpbB04 (B:387-526)
3a: PFAM_TPP_enzyme_N_1qpbB05 (B:4-180)
3b: PFAM_TPP_enzyme_N_1qpbB06 (B:4-180)
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)
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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-1qpbB01
B:201-339
1b
TPP_enzyme_M-1qpbB02
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-1qpbB03
B:387-526
2b
TPP_enzyme_C-1qpbB04
B:387-526
Family
:
TPP_enzyme_N
(54)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(12)
3a
TPP_enzyme_N-1qpbB05
B:4-180
3b
TPP_enzyme_N-1qpbB06
B:4-180
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Show PDB file:
Asym.Unit (184 KB)
Header - Asym.Unit
Biol.Unit 1 (351 KB)
Header - Biol.Unit 1
Biol.Unit 2 (178 KB)
Header - Biol.Unit 2
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