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2WVA
Biol. Unit 2
Info
Asym.Unit (1.4 MB)
Biol.Unit 1 (735 KB)
Biol.Unit 2 (730 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
:
15 Oct 09 (Deposition) - 09 Feb 10 (Release) - 19 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,E,F,V,X,Y,Z
Biol. Unit 1: V,X,Y,Z (1x)
Biol. Unit 2: A,B,E,F (1x)
Keywords
:
Thiamin 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
(2, 5)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
2a: PYRUVIC ACID (PYRa)
2b: PYRUVIC ACID (PYRb)
2c: PYRUVIC ACID (PYRc)
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)
3e: 2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPUe)
3f: 2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPUf)
3g: 2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPUg)
3h: 2-{1-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPUh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
PYR
1
Ligand/Ion
PYRUVIC ACID
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
(9, 9)
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)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
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:2307 , HOH A:2332 , HOH A:2388 , ALA B:25 , GLY B:26 , GLU B:50 , VAL B:75 , HIS B:114
BINDING SITE FOR RESIDUE TPU A 600
2
AC2
SOFTWARE
ASP A:440 , ASN A:467 , GLY A:469 , TPU A:600 , HOH A:2332
BINDING SITE FOR RESIDUE MG A 601
3
AC3
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:2231 , HOH B:2292 , HOH B:2293
BINDING SITE FOR RESIDUE TPU B 600
4
AC4
SOFTWARE
ASP B:440 , ASN B:467 , GLY B:469 , TPU B:600 , HOH B:2293
BINDING SITE FOR RESIDUE MG B 601
5
AC5
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:2238 , HOH E:2246 , HOH E:2294 , HOH E:2295 , ALA F:25 , GLU F:50 , VAL F:75 , HIS F:114
BINDING SITE FOR RESIDUE TPU E 600
6
AC6
SOFTWARE
ASP E:440 , ASN E:467 , GLY E:469 , TPU E:600 , HOH E:2246
BINDING SITE FOR RESIDUE MG E 601
7
AC7
SOFTWARE
ASP F:440 , ASN F:467 , GLY F:469 , TPU F:600 , HOH F:2332
BINDING SITE FOR RESIDUE MG F 569
8
AC8
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 , PYR F:602 , HOH F:2266 , HOH F:2332 , HOH F:2333
BINDING SITE FOR RESIDUE TPU F 600
9
AC9
SOFTWARE
ASP E:27 , HIS E:114 , HOH E:2043 , TYR F:290 , ILE F:472 , GLU F:473 , ILE F:476 , TPU F:600 , HOH F:2334
BINDING SITE FOR RESIDUE PYR F 602
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 24)
Info
All SCOP Domains
1a: SCOP_d2wvaa2 (A:188-362)
1b: SCOP_d2wvab2 (B:188-362)
1c: SCOP_d2wvae2 (E:188-362)
1d: SCOP_d2wvaf2 (F:188-362)
1e: SCOP_d2wvav2 (V:188-362)
1f: SCOP_d2wvax2 (X:188-362)
1g: SCOP_d2wvay2 (Y:188-362)
1h: SCOP_d2wvaz2 (Z:188-362)
2a: SCOP_d2wvaa1 (A:2-187)
2b: SCOP_d2wvaa3 (A:363-566)
2c: SCOP_d2wvab1 (B:2-187)
2d: SCOP_d2wvab3 (B:363-566)
2e: SCOP_d2wvae1 (E:2-187)
2f: SCOP_d2wvae3 (E:363-566)
2g: SCOP_d2wvaf1 (F:2-187)
2h: SCOP_d2wvaf3 (F:363-566)
2i: SCOP_d2wvav1 (V:2-187)
2j: SCOP_d2wvav3 (V:363-566)
2k: SCOP_d2wvax1 (X:1-187)
2l: SCOP_d2wvax3 (X:363-566)
2m: SCOP_d2wvay1 (Y:2-187)
2n: SCOP_d2wvay3 (Y:363-566)
2o: SCOP_d2wvaz1 (Z:2-187)
2p: SCOP_d2wvaz3 (Z:363-566)
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)
(
)
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)
(
)
Superfamilies
(
)
(
)
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
d2wvaa2
A:188-362
1b
d2wvab2
B:188-362
1c
d2wvae2
E:188-362
1d
d2wvaf2
F:188-362
1e
d2wvav2
V:188-362
1f
d2wvax2
X:188-362
1g
d2wvay2
Y:188-362
1h
d2wvaz2
Z: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
d2wvaa1
A:2-187
2b
d2wvaa3
A:363-566
2c
d2wvab1
B:2-187
2d
d2wvab3
B:363-566
2e
d2wvae1
E:2-187
2f
d2wvae3
E:363-566
2g
d2wvaf1
F:2-187
2h
d2wvaf3
F:363-566
2i
d2wvav1
V:2-187
2j
d2wvav3
V:363-566
2k
d2wvax1
X:1-187
2l
d2wvax3
X:363-566
2m
d2wvay1
Y:2-187
2n
d2wvay3
Y:363-566
2o
d2wvaz1
Z:2-187
2p
d2wvaz3
Z:363-566
[
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]
CATH Domains
(2, 24)
Info
all CATH domains
1a: CATH_2wvaA03 (A:355-548)
1b: CATH_2wvaY03 (Y:355-548)
1c: CATH_2wvaZ03 (Z:355-548)
1d: CATH_2wvaX01 (X:1-186)
1e: CATH_2wvaA01 (A:2-186)
1f: CATH_2wvaB01 (B:2-186)
1g: CATH_2wvaE01 (E:2-186)
1h: CATH_2wvaF01 (F:2-186)
1i: CATH_2wvaV01 (V:2-186)
1j: CATH_2wvaY01 (Y:2-186)
1k: CATH_2wvaZ01 (Z:2-186)
1l: CATH_2wvaB03 (B:355-548)
1m: CATH_2wvaE03 (E:355-548)
1n: CATH_2wvaF03 (F:355-548)
1o: CATH_2wvaV03 (V:355-548)
1p: CATH_2wvaX03 (X:355-548)
2a: CATH_2wvaA02 (A:188-350)
2b: CATH_2wvaY02 (Y:188-350)
2c: CATH_2wvaZ02 (Z:188-350)
2d: CATH_2wvaB02 (B:188-350)
2e: CATH_2wvaE02 (E:188-350)
2f: CATH_2wvaF02 (F:188-350)
2g: CATH_2wvaV02 (V:188-350)
2h: CATH_2wvaX02 (X: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
2wvaA03
A:355-548
1b
2wvaY03
Y:355-548
1c
2wvaZ03
Z:355-548
1d
2wvaX01
X:1-186
1e
2wvaA01
A:2-186
1f
2wvaB01
B:2-186
1g
2wvaE01
E:2-186
1h
2wvaF01
F:2-186
1i
2wvaV01
V:2-186
1j
2wvaY01
Y:2-186
1k
2wvaZ01
Z:2-186
1l
2wvaB03
B:355-548
1m
2wvaE03
E:355-548
1n
2wvaF03
F:355-548
1o
2wvaV03
V:355-548
1p
2wvaX03
X:355-548
Homologous Superfamily
:
TPP-binding domain
(120)
Zymomonas mobilis. Organism_taxid: 542.
(4)
2a
2wvaA02
A:188-350
2b
2wvaY02
Y:188-350
2c
2wvaZ02
Z:188-350
2d
2wvaB02
B:188-350
2e
2wvaE02
E:188-350
2f
2wvaF02
F:188-350
2g
2wvaV02
V:188-350
2h
2wvaX02
X:188-350
[
close CATH info
]
Pfam Domains
(3, 24)
Info
all PFAM domains
1a: PFAM_TPP_enzyme_M_2wvaZ01 (Z:199-360)
1b: PFAM_TPP_enzyme_M_2wvaZ02 (Z:199-360)
1c: PFAM_TPP_enzyme_M_2wvaZ03 (Z:199-360)
1d: PFAM_TPP_enzyme_M_2wvaZ04 (Z:199-360)
1e: PFAM_TPP_enzyme_M_2wvaZ05 (Z:199-360)
1f: PFAM_TPP_enzyme_M_2wvaZ06 (Z:199-360)
1g: PFAM_TPP_enzyme_M_2wvaZ07 (Z:199-360)
1h: PFAM_TPP_enzyme_M_2wvaZ08 (Z:199-360)
2a: PFAM_TPP_enzyme_C_2wvaZ09 (Z:387-537)
2b: PFAM_TPP_enzyme_C_2wvaZ10 (Z:387-537)
2c: PFAM_TPP_enzyme_C_2wvaZ11 (Z:387-537)
2d: PFAM_TPP_enzyme_C_2wvaZ12 (Z:387-537)
2e: PFAM_TPP_enzyme_C_2wvaZ13 (Z:387-537)
2f: PFAM_TPP_enzyme_C_2wvaZ14 (Z:387-537)
2g: PFAM_TPP_enzyme_C_2wvaZ15 (Z:387-537)
2h: PFAM_TPP_enzyme_C_2wvaZ16 (Z:387-537)
3a: PFAM_TPP_enzyme_N_2wvaZ17 (Z:3-179)
3b: PFAM_TPP_enzyme_N_2wvaZ18 (Z:3-179)
3c: PFAM_TPP_enzyme_N_2wvaZ19 (Z:3-179)
3d: PFAM_TPP_enzyme_N_2wvaZ20 (Z:3-179)
3e: PFAM_TPP_enzyme_N_2wvaZ21 (Z:3-179)
3f: PFAM_TPP_enzyme_N_2wvaZ22 (Z:3-179)
3g: PFAM_TPP_enzyme_N_2wvaZ23 (Z:3-179)
3h: PFAM_TPP_enzyme_N_2wvaZ24 (Z:3-179)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FAD_DHS
(82)
Family
:
TPP_enzyme_M
(50)
Zymomonas mobilis
(5)
1a
TPP_enzyme_M-2wvaZ01
Z:199-360
1b
TPP_enzyme_M-2wvaZ02
Z:199-360
1c
TPP_enzyme_M-2wvaZ03
Z:199-360
1d
TPP_enzyme_M-2wvaZ04
Z:199-360
1e
TPP_enzyme_M-2wvaZ05
Z:199-360
1f
TPP_enzyme_M-2wvaZ06
Z:199-360
1g
TPP_enzyme_M-2wvaZ07
Z:199-360
1h
TPP_enzyme_M-2wvaZ08
Z:199-360
Clan
:
THDP-binding
(106)
Family
:
TPP_enzyme_C
(54)
Zymomonas mobilis
(5)
2a
TPP_enzyme_C-2wvaZ09
Z:387-537
2b
TPP_enzyme_C-2wvaZ10
Z:387-537
2c
TPP_enzyme_C-2wvaZ11
Z:387-537
2d
TPP_enzyme_C-2wvaZ12
Z:387-537
2e
TPP_enzyme_C-2wvaZ13
Z:387-537
2f
TPP_enzyme_C-2wvaZ14
Z:387-537
2g
TPP_enzyme_C-2wvaZ15
Z:387-537
2h
TPP_enzyme_C-2wvaZ16
Z:387-537
Family
:
TPP_enzyme_N
(54)
Zymomonas mobilis
(5)
3a
TPP_enzyme_N-2wvaZ17
Z:3-179
3b
TPP_enzyme_N-2wvaZ18
Z:3-179
3c
TPP_enzyme_N-2wvaZ19
Z:3-179
3d
TPP_enzyme_N-2wvaZ20
Z:3-179
3e
TPP_enzyme_N-2wvaZ21
Z:3-179
3f
TPP_enzyme_N-2wvaZ22
Z:3-179
3g
TPP_enzyme_N-2wvaZ23
Z:3-179
3h
TPP_enzyme_N-2wvaZ24
Z:3-179
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