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1BFD
Asym. Unit
Info
Asym.Unit (93 KB)
Biol.Unit 1 (344 KB)
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(1)
Title
:
BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
Authors
:
M. S. Hasson, A. Muscate, M. J. Mcleish, L. S. Polovnikova, J. A. Gerlt, G. L. Kenyon, G. A. Petsko, D. Ringe
Date
:
30 Apr 98 (Deposition) - 24 Jun 98 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A
Biol. Unit 1: A (4x)
Keywords
:
Lyase, Carbon-Carbon, Decarboxylase, Mandelate Catabolism, Thiamin Diphosphate
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. S. Hasson, A. Muscate, M. J. Mcleish, L. S. Polovnikova, J. A. Gerlt, G. L. Kenyon, G. A. Petsko, D. Ringe
The Crystal Structure Of Benzoylformate Decarboxylase At 1. A Resolution: Diversity Of Catalytic Residues In Thiamin Diphosphate-Dependent Enzymes.
Biochemistry V. 37 9918 1998
(for further references see the
PDB file header
)
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: MAGNESIUM ION (MGa)
3a: THIAMINE DIPHOSPHATE (TPPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
MG
1
Ligand/Ion
MAGNESIUM ION
3
TPP
1
Ligand/Ion
THIAMINE DIPHOSPHATE
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: CA1 (UNKNOWN)
6: CA2 (UNKNOWN)
7: MG1 (UNKNOWN)
8: PP2 (UNKNOWN)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:428 , ASN A:455 , THR A:457 , TPP A:530 , HOH A:533
BINDING SITE FOR RESIDUE CA A 529
2
AC2
SOFTWARE
ASN A:117 , LEU A:118 , ARG A:120 , HOH A:803
BINDING SITE FOR RESIDUE MG A 531
3
AC3
SOFTWARE
GLU A:37 , ASP A:364 , HOH A:691 , HOH A:700 , HOH A:703 , HOH A:844 , HOH A:845
BINDING SITE FOR RESIDUE CA A 532
4
AC4
SOFTWARE
ASN A:23 , PRO A:24 , GLY A:25 , GLU A:47 , HIS A:70 , ASN A:77 , THR A:377 , SER A:378 , GLY A:401 , LEU A:403 , GLY A:427 , ASP A:428 , GLY A:429 , SER A:430 , TYR A:433 , ASN A:455 , THR A:457 , TYR A:458 , GLY A:459 , ALA A:460 , CA A:529 , HOH A:540
BINDING SITE FOR RESIDUE TPP A 530
5
CA1
UNKNOWN
CA A:529
DIVALENT CATION BOUND TO PYROPHOSPHATE OF TPP (CA 529).
6
CA2
UNKNOWN
CA A:532
CALCIUM ION AT CRYSTAL CONTACT (CA 532).
7
MG1
UNKNOWN
MG A:531
MAGNESIUM ION ON CRYSTALLOGRAPHIC TWO-FOLD AT DIMER INTERFACE (MG 531).
8
PP2
UNKNOWN
ARG A:334 , GLN A:335 , LEU A:336 , PRO A:337 , THR A:338 , ALA A:339 , ALA A:340 , PRO A:341 , GLU A:342 , PRO A:343 , ALA A:344 , LYS A:345 , VAL A:346
POLYPROLINE TYPE II HELIX FROM ARG 334 THROUGH VAL 346.
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: TPP_ENZYMES (A:411-430)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TPP_ENZYMES
PS00187
Thiamine pyrophosphate enzymes signature.
MDLC_PSEPU
411-430
1
A:411-430
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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
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1bfda1 (A:182-341)
2a: SCOP_d1bfda3 (A:342-524)
3a: SCOP_d1bfda2 (A:2-181)
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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
:
Benzoylformate decarboxylase
(32)
Pseudomonas putida [TaxId: 303]
(32)
1a
d1bfda1
A:182-341
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
:
Benzoylformate decarboxylase
(7)
Pseudomonas putida [TaxId: 303]
(7)
2a
d1bfda3
A:342-524
Family
:
Pyruvate oxidase and decarboxylase Pyr module
(43)
Protein domain
:
Benzoylformate decarboxylase
(7)
Pseudomonas putida [TaxId: 303]
(7)
3a
d1bfda2
A:2-181
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CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_1bfdA03 (A:342-524)
1b: CATH_1bfdA02 (A:2-179)
2a: CATH_1bfdA01 (A:180-341)
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)
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)
Pseudomonas putida. Organism_taxid: 303. Strain: rf4738.
(2)
1a
1bfdA03
A:342-524
1b
1bfdA02
A:2-179
Homologous Superfamily
:
TPP-binding domain
(120)
Pseudomonas putida. Organism_taxid: 303. Strain: rf4738.
(2)
2a
1bfdA01
A:180-341
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Pfam Domains
(0, 0)
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Chain A
Asymmetric Unit 1
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