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Asym. Unit
Info
Asym.Unit (379 KB)
Biol.Unit 1 (188 KB)
Biol.Unit 2 (191 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PYRUVATE DECARBOXYLASE FROM KLUYVEROMYCES LACTIS
Authors
:
S. Kutter, S. Relle, G. Wille, M. S. Weiss, S. Konig
Date
:
17 Dec 07 (Deposition) - 27 Jan 09 (Release) - 27 Jan 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Metal-Binding, Decarboxylase, Dimer Of Dimers, Substrate Activation, Thiamine Diphosphate, Tdp, Tpp, Lyase, Magnesium, Flavoprotein, Thiamine Pyrophosphate, Asymmetric Active Sites
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
S. Konig, M. Spinka, S. Kutter
Allosteric Activation Of Pyruvate Decarboxylases. A Never-Ending Story?
To Be Published
(for further references see the
PDB file header
)
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
2a: THIAMINE DIPHOSPHATE (TPPa)
2b: THIAMINE DIPHOSPHATE (TPPb)
2c: THIAMINE DIPHOSPHATE (TPPc)
2d: THIAMINE DIPHOSPHATE (TPPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
4
Ligand/Ion
MAGNESIUM ION
2
TPP
4
Ligand/Ion
THIAMINE DIPHOSPHATE
[
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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:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
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:601 , HOH A:2238 , HOH A:2309 , HOH A:2310 , PRO B:26 , GLY B:27 , GLU B:51 , VAL B:76
BINDING SITE FOR RESIDUE TPP A 600
2
AC2
SOFTWARE
ASP A:444 , ASN A:471 , GLY A:473 , TPP A:600 , HOH A:2238
BINDING SITE FOR RESIDUE MG A 601
3
AC3
SOFTWARE
PRO A:26 , GLY A:27 , 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:601 , HOH B:2215 , HOH B:2256 , HOH B:2325 , HOH B:2326
BINDING SITE FOR RESIDUE TPP B 600
4
AC4
SOFTWARE
ASP B:444 , ASN B:471 , GLY B:473 , TPP B:600 , HOH B:2256
BINDING SITE FOR RESIDUE MG B 601
5
AC5
SOFTWARE
THR C:390 , GLY C:413 , SER C:414 , ILE C:415 , GLY C:443 , ASP C:444 , GLY C:445 , SER C:446 , ASN C:471 , GLY C:473 , TYR C:474 , THR C:475 , ILE C:476 , GLU C:477 , MG C:601 , HOH C:2260 , HOH C:2374 , HOH C:2375 , HOH C:2376 , PRO D:26 , GLY D:27 , GLU D:51 , VAL D:76
BINDING SITE FOR RESIDUE TPP C 600
6
AC6
SOFTWARE
ASP C:444 , ASN C:471 , GLY C:473 , TPP C:600 , HOH C:2374
BINDING SITE FOR RESIDUE MG C 601
7
AC7
SOFTWARE
PRO C:26 , GLY C:27 , GLU C:51 , VAL C:76 , GLY D:389 , THR D:390 , GLY D:413 , SER D:414 , ILE D:415 , GLY D:443 , ASP D:444 , GLY D:445 , SER D:446 , ASN D:471 , GLY D:473 , TYR D:474 , THR D:475 , ILE D:476 , GLU D:477 , MG D:601 , HOH D:2196 , HOH D:2197 , HOH D:2237 , HOH D:2307
BINDING SITE FOR RESIDUE TPP D 600
8
AC8
SOFTWARE
ASP D:444 , ASN D:471 , GLY D:473 , TPP D:600 , HOH D:2237
BINDING SITE FOR RESIDUE MG D 601
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: TPP_ENZYMES (A:427-446,B:427-446,C:427-446,D:42...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TPP_ENZYMES
PS00187
Thiamine pyrophosphate enzymes signature.
PDC1_KLULA
427-446
4
A:427-446
B:427-446
C:427-446
D:427-446
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d2vk4a2 (A:182-360)
1b: SCOP_d2vk4b2 (B:182-360)
1c: SCOP_d2vk4c2 (C:182-360)
1d: SCOP_d2vk4d2 (D:182-360)
2a: SCOP_d2vk4a1 (A:2-181)
2b: SCOP_d2vk4a3 (A:361-563)
2c: SCOP_d2vk4b1 (B:2-181)
2d: SCOP_d2vk4b3 (B:361-561)
2e: SCOP_d2vk4c1 (C:2-181)
2f: SCOP_d2vk4c3 (C:361-560)
2g: SCOP_d2vk4d1 (D:2-181)
2h: SCOP_d2vk4d3 (D:361-563)
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)
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)
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(
)
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)
(
)
Families
(
)
(
)
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
:
automated matches
(36)
Protein domain
:
automated matches
(36)
Milk yeast (Kluyveromyces lactis) [TaxId: 28985]
(2)
1a
d2vk4a2
A:182-360
1b
d2vk4b2
B:182-360
1c
d2vk4c2
C:182-360
1d
d2vk4d2
D:182-360
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
automated matches
(65)
Protein domain
:
automated matches
(65)
Milk yeast (Kluyveromyces lactis) [TaxId: 28985]
(2)
2a
d2vk4a1
A:2-181
2b
d2vk4a3
A:361-563
2c
d2vk4b1
B:2-181
2d
d2vk4b3
B:361-561
2e
d2vk4c1
C:2-181
2f
d2vk4c3
C:361-560
2g
d2vk4d1
D:2-181
2h
d2vk4d3
D:361-563
[
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2vk4A03 (A:353-554)
1b: CATH_2vk4B03 (B:353-554)
1c: CATH_2vk4C03 (C:353-554)
1d: CATH_2vk4D03 (D:353-554)
1e: CATH_2vk4A01 (A:2-188)
1f: CATH_2vk4D01 (D:2-188)
1g: CATH_2vk4B01 (B:2-188)
1h: CATH_2vk4C01 (C:2-188)
2a: CATH_2vk4A02 (A:189-352)
2b: CATH_2vk4B02 (B:189-352)
2c: CATH_2vk4C02 (C:189-352)
2d: CATH_2vk4D02 (D:189-352)
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)
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)
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)
Homologous Superfamilies
(
)
(
)
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)
Kluyveromyces lactis. Organism_taxid: 28985
(1)
1a
2vk4A03
A:353-554
1b
2vk4B03
B:353-554
1c
2vk4C03
C:353-554
1d
2vk4D03
D:353-554
1e
2vk4A01
A:2-188
1f
2vk4D01
D:2-188
1g
2vk4B01
B:2-188
1h
2vk4C01
C:2-188
Homologous Superfamily
:
TPP-binding domain
(120)
Kluyveromyces lactis. Organism_taxid: 28985
(1)
2a
2vk4A02
A:189-352
2b
2vk4B02
B:189-352
2c
2vk4C02
C:189-352
2d
2vk4D02
D:189-352
[
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Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_TPP_enzyme_M_2vk4D01 (D:201-337)
1b: PFAM_TPP_enzyme_M_2vk4D02 (D:201-337)
1c: PFAM_TPP_enzyme_M_2vk4D03 (D:201-337)
1d: PFAM_TPP_enzyme_M_2vk4D04 (D:201-337)
2a: PFAM_TPP_enzyme_C_2vk4D05 (D:387-538)
2b: PFAM_TPP_enzyme_C_2vk4D06 (D:387-538)
2c: PFAM_TPP_enzyme_C_2vk4D07 (D:387-538)
2d: PFAM_TPP_enzyme_C_2vk4D08 (D:387-538)
3a: PFAM_TPP_enzyme_N_2vk4D09 (D:4-180)
3b: PFAM_TPP_enzyme_N_2vk4D10 (D:4-180)
3c: PFAM_TPP_enzyme_N_2vk4D11 (D:4-180)
3d: PFAM_TPP_enzyme_N_2vk4D12 (D:4-180)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FAD_DHS
(82)
Family
:
TPP_enzyme_M
(50)
Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (Yea
(1)
1a
TPP_enzyme_M-2vk4D01
D:201-337
1b
TPP_enzyme_M-2vk4D02
D:201-337
1c
TPP_enzyme_M-2vk4D03
D:201-337
1d
TPP_enzyme_M-2vk4D04
D:201-337
Clan
:
THDP-binding
(106)
Family
:
TPP_enzyme_C
(54)
Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (Yea
(1)
2a
TPP_enzyme_C-2vk4D05
D:387-538
2b
TPP_enzyme_C-2vk4D06
D:387-538
2c
TPP_enzyme_C-2vk4D07
D:387-538
2d
TPP_enzyme_C-2vk4D08
D:387-538
Family
:
TPP_enzyme_N
(54)
Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (Yea
(1)
3a
TPP_enzyme_N-2vk4D09
D:4-180
3b
TPP_enzyme_N-2vk4D10
D:4-180
3c
TPP_enzyme_N-2vk4D11
D:4-180
3d
TPP_enzyme_N-2vk4D12
D:4-180
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (379 KB)
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