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2JI9
Asym. Unit
Info
Asym.Unit (186 KB)
Biol.Unit 1 (355 KB)
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(1)
Title
:
X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH 3-DEAZA-THDP
Authors
:
C. L. Berthold, C. G. Toyota, P. Moussatche, M. D. Wood, F. Leeper, N. G. J. Richards, Y. Lindqvist
Date
:
26 Feb 07 (Deposition) - 17 Jul 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Oxalate Degradation, Thiamine Pyrophosphate, Lyase, Flavoprotein, Decarboxylase, Cofactor Analogue Inhibitor Complex, Non- Oxidative Decarboxylase, Thiamin Diphosphate-Dependent
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
C. L. Berthold, C. G. Toyota, P. Moussatche, M. D. Wood, F. Leeper, N. G. J. Richards, Y. Lindqvist
Crystallographic Snapshots Of Oxalyl-Coa Decarboxylase Give Insights Into Catalysis By Nonoxidative Thdp-Dependent Decarboxylases
Structure V. 15 853 2007
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Hetero Components
(4, 8)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
2a: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHY... (B3Pa)
2b: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHY... (B3Pb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
4a: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPWa)
4b: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPWb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
ADP
2
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
B3P
2
Ligand/Ion
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3
MG
2
Ligand/Ion
MAGNESIUM ION
4
TPW
2
Ligand/Ion
2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGENDIPHOSPHATE
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Sites
(8, 8)
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)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
VAL A:32 , GLU A:56 , ASN A:86 , GLU A:121 , TYR B:377 , GLY B:400 , ALA B:401 , ASN B:402 , ALA B:403 , GLY B:426 , MET B:428 , GLY B:451 , ASP B:452 , SER B:453 , ALA B:454 , PHE B:457 , ASN B:479 , GLY B:481 , ILE B:482 , TYR B:483 , MG B:1555 , HOH B:2251 , HOH B:2269
BINDING SITE FOR RESIDUE TPW B1554
2
AC2
SOFTWARE
TYR A:377 , GLY A:400 , ALA A:401 , ASN A:402 , ALA A:403 , GLY A:426 , MET A:428 , GLY A:451 , ASP A:452 , SER A:453 , ALA A:454 , PHE A:457 , ASN A:479 , GLY A:481 , ILE A:482 , TYR A:483 , MG A:1555 , HOH A:2245 , HOH A:2250 , VAL B:32 , GLU B:56 , VAL B:79 , ASN B:86 , GLU B:121
BINDING SITE FOR RESIDUE TPW A1554
3
AC3
SOFTWARE
ASP B:452 , ASN B:479 , GLY B:481 , TPW B:1554 , HOH B:2269
BINDING SITE FOR RESIDUE MG B1555
4
AC4
SOFTWARE
ASP A:452 , ASN A:479 , GLY A:481 , TPW A:1554 , HOH A:2250
BINDING SITE FOR RESIDUE MG A1555
5
AC5
SOFTWARE
ARG B:160 , GLY B:221 , LYS B:222 , GLY B:223 , TYR B:226 , MET B:247 , GLY B:280 , ALA B:281 , ARG B:282 , ASP B:306 , ILE B:307 , GLY B:324 , ASP B:325 , ILE B:326 , HOH B:2311 , HOH B:2312
BINDING SITE FOR RESIDUE ADP B1556
6
AC6
SOFTWARE
ARG A:160 , GLY A:221 , LYS A:222 , GLY A:223 , MET A:247 , GLY A:280 , ALA A:281 , ARG A:282 , LEU A:286 , ASP A:306 , ILE A:307 , GLY A:324 , ASP A:325 , ILE A:326 , HOH A:2244 , HOH A:2300 , HOH A:2301 , HOH A:2302
BINDING SITE FOR RESIDUE ADP A1556
7
AC7
SOFTWARE
ASP A:489 , GLY A:493 , VAL A:494 , ARG A:499
BINDING SITE FOR RESIDUE B3P A1557
8
AC8
SOFTWARE
ASP B:489 , GLY B:493 , ARG B:499
BINDING SITE FOR RESIDUE B3P B1557
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2ji9a1 (A:195-369)
1b: SCOP_d2ji9b1 (B:195-369)
2a: SCOP_d2ji9a3 (A:370-553)
2b: SCOP_d2ji9b3 (B:370-553)
3a: SCOP_d2ji9a2 (A:7-194)
3b: SCOP_d2ji9b2 (B:7-194)
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Classes
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Folds
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Superfamilies
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)
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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
:
Pyruvate oxidase and decarboxylase, middle domain
(74)
Protein domain
:
Oxalyl-CoA decarboxylase
(6)
Oxalobacter formigenes [TaxId: 847]
(6)
1a
d2ji9a1
A:195-369
1b
d2ji9b1
B:195-369
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
Pyruvate oxidase and decarboxylase PP module
(43)
Protein domain
:
Oxalyl-CoA decarboxylase
(6)
Oxalobacter formigenes [TaxId: 847]
(6)
2a
d2ji9a3
A:370-553
2b
d2ji9b3
B:370-553
Family
:
Pyruvate oxidase and decarboxylase Pyr module
(43)
Protein domain
:
Oxalyl-CoA decarboxylase
(6)
Oxalobacter formigenes [TaxId: 847]
(6)
3a
d2ji9a2
A:7-194
3b
d2ji9b2
B:7-194
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_TPP_enzyme_M_2ji9B01 (B:203-335)
1b: PFAM_TPP_enzyme_M_2ji9B02 (B:203-335)
2a: PFAM_TPP_enzyme_C_2ji9B03 (B:400-543)
2b: PFAM_TPP_enzyme_C_2ji9B04 (B:400-543)
3a: PFAM_TPP_enzyme_N_2ji9B05 (B:10-181)
3b: PFAM_TPP_enzyme_N_2ji9B06 (B:10-181)
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)
Clan
:
FAD_DHS
(82)
Family
:
TPP_enzyme_M
(50)
Oxalobacter formigenes
(4)
1a
TPP_enzyme_M-2ji9B01
B:203-335
1b
TPP_enzyme_M-2ji9B02
B:203-335
Clan
:
THDP-binding
(106)
Family
:
TPP_enzyme_C
(54)
Oxalobacter formigenes
(4)
2a
TPP_enzyme_C-2ji9B03
B:400-543
2b
TPP_enzyme_C-2ji9B04
B:400-543
Family
:
TPP_enzyme_N
(54)
Oxalobacter formigenes
(4)
3a
TPP_enzyme_N-2ji9B05
B:10-181
3b
TPP_enzyme_N-2ji9B06
B:10-181
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (186 KB)
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