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Asym. Unit
Info
Asym.Unit (751 KB)
Biol.Unit 1 (743 KB)
Biol.Unit 2 (377 KB)
Biol.Unit 3 (374 KB)
Biol.Unit 4 (375 KB)
Biol.Unit 5 (376 KB)
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(1)
Title
:
STRUCTURAL INSIGHTS INTO THE PRE-REACTION STATE OF PYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS
Authors
:
X. Y. Pei, K. Erixon, B. F. Luisi, F. J. Leeper
Date
:
16 Oct 09 (Deposition) - 09 Feb 10 (Release) - 19 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,E,F
Biol. Unit 1: A,B,E,F (1x)
Biol. Unit 2: A,B (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: A,F (1x)
Biol. Unit 5: B,E (1x)
Keywords
:
Thiamine Diphosphate, Lyase, Flavoprotein, Metal-Binding, Alcohol Fermentation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Y. Pei, K. Erixon, B. F. Luisi, F. J. Leeper
Structural Insights Into The Pre-Reaction State Of Pyruvate Decarboxylase From Zymomonas Mobilis
Biochemistry V. 49 1727 2010
[
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: FLUORIDE ION (Fa)
1b: FLUORIDE ION (Fb)
1c: FLUORIDE ION (Fc)
1d: FLUORIDE ION (Fd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: 2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPUa)
3b: 2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPUb)
3c: 2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPUc)
3d: 2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPUd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
F
4
Ligand/Ion
FLUORIDE ION
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
TPU
4
Ligand/Ion
2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-METHYL-1H-1,2,3-TRIAZOL-4-YL}ETHYLTRIHYDROGEN DIPHOSPHATE
[
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Sites
(12, 12)
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: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:26 , ASP A:27 , THR A:72 , HIS A:114
BINDING SITE FOR RESIDUE F A 569
02
AC2
SOFTWARE
GLY A:389 , ASP A:390 , GLY A:413 , HIS A:414 , ILE A:415 , GLY A:439 , ASP A:440 , GLY A:441 , SER A:442 , ASN A:467 , GLY A:469 , TYR A:470 , THR A:471 , ILE A:472 , GLU A:473 , MG A:601 , HOH A:2443 , HOH A:2489 , HOH A:2572 , ALA B:25 , GLY B:26 , GLU B:50 , VAL B:75 , HIS B:114
BINDING SITE FOR RESIDUE TPU A 600
03
AC3
SOFTWARE
ASP A:440 , ASN A:467 , GLY A:469 , TPU A:600 , HOH A:2489
BINDING SITE FOR RESIDUE MG A 601
04
AC4
SOFTWARE
GLY B:26 , ASP B:27 , THR B:72 , HIS B:114
BINDING SITE FOR RESIDUE F B 569
05
AC5
SOFTWARE
ALA A:25 , GLY A:26 , GLU A:50 , VAL A:75 , HIS A:114 , GLY B:389 , ASP B:390 , GLY B:413 , HIS B:414 , ILE B:415 , GLY B:439 , ASP B:440 , GLY B:441 , SER B:442 , ASN B:467 , GLY B:469 , TYR B:470 , THR B:471 , ILE B:472 , GLU B:473 , MG B:601 , HOH B:2409 , HOH B:2454 , HOH B:2548 , HOH B:2549
BINDING SITE FOR RESIDUE TPU B 600
06
AC6
SOFTWARE
ASP B:440 , ASN B:467 , GLY B:469 , TPU B:600 , HOH B:2448
BINDING SITE FOR RESIDUE MG B 601
07
AC7
SOFTWARE
GLY E:26 , ASP E:27 , THR E:72 , HIS E:114
BINDING SITE FOR RESIDUE F E 569
08
AC8
SOFTWARE
GLY E:389 , ASP E:390 , GLY E:413 , HIS E:414 , ILE E:415 , GLY E:439 , ASP E:440 , GLY E:441 , SER E:442 , ASN E:467 , GLY E:469 , TYR E:470 , THR E:471 , ILE E:472 , GLU E:473 , MG E:601 , HOH E:2478 , HOH E:2481 , HOH E:2628 , HOH E:2629 , ALA F:25 , GLY F:26 , GLU F:50 , VAL F:75 , HIS F:114
BINDING SITE FOR RESIDUE TPU E 600
09
AC9
SOFTWARE
ASP E:440 , ASN E:467 , GLY E:469 , TPU E:600 , HOH E:2528
BINDING SITE FOR RESIDUE MG E 601
10
BC1
SOFTWARE
ASP F:440 , ASN F:467 , GLY F:469 , TPU F:600 , HOH F:2497
BINDING SITE FOR RESIDUE MG F 569
11
BC2
SOFTWARE
GLY F:26 , ASP F:27 , THR F:72 , HIS F:114
BINDING SITE FOR RESIDUE F F 570
12
BC3
SOFTWARE
ALA E:25 , GLY E:26 , GLU E:50 , VAL E:75 , HIS E:114 , GLY F:389 , ASP F:390 , GLY F:413 , HIS F:414 , ILE F:415 , GLY F:439 , ASP F:440 , GLY F:441 , SER F:442 , ASN F:467 , GLY F:469 , TYR F:470 , THR F:471 , ILE F:472 , GLU F:473 , MG F:569 , HOH F:2450 , HOH F:2452 , HOH F:2497 , HOH F:2606
BINDING SITE FOR RESIDUE TPU F 600
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: TPP_ENZYMES (A:423-442,B:423-442,E:423-442,F: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.
PDC_ZYMMO
423-442
4
A:423-442
B:423-442
E:423-442
F:423-442
[
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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_d2wvga2 (A:188-362)
1b: SCOP_d2wvgb2 (B:188-362)
1c: SCOP_d2wvge2 (E:188-362)
1d: SCOP_d2wvgf2 (F:188-362)
2a: SCOP_d2wvga1 (A:2-187)
2b: SCOP_d2wvga3 (A:363-566)
2c: SCOP_d2wvgb1 (B:2-187)
2d: SCOP_d2wvgb3 (B:363-566)
2e: SCOP_d2wvge1 (E:2-187)
2f: SCOP_d2wvge3 (E:363-566)
2g: SCOP_d2wvgf1 (F:2-187)
2h: SCOP_d2wvgf3 (F:363-566)
View:
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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)
Zymomonas mobilis [TaxId: 542]
(4)
1a
d2wvga2
A:188-362
1b
d2wvgb2
B:188-362
1c
d2wvge2
E:188-362
1d
d2wvgf2
F:188-362
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)
Zymomonas mobilis [TaxId: 542]
(4)
2a
d2wvga1
A:2-187
2b
d2wvga3
A:363-566
2c
d2wvgb1
B:2-187
2d
d2wvgb3
B:363-566
2e
d2wvge1
E:2-187
2f
d2wvge3
E:363-566
2g
d2wvgf1
F:2-187
2h
d2wvgf3
F:363-566
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2wvgA03 (A:355-548)
1b: CATH_2wvgB03 (B:355-548)
1c: CATH_2wvgE03 (E:355-548)
1d: CATH_2wvgA01 (A:2-186)
1e: CATH_2wvgB01 (B:2-186)
1f: CATH_2wvgE01 (E:2-186)
1g: CATH_2wvgF01 (F:2-186)
1h: CATH_2wvgF03 (F:355-548)
2a: CATH_2wvgA02 (A:188-350)
2b: CATH_2wvgB02 (B:188-350)
2c: CATH_2wvgE02 (E:188-350)
2d: CATH_2wvgF02 (F:188-350)
View:
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(
)
Topologies
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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)
Zymomonas mobilis. Organism_taxid: 542.
(4)
1a
2wvgA03
A:355-548
1b
2wvgB03
B:355-548
1c
2wvgE03
E:355-548
1d
2wvgA01
A:2-186
1e
2wvgB01
B:2-186
1f
2wvgE01
E:2-186
1g
2wvgF01
F:2-186
1h
2wvgF03
F:355-548
Homologous Superfamily
:
TPP-binding domain
(120)
Zymomonas mobilis. Organism_taxid: 542.
(4)
2a
2wvgA02
A:188-350
2b
2wvgB02
B:188-350
2c
2wvgE02
E:188-350
2d
2wvgF02
F:188-350
[
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]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_TPP_enzyme_M_2wvgF01 (F:199-360)
1b: PFAM_TPP_enzyme_M_2wvgF02 (F:199-360)
1c: PFAM_TPP_enzyme_M_2wvgF03 (F:199-360)
1d: PFAM_TPP_enzyme_M_2wvgF04 (F:199-360)
2a: PFAM_TPP_enzyme_C_2wvgF05 (F:387-537)
2b: PFAM_TPP_enzyme_C_2wvgF06 (F:387-537)
2c: PFAM_TPP_enzyme_C_2wvgF07 (F:387-537)
2d: PFAM_TPP_enzyme_C_2wvgF08 (F:387-537)
3a: PFAM_TPP_enzyme_N_2wvgF09 (F:3-179)
3b: PFAM_TPP_enzyme_N_2wvgF10 (F:3-179)
3c: PFAM_TPP_enzyme_N_2wvgF11 (F:3-179)
3d: PFAM_TPP_enzyme_N_2wvgF12 (F:3-179)
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Clans
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)
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)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FAD_DHS
(82)
Family
:
TPP_enzyme_M
(50)
Zymomonas mobilis
(5)
1a
TPP_enzyme_M-2wvgF01
F:199-360
1b
TPP_enzyme_M-2wvgF02
F:199-360
1c
TPP_enzyme_M-2wvgF03
F:199-360
1d
TPP_enzyme_M-2wvgF04
F:199-360
Clan
:
THDP-binding
(106)
Family
:
TPP_enzyme_C
(54)
Zymomonas mobilis
(5)
2a
TPP_enzyme_C-2wvgF05
F:387-537
2b
TPP_enzyme_C-2wvgF06
F:387-537
2c
TPP_enzyme_C-2wvgF07
F:387-537
2d
TPP_enzyme_C-2wvgF08
F:387-537
Family
:
TPP_enzyme_N
(54)
Zymomonas mobilis
(5)
3a
TPP_enzyme_N-2wvgF09
F:3-179
3b
TPP_enzyme_N-2wvgF10
F:3-179
3c
TPP_enzyme_N-2wvgF11
F:3-179
3d
TPP_enzyme_N-2wvgF12
F:3-179
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]
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Asym.Unit (751 KB)
Header - Asym.Unit
Biol.Unit 1 (743 KB)
Header - Biol.Unit 1
Biol.Unit 2 (377 KB)
Header - Biol.Unit 2
Biol.Unit 3 (374 KB)
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Biol.Unit 4 (375 KB)
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