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3OE1
Asym. Unit
Info
Asym.Unit (731 KB)
Biol.Unit 1 (722 KB)
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(1)
Title
:
PYRUVATE DECARBOXYLASE VARIANT GLU473ASP FROM Z. MOBILIS IN COMPLEX WITH REACTION INTERMEDIATE 2-LACTYL-THDP
Authors
:
D. Meyer, P. Neumann, C. Parthier, K. Tittmann
Date
:
12 Aug 10 (Deposition) - 08 Sep 10 (Release) - 12 Jan 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.99
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Meyer, P. Neumann, C. Parthier, R. Friedemann, N. Nemeria, F. Jordan, K. Tittmann
Double Duty For A Conserved Glutamate In Pyruvate Decarboxylase: Evidence Of The Participation In Stereoelectronically Controlled Decarboxylation And In Protonation Of The Nascent Carbanion/Enamine Intermediate .
Biochemistry V. 49 8197 2010
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Hetero Components
(3, 10)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL... (TDLa)
3b: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL... (TDLb)
3c: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL... (TDLc)
3d: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL... (TDLd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
TDL
4
Ligand/Ion
3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-CARBOXY-1-HYDROXYETHYL)-5-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM
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Sites
(10, 10)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:440 , ASN A:467 , GLY A:469 , TDL A:611 , HOH A:1251
BINDING SITE FOR RESIDUE MG A 601
02
AC2
SOFTWARE
ASP B:440 , ASN B:467 , GLY B:469 , TDL B:611 , HOH B:897
BINDING SITE FOR RESIDUE MG B 601
03
AC3
SOFTWARE
ASP C:440 , ASN C:467 , GLY C:469 , TDL C:611 , HOH C:1252
BINDING SITE FOR RESIDUE MG C 601
04
AC4
SOFTWARE
ASP D:440 , ASN D:467 , GLY D:469 , TDL D:611 , HOH D:898
BINDING SITE FOR RESIDUE MG D 601
05
AC5
SOFTWARE
TYR A:290 , THR A:388 , 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 , ASP A:473 , ILE A:476 , HOH A:599 , MG A:601 , HOH A:627 , HOH A:734 , HOH A:1251 , ALA B:25 , GLY B:26 , ASP B:27 , GLU B:50 , VAL B:75 , HIS B:114
BINDING SITE FOR RESIDUE TDL A 611
06
AC6
SOFTWARE
ALA A:25 , GLY A:26 , ASP A:27 , GLU A:50 , VAL A:75 , HIS A:114 , HOH A:637 , TYR B:290 , THR B:388 , 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 , ASP B:473 , HOH B:578 , MG B:601 , HOH B:635 , HOH B:686 , HOH B:897
BINDING SITE FOR RESIDUE TDL B 611
07
AC7
SOFTWARE
TYR C:290 , THR C:388 , GLY C:389 , ASP C:390 , GLY C:413 , HIS C:414 , ILE C:415 , GLY C:439 , ASP C:440 , GLY C:441 , SER C:442 , ASN C:467 , GLY C:469 , TYR C:470 , THR C:471 , ILE C:472 , ASP C:473 , HOH C:599 , MG C:601 , HOH C:624 , HOH C:1252 , ALA D:25 , GLY D:26 , ASP D:27 , GLU D:50 , THR D:72 , VAL D:75 , HIS D:114 , HOH D:750
BINDING SITE FOR RESIDUE TDL C 611
08
AC8
SOFTWARE
ALA C:25 , GLY C:26 , ASP C:27 , GLU C:50 , VAL C:75 , HIS C:114 , HOH C:615 , TYR D:290 , THR D:388 , GLY D:389 , ASP D:390 , GLY D:413 , HIS D:414 , ILE D:415 , GLY D:439 , ASP D:440 , GLY D:441 , SER D:442 , ASN D:467 , GLY D:469 , TYR D:470 , THR D:471 , ILE D:472 , ASP D:473 , MG D:601 , HOH D:638 , HOH D:753 , HOH D:898
BINDING SITE FOR RESIDUE TDL D 611
09
AC9
SOFTWARE
ALA D:61 , ARG D:62 , GLY D:65 , ARG D:221 , HOH D:623 , HOH D:671 , HOH D:1055
BINDING SITE FOR RESIDUE GOL D 569
10
BC1
SOFTWARE
PRO B:430 , PRO B:459 , THR B:529 , GLU D:369 , ARG D:372
BINDING SITE FOR RESIDUE GOL D 570
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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:423-442,B:423-442,C:423-442,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.
PDC_ZYMMO
423-442
4
A:423-442
B:423-442
C:423-442
D:423-442
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_d3oe1a2 (A:188-362)
1b: SCOP_d3oe1b2 (B:188-362)
1c: SCOP_d3oe1c2 (C:188-362)
1d: SCOP_d3oe1d2 (D:188-362)
2a: SCOP_d3oe1a1 (A:2-187)
2b: SCOP_d3oe1b1 (B:2-187)
2c: SCOP_d3oe1b3 (B:363-566)
2d: SCOP_d3oe1c1 (C:2-187)
2e: SCOP_d3oe1c3 (C:363-566)
2f: SCOP_d3oe1d1 (D:2-187)
2g: SCOP_d3oe1d3 (D:363-566)
2h: SCOP_d3oe1a3 (A:363-566)
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Classes
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Protein Domains
(
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(
)
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
d3oe1a2
A:188-362
1b
d3oe1b2
B:188-362
1c
d3oe1c2
C:188-362
1d
d3oe1d2
D: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
d3oe1a1
A:2-187
2b
d3oe1b1
B:2-187
2c
d3oe1b3
B:363-566
2d
d3oe1c1
C:2-187
2e
d3oe1c3
C:363-566
2f
d3oe1d1
D:2-187
2g
d3oe1d3
D:363-566
2h
d3oe1a3
A:363-566
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_TPP_enzyme_M_3oe1D01 (D:199-360)
1b: PFAM_TPP_enzyme_M_3oe1D02 (D:199-360)
1c: PFAM_TPP_enzyme_M_3oe1D03 (D:199-360)
1d: PFAM_TPP_enzyme_M_3oe1D04 (D:199-360)
2a: PFAM_TPP_enzyme_C_3oe1D05 (D:387-537)
2b: PFAM_TPP_enzyme_C_3oe1D06 (D:387-537)
2c: PFAM_TPP_enzyme_C_3oe1D07 (D:387-537)
2d: PFAM_TPP_enzyme_C_3oe1D08 (D:387-537)
3a: PFAM_TPP_enzyme_N_3oe1D09 (D:3-179)
3b: PFAM_TPP_enzyme_N_3oe1D10 (D:3-179)
3c: PFAM_TPP_enzyme_N_3oe1D11 (D:3-179)
3d: PFAM_TPP_enzyme_N_3oe1D12 (D:3-179)
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Clans
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Organisms
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)
Clan
:
FAD_DHS
(82)
Family
:
TPP_enzyme_M
(50)
Zymomonas mobilis
(5)
1a
TPP_enzyme_M-3oe1D01
D:199-360
1b
TPP_enzyme_M-3oe1D02
D:199-360
1c
TPP_enzyme_M-3oe1D03
D:199-360
1d
TPP_enzyme_M-3oe1D04
D:199-360
Clan
:
THDP-binding
(106)
Family
:
TPP_enzyme_C
(54)
Zymomonas mobilis
(5)
2a
TPP_enzyme_C-3oe1D05
D:387-537
2b
TPP_enzyme_C-3oe1D06
D:387-537
2c
TPP_enzyme_C-3oe1D07
D:387-537
2d
TPP_enzyme_C-3oe1D08
D:387-537
Family
:
TPP_enzyme_N
(54)
Zymomonas mobilis
(5)
3a
TPP_enzyme_N-3oe1D09
D:3-179
3b
TPP_enzyme_N-3oe1D10
D:3-179
3c
TPP_enzyme_N-3oe1D11
D:3-179
3d
TPP_enzyme_N-3oe1D12
D:3-179
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