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Asym. Unit
Info
Asym.Unit (484 KB)
Biol.Unit 1 (476 KB)
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(1)
Title
:
BIOSYNTHETIC THIOLASE FROM Z. RAMIGERA. COMPLEX OF THE N316D MUTANT WITH COENZYME A.
Authors
:
G. Merilainen, V. Poikela, P. Kursula, R. K. Wierenga
Date
:
18 Jun 09 (Deposition) - 03 Nov 09 (Release) - 02 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Acyltransferase, Phb Biosynthesis, Cytoplasm, Transferase, Thiolase Fold
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Merilainen, V. Poikela, P. Kursula, R. K. Wierenga
The Thiolase Reaction Mechanism: The Importance Of Asn316 And His348 For Stabilizing The Enolate Intermediate Of The Claisen Condensation.
Biochemistry V. 48 11011 2009
[
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Hetero Components
(3, 16)
Info
All Hetero Components
1a: COENZYME A (COAa)
1b: COENZYME A (COAb)
1c: COENZYME A (COAc)
1d: COENZYME A (COAd)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
COA
4
Ligand/Ion
COENZYME A
2
NA
2
Ligand/Ion
SODIUM ION
3
SO4
10
Ligand/Ion
SULFATE ION
[
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Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER B:260 , ALA B:262 , ARG B:266 , HOH B:2257 , HOH B:2258
BINDING SITE FOR RESIDUE SO4 B1393
02
AC2
SOFTWARE
LYS B:298 , ARG B:302 , HOH B:2259
BINDING SITE FOR RESIDUE SO4 B1394
03
AC3
SOFTWARE
LYS A:298 , ARG A:302 , HOH A:2197 , HOH A:2237
BINDING SITE FOR RESIDUE SO4 A1393
04
AC4
SOFTWARE
ARG B:41 , ILE B:199 , PRO B:201 , HOH B:2260
BINDING SITE FOR RESIDUE SO4 B1395
05
AC5
SOFTWARE
LYS A:366
BINDING SITE FOR RESIDUE SO4 A1394
06
AC6
SOFTWARE
TYR B:153 , LYS B:286 , HOH B:2261 , HOH B:2262
BINDING SITE FOR RESIDUE SO4 B1396
07
AC7
SOFTWARE
SER A:260 , GLU A:263 , ARG A:266 , HOH A:2183 , HOH A:2239 , HOH A:2240
BINDING SITE FOR RESIDUE SO4 A1395
08
AC8
SOFTWARE
ARG D:41 , VAL D:200 , PRO D:201 , HOH D:2133 , HOH D:2134
BINDING SITE FOR RESIDUE SO4 D1393
09
AC9
SOFTWARE
PHE B:137 , LYS B:138 , HOH B:2263
BINDING SITE FOR RESIDUE SO4 B1397
10
BC1
SOFTWARE
ALA D:8 , SER D:9 , ARG D:41 , GLN D:270 , LEU D:272 , HOH D:2135
BINDING SITE FOR RESIDUE SO4 D1394
11
BC2
SOFTWARE
LEU A:88 , GLY A:380 , MET A:383 , ASN B:65 , ARG B:68
BINDING SITE FOR RESIDUE NA A1396
12
BC3
SOFTWARE
CYS A:89 , LEU A:148 , HIS A:156 , MET A:157 , GLN A:183 , ARG A:220 , SER A:227 , PHE A:235 , ALA A:243 , GLY A:244 , SER A:247 , MET A:288 , PHE A:319 , HOH A:2153 , HOH A:2160 , HOH A:2241 , HOH A:2242 , HOH A:2243 , HOH A:2244 , HOH A:2245 , HOH A:2246
BINDING SITE FOR RESIDUE COA A1397
13
BC4
SOFTWARE
CYS B:89 , HIS B:156 , MET B:157 , ARG B:220 , SER B:227 , MET B:228 , LEU B:231 , ALA B:243 , SER B:247 , GLY B:248 , LEU B:249 , PHE B:319 , HOH B:2192 , HOH B:2264 , HOH B:2265 , HOH B:2266 , HOH B:2267 , LYS C:133 , MET C:134
BINDING SITE FOR RESIDUE COA B1399
14
BC5
SOFTWARE
CYS C:89 , LEU C:148 , HIS C:156 , MET C:157 , ARG C:220 , SER C:227 , MET C:228 , LEU C:231 , ALA C:243 , GLY C:244 , SER C:247 , GLY C:248 , LEU C:249 , MET C:288 , PHE C:319 , HIS C:348 , HOH C:2089 , HOH C:2090 , HOH C:2091 , HOH C:2133 , HOH C:2134 , HOH C:2135 , HOH C:2136
BINDING SITE FOR RESIDUE COA C1393
15
BC6
SOFTWARE
CYS D:89 , LEU D:148 , HIS D:156 , MET D:157 , ARG D:220 , SER D:227 , MET D:228 , LEU D:231 , GLY D:244 , SER D:247 , PHE D:319 , HIS D:348 , HOH D:2129 , HOH D:2136
BINDING SITE FOR RESIDUE COA D1395
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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]
PROSITE Patterns/Profiles
(3, 12)
Info
All PROSITE Patterns/Profiles
1: THIOLASE_1 (A:85-103,B:85-103,C:85-103,D:85-10...)
2: THIOLASE_2 (A:338-354,B:338-354,C:338-354,D:33...)
3: THIOLASE_3 (A:373-386,B:373-386,C:373-386,D:37...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THIOLASE_1
PS00098
Thiolases acyl-enzyme intermediate signature.
THIL_ZOORA
85-103
4
A:85-103
B:85-103
C:85-103
D:85-103
2
THIOLASE_2
PS00737
Thiolases signature 2.
THIL_ZOORA
338-354
4
A:338-354
B:338-354
C:338-354
D:338-354
3
THIOLASE_3
PS00099
Thiolases active site.
THIL_ZOORA
373-386
4
A:373-386
B:373-386
C:373-386
D:373-386
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2wkva2 (A:269-392)
1b: SCOP_d2wkvb2 (B:269-392)
1c: SCOP_d2wkvc2 (C:269-392)
1d: SCOP_d2wkvd2 (D:269-392)
2a: SCOP_d2wkva1 (A:4-268)
2b: SCOP_d2wkvb1 (B:4-268)
2c: SCOP_d2wkvc1 (C:4-268)
2d: SCOP_d2wkvd1 (D:4-268)
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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
:
Thiolase-like
(231)
Superfamily
:
Thiolase-like
(231)
Family
:
automated matches
(108)
Protein domain
:
automated matches
(108)
Zoogloea ramigera [TaxId: 350]
(6)
1a
d2wkva2
A:269-392
1b
d2wkvb2
B:269-392
1c
d2wkvc2
C:269-392
1d
d2wkvd2
D:269-392
Family
:
Thiolase-related
(67)
Protein domain
:
automated matches
(12)
Zoogloea ramigera [TaxId: 350]
(6)
2a
d2wkva1
A:4-268
2b
d2wkvb1
B:4-268
2c
d2wkvc1
C:4-268
2d
d2wkvd1
D:4-268
[
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]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_2wkvA01 (A:4-124,A:194-275)
1b: CATH_2wkvA02 (A:152-193,A:276-389)
1c: CATH_2wkvB02 (B:152-193,B:276-389)
1d: CATH_2wkvC02 (C:152-193,C:276-389)
1e: CATH_2wkvD02 (D:152-193,D:276-389)
1f: CATH_2wkvB01 (B:4-124,B:194-275)
1g: CATH_2wkvC01 (C:4-124,C:194-275)
1h: CATH_2wkvD01 (D:4-124,D:194-275)
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Topologies
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(
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Peroxisomal Thiolase; Chain A, domain 1
(130)
Homologous Superfamily
:
[code=3.40.47.10, no name defined]
(130)
Zoogloea ramigera. Organism_taxid: 350.
(19)
1a
2wkvA01
A:4-124,A:194-275
1b
2wkvA02
A:152-193,A:276-389
1c
2wkvB02
B:152-193,B:276-389
1d
2wkvC02
C:152-193,C:276-389
1e
2wkvD02
D:152-193,D:276-389
1f
2wkvB01
B:4-124,B:194-275
1g
2wkvC01
C:4-124,C:194-275
1h
2wkvD01
D:4-124,D:194-275
[
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]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Thiolase_C_2wkvD01 (D:269-391)
1b: PFAM_Thiolase_C_2wkvD02 (D:269-391)
1c: PFAM_Thiolase_C_2wkvD03 (D:269-391)
1d: PFAM_Thiolase_C_2wkvD04 (D:269-391)
2a: PFAM_Thiolase_N_2wkvD05 (D:11-262)
2b: PFAM_Thiolase_N_2wkvD06 (D:11-262)
2c: PFAM_Thiolase_N_2wkvD07 (D:11-262)
2d: PFAM_Thiolase_N_2wkvD08 (D:11-262)
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Clans
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Families
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Organisms
(
)
(
)
Clan
:
Thiolase
(72)
Family
:
Thiolase_C
(23)
Zoogloea ramigera
(15)
1a
Thiolase_C-2wkvD01
D:269-391
1b
Thiolase_C-2wkvD02
D:269-391
1c
Thiolase_C-2wkvD03
D:269-391
1d
Thiolase_C-2wkvD04
D:269-391
Family
:
Thiolase_N
(23)
Zoogloea ramigera
(15)
2a
Thiolase_N-2wkvD05
D:11-262
2b
Thiolase_N-2wkvD06
D:11-262
2c
Thiolase_N-2wkvD07
D:11-262
2d
Thiolase_N-2wkvD08
D:11-262
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Asym.Unit (484 KB)
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