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4K9O
Asym. Unit
Info
Asym.Unit (354 KB)
Biol.Unit 1 (346 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE PHE397ALA MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
Authors
:
H. R. Brodkin, M. J. Mcleish
Date
:
20 Apr 13 (Deposition) - 08 May 13 (Release) - 08 May 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.89
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Thiamine Diphosphate, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. R. Brodkin, F. H. Andrews, A. C. Milne, G. A. Petsko, D. Ringe, M. J. Mcleish
Crystal Structure Of The Phe397Ala Mutant Of Benzoylformate Decarboxylase From Pseudomonas Putida
To Be Published
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close entry info
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Hetero Components
(4, 16)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
4a: THIAMINE DIPHOSPHATE (TPPa)
4b: THIAMINE DIPHOSPHATE (TPPb)
4c: THIAMINE DIPHOSPHATE (TPPc)
4d: THIAMINE DIPHOSPHATE (TPPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
GOL
6
Ligand/Ion
GLYCEROL
3
MG
2
Ligand/Ion
MAGNESIUM ION
4
TPP
4
Ligand/Ion
THIAMINE DIPHOSPHATE
[
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Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:117 , LEU A:118 , ARG A:120 , HOH A:789 , ASN C:117 , LEU C:118 , ARG C:120
BINDING SITE FOR RESIDUE MG A 601
02
AC2
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 , LEU A:461 , CA A:603 , HOH A:735 , HOH A:745 , ASN C:23 , PRO C:24 , GLY C:25 , GLU C:47 , HIS C:70 , ASN C:77 , HOH C:1016
BINDING SITE FOR RESIDUE TPP A 602
03
AC3
SOFTWARE
ASP A:428 , ASN A:455 , THR A:457 , TPP A:602 , HOH A:735
BINDING SITE FOR RESIDUE CA A 603
04
AC4
SOFTWARE
ASP B:428 , ASN B:455 , THR B:457 , TPP B:603 , HOH B:765
BINDING SITE FOR RESIDUE CA B 601
05
AC5
SOFTWARE
ASN B:117 , LEU B:118 , ARG B:120 , HOH B:712 , ASN D:117 , LEU D:118 , ARG D:120
BINDING SITE FOR RESIDUE MG B 602
06
AC6
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 , LEU B:461 , CA B:601 , HOH B:765 , HOH B:881 , ASN D:23 , PRO D:24 , GLY D:25 , GLU D:47 , HIS D:70 , ASN D:77 , HOH D:997
BINDING SITE FOR RESIDUE TPP B 603
07
AC7
SOFTWARE
HIS B:281 , GLN B:282 , PHE B:464 , SER D:26
BINDING SITE FOR RESIDUE GOL B 604
08
AC8
SOFTWARE
ARG B:14 , ASP B:176 , ARG B:177 , HIS B:178 , HOH B:807 , HOH B:997
BINDING SITE FOR RESIDUE GOL B 605
09
AC9
SOFTWARE
ASP B:364 , HOH B:1024 , GLU C:37
BINDING SITE FOR RESIDUE GOL B 606
10
BC1
SOFTWARE
ARG B:101 , GLU B:128 , PRO B:129 , ALA B:130 , HOH B:1015 , ARG C:101 , GLU C:128 , PRO C:129 , ALA C:130
BINDING SITE FOR RESIDUE GOL B 607
11
BC2
SOFTWARE
ASP C:428 , ASN C:455 , THR C:457 , TPP C:602 , HOH C:766
BINDING SITE FOR RESIDUE CA C 601
12
BC3
SOFTWARE
ASN A:23 , PRO A:24 , GLY A:25 , GLU A:47 , HIS A:70 , ASN A:77 , 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 , LEU C:461 , CA C:601 , HOH C:766 , HOH C:782 , HOH C:1022
BINDING SITE FOR RESIDUE TPP C 602
13
BC4
SOFTWARE
ARG C:294 , ASP C:312
BINDING SITE FOR RESIDUE GOL C 603
14
BC5
SOFTWARE
ASP D:428 , ASN D:455 , THR D:457 , TPP D:602 , HOH D:716
BINDING SITE FOR RESIDUE CA D 601
15
BC6
SOFTWARE
ASN B:23 , PRO B:24 , GLY B:25 , GLU B:47 , HIS B:70 , ASN B:77 , 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 , LEU D:461 , CA D:601 , HOH D:716 , HOH D:981 , HOH D:1000
BINDING SITE FOR RESIDUE TPP D 602
16
BC7
SOFTWARE
ARG A:101 , GLU A:128 , PRO A:129 , ALA A:130 , ARG D:101 , GLU D:128 , PRO D:129 , ALA D:130 , HOH D:815
BINDING SITE FOR RESIDUE GOL D 603
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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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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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_d4k9oa2 (A:182-341)
1b: SCOP_d4k9ob2 (B:182-341)
1c: SCOP_d4k9oc2 (C:182-341)
1d: SCOP_d4k9od2 (D:182-341)
2a: SCOP_d4k9oa1 (A:2-181)
2b: SCOP_d4k9oa3 (A:342-526)
2c: SCOP_d4k9ob1 (B:2-181)
2d: SCOP_d4k9ob3 (B:342-526)
2e: SCOP_d4k9oc1 (C:2-181)
2f: SCOP_d4k9oc3 (C:342-525)
2g: SCOP_d4k9od1 (D:2-181)
2h: SCOP_d4k9od3 (D:342-525)
View:
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Classes
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Folds
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(
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Superfamilies
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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
:
Pyruvate oxidase and decarboxylase, middle domain
(74)
Protein domain
:
Benzoylformate decarboxylase
(32)
Pseudomonas putida [TaxId: 303]
(32)
1a
d4k9oa2
A:182-341
1b
d4k9ob2
B:182-341
1c
d4k9oc2
C:182-341
1d
d4k9od2
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
d4k9oa1
A:2-181
2b
d4k9oa3
A:342-526
2c
d4k9ob1
B:2-181
2d
d4k9ob3
B:342-526
2e
d4k9oc1
C:2-181
2f
d4k9oc3
C:342-525
2g
d4k9od1
D:2-181
2h
d4k9od3
D:342-525
[
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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
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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