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1Y9D
Asym. Unit
Info
Asym.Unit (400 KB)
Biol.Unit 1 (390 KB)
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(1)
Title
:
PYRUVATE OXIDASE VARIANT V265A FROM LACTOBACILLUS PLANTARUM
Authors
:
G. Wille, M. Ritter, M. S. Weiss, S. Konig, W. Mantele, G. Hubner
Date
:
15 Dec 04 (Deposition) - 05 Apr 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Oxidoreductase, Pyruvate Oxidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Wille, M. Ritter, M. S. Weiss, S. Konig, W. Mantele, G. Hubner
The Role Of Val-265 For Flavin Adenine Dinulceotide (Fad) Binding In Pyruvate Oxidase: Ftir, Kinetic And Crystallographic Studies On The Enzyme Variant V265A
Biochemistry V. 44 5086 2005
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 18)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
1c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
1d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
5a: THIAMINE DIPHOSPHATE (TPPa)
5b: THIAMINE DIPHOSPHATE (TPPb)
5c: THIAMINE DIPHOSPHATE (TPPc)
5d: THIAMINE DIPHOSPHATE (TPPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
NA
2
Ligand/Ion
SODIUM ION
4
SO4
4
Ligand/Ion
SULFATE ION
5
TPP
4
Ligand/Ion
THIAMINE DIPHOSPHATE
[
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Sites
(18, 18)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:447 , ASN A:474 , GLN A:476 , TPP A:2602
BINDING SITE FOR RESIDUE MG A 2601
02
AC2
SOFTWARE
ILE A:480 , TPP A:2602 , GLY C:34 , GLY C:35 , SER C:36 , SER C:82 , HOH C:2843 , HOH C:2868 , HOH C:2896 , HOH C:2938 , HOH C:2989
BINDING SITE FOR RESIDUE SO4 C 2604
03
AC3
SOFTWARE
MET A:452 , GLN A:455 , HOH A:2858 , MET C:452 , GLN C:455 , HOH C:2859
BINDING SITE FOR RESIDUE NA A 2605
04
AC4
SOFTWARE
ASP B:447 , ASN B:474 , GLN B:476 , TPP B:2702
BINDING SITE FOR RESIDUE MG B 2701
05
AC5
SOFTWARE
ILE B:480 , TPP B:2702 , GLY D:34 , GLY D:35 , SER D:36 , SER D:82 , HOH D:2937 , HOH D:2978 , HOH D:3054 , HOH D:3072
BINDING SITE FOR RESIDUE SO4 D 2704
06
AC6
SOFTWARE
MET B:452 , GLN B:455 , HOH B:2971 , MET D:452 , GLN D:455 , HOH D:2971
BINDING SITE FOR RESIDUE NA B 2705
07
AC7
SOFTWARE
ASP C:447 , ASN C:474 , GLN C:476 , TPP C:2802
BINDING SITE FOR RESIDUE MG C 2801
08
AC8
SOFTWARE
GLY A:34 , GLY A:35 , SER A:36 , SER A:82 , HOH A:2827 , HOH A:2832 , HOH A:2977 , HOH A:3050 , ILE C:480 , TPP C:2802
BINDING SITE FOR RESIDUE SO4 A 2804
09
AC9
SOFTWARE
ASP D:447 , ASN D:474 , GLN D:476 , TPP D:2902 , HOH D:2946
BINDING SITE FOR RESIDUE MG D 2901
10
BC1
SOFTWARE
GLY B:34 , GLY B:35 , SER B:36 , SER B:82 , PHE B:111 , HOH B:2937 , HOH B:2939 , HOH B:3108 , HOH B:3151 , ILE D:480 , TPP D:2902
BINDING SITE FOR RESIDUE SO4 B 2904
11
BC2
SOFTWARE
VAL A:394 , ASP A:396 , ALA A:420 , MET A:422 , GLY A:446 , ASP A:447 , GLY A:448 , GLY A:449 , ASN A:474 , GLN A:476 , TYR A:477 , GLY A:478 , PHE A:479 , ILE A:480 , MG A:2601 , HOH A:2843 , HOH A:2846 , HOH A:2882 , PRO C:33 , GLU C:59 , SER C:82 , PRO C:85 , HIS C:89 , SO4 C:2604 , HOH C:2896
BINDING SITE FOR RESIDUE TPP A 2602
12
BC3
SOFTWARE
GLY A:220 , ILE A:221 , GLY A:222 , THR A:244 , PRO A:246 , GLY A:284 , ASN A:285 , ASN A:286 , ASP A:306 , ILE A:307 , LYS A:311 , ASP A:325 , ALA A:326 , HOH A:2901
BINDING SITE FOR RESIDUE FAD A 2603
13
BC4
SOFTWARE
VAL B:394 , ASP B:396 , ALA B:420 , MET B:422 , ASP B:447 , GLY B:448 , GLY B:449 , ASN B:474 , GLN B:476 , TYR B:477 , GLY B:478 , PHE B:479 , ILE B:480 , MG B:2701 , HOH B:2906 , HOH B:2915 , HOH B:3007 , PRO D:33 , GLU D:59 , SER D:82 , PRO D:85 , HIS D:89 , SO4 D:2704 , HOH D:2978
BINDING SITE FOR RESIDUE TPP B 2702
14
BC5
SOFTWARE
GLY B:220 , ILE B:221 , GLY B:222 , THR B:244 , PRO B:246 , GLY B:284 , ASN B:285 , ASN B:286 , ASP B:306 , ILE B:307 , ASP B:308 , LYS B:311 , ALA B:324 , ASP B:325 , ALA B:326 , HOH B:2953 , HOH B:3059 , HOH B:3379
BINDING SITE FOR RESIDUE FAD B 2703
15
BC6
SOFTWARE
PRO A:33 , GLU A:59 , SER A:82 , PRO A:85 , HIS A:89 , SO4 A:2804 , HOH A:2832 , VAL C:394 , GLY C:395 , ASP C:396 , ALA C:420 , MET C:422 , GLY C:446 , ASP C:447 , GLY C:448 , GLY C:449 , ASN C:474 , GLN C:476 , TYR C:477 , GLY C:478 , PHE C:479 , ILE C:480 , MG C:2801 , HOH C:2848 , HOH C:2854 , HOH C:2855
BINDING SITE FOR RESIDUE TPP C 2802
16
BC7
SOFTWARE
GLY C:220 , ILE C:221 , GLY C:222 , THR C:244 , PRO C:246 , GLY C:284 , ASN C:285 , ASN C:286 , ASP C:306 , ILE C:307 , LYS C:311 , ALA C:324 , ASP C:325 , ALA C:326 , HOH C:2931 , HOH C:3007 , HOH C:3015
BINDING SITE FOR RESIDUE FAD C 2803
17
BC8
SOFTWARE
PRO B:33 , GLU B:59 , SER B:82 , PRO B:85 , HIS B:89 , SO4 B:2904 , HOH B:2937 , VAL D:394 , ASP D:396 , ALA D:420 , MET D:422 , GLY D:446 , ASP D:447 , GLY D:448 , GLY D:449 , ASN D:474 , GLN D:476 , TYR D:477 , GLY D:478 , PHE D:479 , ILE D:480 , MG D:2901 , HOH D:2907 , HOH D:2946 , HOH D:2947 , HOH D:2976
BINDING SITE FOR RESIDUE TPP D 2902
18
BC9
SOFTWARE
GLY D:220 , ILE D:221 , GLY D:222 , THR D:244 , PRO D:246 , GLY D:284 , ASN D:285 , ASN D:286 , ASP D:306 , ILE D:307 , ASP D:308 , LYS D:311 , ALA D:324 , ASP D:325 , ALA D:326 , HOH D:3020
BINDING SITE FOR RESIDUE FAD D 2903
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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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:430-449,B:430-449,C:430-449,D:43...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TPP_ENZYMES
PS00187
Thiamine pyrophosphate enzymes signature.
POXB_LACPL
430-449
4
A:430-449
B:430-449
C:430-449
D:430-449
[
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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_d1y9da2 (A:192-365)
1b: SCOP_d1y9db2 (B:183-365)
1c: SCOP_d1y9dc2 (C:194-365)
1d: SCOP_d1y9dd2 (D:183-365)
2a: SCOP_d1y9da1 (A:9-182)
2b: SCOP_d1y9da3 (A:366-593)
2c: SCOP_d1y9db1 (B:9-182)
2d: SCOP_d1y9db3 (B:366-597)
2e: SCOP_d1y9dc1 (C:9-180)
2f: SCOP_d1y9dc3 (C:366-593)
2g: SCOP_d1y9dd1 (D:9-182)
2h: SCOP_d1y9dd3 (D:366-593)
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Classes
(
)
(
)
Folds
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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
:
Pyruvate oxidase and decarboxylase, middle domain
(74)
Protein domain
:
Pyruvate oxidase
(10)
Lactobacillus plantarum [TaxId: 1590]
(8)
1a
d1y9da2
A:192-365
1b
d1y9db2
B:183-365
1c
d1y9dc2
C:194-365
1d
d1y9dd2
D:183-365
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)
Lactobacillus plantarum [TaxId: 1590]
(6)
2a
d1y9da1
A:9-182
2b
d1y9da3
A:366-593
2c
d1y9db1
B:9-182
2d
d1y9db3
B:366-597
2e
d1y9dc1
C:9-180
2f
d1y9dc3
C:366-593
2g
d1y9dd1
D:9-182
2h
d1y9dd3
D:366-593
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1y9dA03 (A:360-549)
1b: CATH_1y9dB03 (B:360-549)
1c: CATH_1y9dC03 (C:360-549)
1d: CATH_1y9dD03 (D:360-549)
1e: CATH_1y9dB01 (B:9-192)
1f: CATH_1y9dD01 (D:9-186)
1g: CATH_1y9dA01 (A:9-192)
1h: CATH_1y9dC01 (C:9-180)
2a: CATH_1y9dB02 (B:193-359)
2b: CATH_1y9dC02 (C:194-359)
2c: CATH_1y9dA02 (A:193-359)
2d: CATH_1y9dD02 (D:195-359)
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)
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)
Architectures
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)
(
)
Topologies
(
)
(
)
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)
Lactobacillus plantarum. Organism_taxid: 1590.
(6)
1a
1y9dA03
A:360-549
1b
1y9dB03
B:360-549
1c
1y9dC03
C:360-549
1d
1y9dD03
D:360-549
1e
1y9dB01
B:9-192
1f
1y9dD01
D:9-186
1g
1y9dA01
A:9-192
1h
1y9dC01
C:9-180
Homologous Superfamily
:
TPP-binding domain
(120)
Lactobacillus plantarum. Organism_taxid: 1590.
(6)
2a
1y9dB02
B:193-359
2b
1y9dC02
C:194-359
2c
1y9dA02
A:193-359
2d
1y9dD02
D:195-359
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_TPP_enzyme_M_1y9dD01 (D:202-333)
1b: PFAM_TPP_enzyme_M_1y9dD02 (D:202-333)
1c: PFAM_TPP_enzyme_M_1y9dD03 (D:202-333)
1d: PFAM_TPP_enzyme_M_1y9dD04 (D:202-333)
2a: PFAM_TPP_enzyme_C_1y9dD05 (D:393-542)
2b: PFAM_TPP_enzyme_C_1y9dD06 (D:393-542)
2c: PFAM_TPP_enzyme_C_1y9dD07 (D:393-542)
2d: PFAM_TPP_enzyme_C_1y9dD08 (D:393-542)
3a: PFAM_TPP_enzyme_N_1y9dD09 (D:11-181)
3b: PFAM_TPP_enzyme_N_1y9dD10 (D:11-181)
3c: PFAM_TPP_enzyme_N_1y9dD11 (D:11-181)
3d: PFAM_TPP_enzyme_N_1y9dD12 (D:11-181)
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Clans
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Families
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)
(
)
Organisms
(
)
(
)
Clan
:
FAD_DHS
(82)
Family
:
TPP_enzyme_M
(50)
Lactobacillus plantarum
(3)
1a
TPP_enzyme_M-1y9dD01
D:202-333
1b
TPP_enzyme_M-1y9dD02
D:202-333
1c
TPP_enzyme_M-1y9dD03
D:202-333
1d
TPP_enzyme_M-1y9dD04
D:202-333
Clan
:
THDP-binding
(106)
Family
:
TPP_enzyme_C
(54)
Lactobacillus plantarum
(3)
2a
TPP_enzyme_C-1y9dD05
D:393-542
2b
TPP_enzyme_C-1y9dD06
D:393-542
2c
TPP_enzyme_C-1y9dD07
D:393-542
2d
TPP_enzyme_C-1y9dD08
D:393-542
Family
:
TPP_enzyme_N
(54)
Lactobacillus plantarum
(3)
3a
TPP_enzyme_N-1y9dD09
D:11-181
3b
TPP_enzyme_N-1y9dD10
D:11-181
3c
TPP_enzyme_N-1y9dD11
D:11-181
3d
TPP_enzyme_N-1y9dD12
D:11-181
[
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