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Asym. Unit
Info
Asym.Unit (483 KB)
Biol.Unit 1 (946 KB)
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(1)
Title
:
HIGH-RESOLUTION CRYSTAL STRUCTURE OF PYRUVATE OXIDASE FROM L. PLANTARUM IN COMPLEX WITH PHOSPHATE
Authors
:
P. Neumann, K. Tittmann
Date
:
29 Apr 13 (Deposition) - 12 Jun 13 (Release) - 07 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.06
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Carbanion, Structure Activity Relationship, Oxidation-Reduction, Umpolung, Thiamine Diphosphate, Reaction Intermediate, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Meyer, P. Neumann, R. Ficner, K. Tittmann
Observation Of A Stable Carbene At The Active Site Of A Thiamin Enzyme.
Nat. Chem. Biol. V. 9 488 2013
[
close entry info
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Hetero Components
(6, 18)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
3a: POTASSIUM ION (Ka)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
6a: THIAMIN DIPHOSPHATE (TDPa)
6b: THIAMIN DIPHOSPHATE (TDPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
GOL
9
Ligand/Ion
GLYCEROL
3
K
1
Ligand/Ion
POTASSIUM ION
4
MG
2
Ligand/Ion
MAGNESIUM ION
5
PO4
2
Ligand/Ion
PHOSPHATE ION
6
TDP
2
Ligand/Ion
THIAMIN 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
HIS A:101 , PHE A:121 , GLY A:220 , ILE A:221 , GLY A:222 , THR A:244 , TYR A:245 , ALA A:262 , ASN A:263 , ARG A:264 , VAL A:265 , GLY A:284 , ASN A:285 , ASN A:286 , TYR A:287 , PRO A:288 , PHE A:289 , ASP A:306 , ILE A:307 , ASP A:308 , LYS A:311 , ASP A:325 , ALA A:326 , ASN A:398 , SER A:416 , ASN A:417 , HOH A:802 , HOH A:811 , HOH A:847 , HOH A:1078 , HOH A:1079 , HOH A:1184 , HOH A:1202 , HOH A:1342 , HOH A:1485
BINDING SITE FOR RESIDUE FAD A 701
02
AC2
SOFTWARE
ASP A:447 , ASN A:474 , GLN A:476 , TDP A:704 , HOH A:803
BINDING SITE FOR RESIDUE MG A 702
03
AC3
SOFTWARE
GLY A:34 , GLY A:35 , SER A:36 , SER A:82 , PHE A:111 , GLN A:122 , ILE A:480 , TDP A:704 , HOH A:912 , HOH A:1019 , HOH A:1487 , HOH A:1598
BINDING SITE FOR RESIDUE PO4 A 703
04
AC4
SOFTWARE
PRO A:33 , GLU A:59 , SER A:82 , PRO A:85 , HIS A:89 , GLN A:122 , 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:702 , PO4 A:703 , HOH A:803 , HOH A:820 , HOH A:824 , HOH A:846 , HOH A:1487
BINDING SITE FOR RESIDUE TDP A 704
05
AC5
SOFTWARE
ALA A:23 , TRP A:24 , LYS A:75 , TYR A:158 , ALA A:186 , TYR A:189 , HOH A:1024 , HOH A:1421
BINDING SITE FOR RESIDUE GOL A 705
06
AC6
SOFTWARE
LYS A:433 , PRO A:437 , GLU A:438 , PRO A:466 , ALA A:533 , GLN A:534 , HOH A:1089 , HOH A:1121 , HOH A:1373
BINDING SITE FOR RESIDUE GOL A 706
07
AC7
SOFTWARE
TRP A:174 , THR A:487 , GLN A:489 , HOH A:1291 , HOH A:1444
BINDING SITE FOR RESIDUE GOL A 707
08
AC8
SOFTWARE
ARG A:264 , GLU A:483 , ASP A:486 , GLU A:553 , HOH A:1029 , HOH A:1222 , HOH A:1347 , HOH A:1483 , HOH A:1496 , HOH A:1629
BINDING SITE FOR RESIDUE GOL A 708
09
AC9
SOFTWARE
MET A:452 , GLN A:455 , HOH A:825
BINDING SITE FOR RESIDUE K A 709
10
BC1
SOFTWARE
HIS B:101 , PHE B:121 , GLY B:220 , ILE B:221 , GLY B:222 , THR B:244 , TYR B:245 , PRO B:246 , ALA B:262 , ASN B:263 , ARG B:264 , VAL B:265 , GLY B:284 , ASN B:285 , ASN B:286 , TYR B:287 , PRO B:288 , PHE B:289 , ASP B:306 , ILE B:307 , ASP B:308 , LYS B:311 , ASP B:325 , ALA B:326 , ASN B:398 , SER B:416 , ASN B:417 , HOH B:801 , HOH B:807 , HOH B:816 , HOH B:819 , HOH B:1132 , HOH B:1133 , HOH B:1336 , HOH B:1498 , HOH B:1553
BINDING SITE FOR RESIDUE FAD B 701
11
BC2
SOFTWARE
ASP B:447 , ASN B:474 , GLN B:476 , TDP B:703 , HOH B:802
BINDING SITE FOR RESIDUE MG B 702
12
BC3
SOFTWARE
PRO B:33 , GLU B:59 , SER B:82 , PRO B:85 , HIS B:89 , GLN B:122 , VAL B:394 , ASP B:396 , ALA B:420 , MET B:422 , GLY B:446 , 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:702 , PO4 B:704 , HOH B:802 , HOH B:817 , HOH B:821 , HOH B:855 , HOH B:1496
BINDING SITE FOR RESIDUE TDP B 703
13
BC4
SOFTWARE
GLY B:34 , GLY B:35 , SER B:36 , SER B:82 , PHE B:111 , GLN B:122 , ILE B:480 , TDP B:703 , HOH B:873 , HOH B:1030 , HOH B:1356 , HOH B:1496
BINDING SITE FOR RESIDUE PO4 B 704
14
BC5
SOFTWARE
LYS B:433 , PRO B:437 , GLU B:438 , PRO B:466 , ALA B:533 , GLN B:534 , HOH B:1176 , HOH B:1235
BINDING SITE FOR RESIDUE GOL B 705
15
BC6
SOFTWARE
THR B:487 , HOH B:1306 , HOH B:1712
BINDING SITE FOR RESIDUE GOL B 706
16
BC7
SOFTWARE
HOH A:1083 , ALA B:569 , PHE B:570 , ARG B:573 , TYR B:574 , HOH B:961 , HOH B:980 , HOH B:1187 , HOH B:1379
BINDING SITE FOR RESIDUE GOL B 707
17
BC8
SOFTWARE
PRO B:409 , SER B:410 , ASN B:411 , ARG B:412 , TYR B:436 , ARG B:439 , GOL B:709
BINDING SITE FOR RESIDUE GOL B 708
18
BC9
SOFTWARE
PRO B:409 , ARG B:412 , GOL B:708 , HOH B:917 , HOH B:939 , HOH B:996 , HOH B:1558
BINDING SITE FOR RESIDUE GOL B 709
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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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, 6)
Info
All SCOP Domains
1a: SCOP_d4kgda2 (A:183-365)
1b: SCOP_d4kgdb2 (B:183-365)
2a: SCOP_d4kgda1 (A:9-182)
2b: SCOP_d4kgda3 (A:366-594)
2c: SCOP_d4kgdb1 (B:9-182)
2d: SCOP_d4kgdb3 (B:366-593)
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(
)
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)
Lactobacillus plantarum [TaxId: 644042]
(3)
1a
d4kgda2
A:183-365
1b
d4kgdb2
B: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: 644042]
(3)
2a
d4kgda1
A:9-182
2b
d4kgda3
A:366-594
2c
d4kgdb1
B:9-182
2d
d4kgdb3
B:366-593
[
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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
(0, 0)
Info
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Sorry, no Info available
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Asymmetric Unit 1
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