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2V3W
Asym. Unit
Info
Asym.Unit (343 KB)
Biol.Unit 1 (336 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE BENZOYLFORMATE DECARBOXYLASE VARIANT L461A FROM PSEUDOMONAS PUTIDA
Authors
:
D. Gocke, L. Walter, K. Gauchenova, G. Kolter, M. Knoll, C. L. Berthold, G. Schneider, J. Pleiss, M. Mueller, M. Pohl
Date
:
25 Jun 07 (Deposition) - 22 Jan 08 (Release) - 10 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Lyase, Calcium, Magnesium, Flavoprotein, Thiamine Pyrophosphate, Rational Protein Design, Aromatic Hydrocarbons Catabolism, Thdp-Dependent, Mandelate Pathway, Metal-Binding, Decarboxylase, Carboligation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Gocke, L. Walter, K. Gauchenova, G. Kolter, M. Knoll, C. L. Berthold G. Schneider, J. Pleiss, M. Muller, M. Pohl
Rational Protein Design Of Thdp-Dependent Enzymes- Engineering Stereoselectivity.
Chembiochem V. 9 406 2008
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Hetero Components
(3, 14)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
3a: THIAMINE DIPHOSPHATE (TPPa)
3b: THIAMINE DIPHOSPHATE (TPPb)
3c: THIAMINE DIPHOSPHATE (TPPc)
3d: THIAMINE DIPHOSPHATE (TPPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
6
Ligand/Ion
MAGNESIUM ION
2
SO4
4
Ligand/Ion
SULFATE ION
3
TPP
4
Ligand/Ion
THIAMINE DIPHOSPHATE
[
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Sites
(14, 14)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:428 , ASN A:455 , THR A:457 , TPP A:1531 , HOH A:2226
BINDING SITE FOR RESIDUE MG A1528
02
AC2
SOFTWARE
ASN A:117 , LEU A:118 , ARG A:120 , ASN C:117 , LEU C:118 , ARG C:120
BINDING SITE FOR RESIDUE MG A1529
03
AC3
SOFTWARE
ASP B:428 , ASN B:455 , THR B:457 , TPP B:1531 , HOH B:2214
BINDING SITE FOR RESIDUE MG B1528
04
AC4
SOFTWARE
ASN B:117 , LEU B:118 , ARG B:120 , ASN D:117 , LEU D:118 , ARG D:120
BINDING SITE FOR RESIDUE MG B1529
05
AC5
SOFTWARE
ASP C:428 , ASN C:455 , THR C:457 , TPP C:1530 , HOH C:2206
BINDING SITE FOR RESIDUE MG C1528
06
AC6
SOFTWARE
ASP D:428 , ASN D:455 , THR D:457 , TPP D:1530 , HOH D:2192
BINDING SITE FOR RESIDUE MG D1528
07
AC7
SOFTWARE
HIS A:281 , PHE A:464 , TPP A:1531 , GLY C:25 , SER C:26 , HIS C:70 , LEU C:110 , HOH C:2246
BINDING SITE FOR RESIDUE SO4 C1529
08
AC8
SOFTWARE
HIS B:281 , TPP B:1531 , GLY D:25 , SER D:26 , HIS D:70 , LEU D:110
BINDING SITE FOR RESIDUE SO4 D1529
09
AC9
SOFTWARE
GLY A:25 , SER A:26 , HIS A:70 , LEU A:110 , HIS C:281 , PHE C:464 , TPP C:1530
BINDING SITE FOR RESIDUE SO4 A1530
10
BC1
SOFTWARE
GLY B:25 , SER B:26 , HIS B:70 , LEU B:110 , HOH B:2240 , HIS D:281 , TPP D:1530
BINDING SITE FOR RESIDUE SO4 B1530
11
BC2
SOFTWARE
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 , MG A:1528 , HOH A:2190 , HOH A:2226 , ASN C:23 , PRO C:24 , GLU C:47 , HIS C:70 , ASN C:77 , SO4 C:1529
BINDING SITE FOR RESIDUE TPP A1531
12
BC3
SOFTWARE
THR B:377 , SER B:378 , GLY B:401 , LEU B:403 , GLY B:427 , ASP B:428 , GLY B:429 , SER B:430 , TYR B:433 , ASN B:455 , THR B:457 , TYR B:458 , GLY B:459 , ALA B:460 , MG B:1528 , HOH B:2176 , HOH B:2214 , ASN D:23 , PRO D:24 , GLY D:25 , GLU D:47 , HIS D:70 , ASN D:77 , SO4 D:1529
BINDING SITE FOR RESIDUE TPP B1531
13
BC4
SOFTWARE
ASN A:23 , PRO A:24 , GLY A:25 , GLU A:47 , HIS A:70 , ASN A:77 , SO4 A:1530 , THR C:377 , SER C:378 , GLY C:401 , LEU C:403 , GLY C:427 , ASP C:428 , GLY C:429 , SER C:430 , TYR C:433 , ASN C:455 , THR C:457 , TYR C:458 , GLY C:459 , ALA C:460 , MG C:1528 , HOH C:2206 , HOH C:2247
BINDING SITE FOR RESIDUE TPP C1530
14
BC5
SOFTWARE
ASN B:23 , PRO B:24 , GLU B:47 , HIS B:70 , ASN B:77 , SO4 B:1530 , THR D:377 , SER D:378 , GLY D:401 , LEU D:403 , GLY D:427 , ASP D:428 , GLY D:429 , SER D:430 , TYR D:433 , ASN D:455 , THR D:457 , TYR D:458 , GLY D:459 , ALA D:460 , MG D:1528 , HOH D:2158 , HOH D:2192
BINDING SITE FOR RESIDUE TPP D1530
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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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:411-430,B:411-430,C:411-430,D:41...)
;
View:
Select:
Label:
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
4
A:411-430
B:411-430
C:411-430
D: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
(2, 12)
Info
All SCOP Domains
1a: SCOP_d2v3wa1 (A:182-341)
1b: SCOP_d2v3wb1 (B:182-341)
1c: SCOP_d2v3wc1 (C:182-341)
1d: SCOP_d2v3wd1 (D:182-341)
2a: SCOP_d2v3wa2 (A:2-181)
2b: SCOP_d2v3wa3 (A:342-527)
2c: SCOP_d2v3wb2 (B:2-181)
2d: SCOP_d2v3wb3 (B:342-527)
2e: SCOP_d2v3wc2 (C:2-181)
2f: SCOP_d2v3wc3 (C:342-527)
2g: SCOP_d2v3wd2 (D:2-181)
2h: SCOP_d2v3wd3 (D:342-527)
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Classes
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Folds
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)
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Families
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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)
Pseudomonas putida [TaxId: 303]
(1)
1a
d2v3wa1
A:182-341
1b
d2v3wb1
B:182-341
1c
d2v3wc1
C:182-341
1d
d2v3wd1
D: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
d2v3wa2
A:2-181
2b
d2v3wa3
A:342-527
2c
d2v3wb2
B:2-181
2d
d2v3wb3
B:342-527
2e
d2v3wc2
C:2-181
2f
d2v3wc3
C:342-527
2g
d2v3wd2
D:2-181
2h
d2v3wd3
D:342-527
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2v3wA03 (A:342-527)
1b: CATH_2v3wB03 (B:342-527)
1c: CATH_2v3wC03 (C:342-527)
1d: CATH_2v3wD03 (D:342-527)
1e: CATH_2v3wA01 (A:2-179)
1f: CATH_2v3wB01 (B:2-179)
1g: CATH_2v3wC01 (C:2-179)
1h: CATH_2v3wD01 (D:2-179)
2a: CATH_2v3wA02 (A:180-341)
2b: CATH_2v3wB02 (B:180-341)
2c: CATH_2v3wC02 (C:180-341)
2d: CATH_2v3wD02 (D:180-341)
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Topologies
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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)
Pseudomonas putida. Organism_taxid: 303.
(8)
1a
2v3wA03
A:342-527
1b
2v3wB03
B:342-527
1c
2v3wC03
C:342-527
1d
2v3wD03
D:342-527
1e
2v3wA01
A:2-179
1f
2v3wB01
B:2-179
1g
2v3wC01
C:2-179
1h
2v3wD01
D:2-179
Homologous Superfamily
:
TPP-binding domain
(120)
Pseudomonas putida. Organism_taxid: 303.
(8)
2a
2v3wA02
A:180-341
2b
2v3wB02
B:180-341
2c
2v3wC02
C:180-341
2d
2v3wD02
D:180-341
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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