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3F6B
Biol. Unit 1
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Asym.Unit (96 KB)
Biol.Unit 1 (353 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BENZOYLFORMATE DECARBOXYLASE IN COMPLEX WITH THE PYRIDYL INHIBITOR PAA
Authors
:
G. S. Brandt, M. J. Mcleish, G. L. Kenyon, G. A. Petsko, D. Ringe, F. Jordan
Date
:
05 Nov 08 (Deposition) - 09 Dec 08 (Release) - 17 Mar 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.34
Chains
:
Asym. Unit : X
Biol. Unit 1: X (4x)
Keywords
:
Thiamin Adduct, Aromatic Hydrocarbons Catabolism, Calcium, Decarboxylase, Lyase, Magnesium, Mandelate Pathway, Metal- Binding, Thiamine Pyrophosphate
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Chakraborty, N. S. Nemeria, A. Balakrishnan, G. S. Brandt, M. M. Kneen, A. Yep, M. J. Mcleish, G. L. Kenyon, G. A. Petsko, D. Ringe, F. Jordan
Detection And Time Course Of Formation Of Major Thiamin Diphosphate-Bound Covalent Intermediates Derived From A Chromophoric Substrate Analogue On Benzoylformate Decarboxylase.
Biochemistry V. 48 981 2009
(for further references see the
PDB file header
)
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL... (8PAa)
2a: MAGNESIUM ION (MGa)
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No.
Name
Count
Type
Full Name
1
8PA
4
Ligand/Ion
3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-[(1S,2E)-1-HYDROXY-3-PYRIDIN-3-YLPROP-2-EN-1-YL]-4-METHYL-1,3-THIAZOL-3-IUM
2
MG
-1
Ligand/Ion
MAGNESIUM ION
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP X:428 , ASN X:455 , THR X:457 , HOH X:527 , 8PA X:602
BINDING SITE FOR RESIDUE MG X 601
2
AC2
SOFTWARE
ASN X:23 , PRO X:24 , GLY X:25 , SER X:26 , GLU X:47 , HIS X:70 , ASN X:77 , HIS X:281 , GLU X:375 , THR X:377 , SER X:378 , GLY X:401 , LEU X:403 , GLY X:427 , ASP X:428 , GLY X:429 , SER X:430 , TYR X:433 , ASN X:455 , THR X:457 , TYR X:458 , GLY X:459 , ALA X:460 , MG X:601 , HOH X:621 , HOH X:689
BINDING SITE FOR RESIDUE 8PA X 602
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: TPP_ENZYMES (X:411-430)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TPP_ENZYMES
PS00187
Thiamine pyrophosphate enzymes signature.
MDLC_PSEPU
411-430
4
X:411-430
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Exons
(0, 0)
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SCOP Domains
(2, 3)
Info
All SCOP Domains
1a: SCOP_d3f6bx2 (X:182-341)
2a: SCOP_d3f6bx1 (X:2-181)
2b: SCOP_d3f6bx3 (X:342-526)
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Protein Domains
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Organisms
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(
)
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
:
Benzoylformate decarboxylase
(32)
Pseudomonas putida [TaxId: 303]
(32)
1a
d3f6bx2
X:182-341
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)
Pseudomonas putida [TaxId: 303]
(26)
2a
d3f6bx1
X:2-181
2b
d3f6bx3
X:342-526
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CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_3f6bX03 (X:342-526)
1b: CATH_3f6bX01 (X:2-179)
2a: CATH_3f6bX02 (X:180-341)
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Organisms
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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)
Pseudomonas putida. Organism_taxid: 303. Strain: dsm 291 / ncib 9494 /nctc 10936 / stanier 90.
(3)
1a
3f6bX03
X:342-526
1b
3f6bX01
X:2-179
Homologous Superfamily
:
TPP-binding domain
(120)
Pseudomonas putida. Organism_taxid: 303. Strain: dsm 291 / ncib 9494 /nctc 10936 / stanier 90.
(3)
2a
3f6bX02
X:180-341
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Pfam Domains
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