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2IB8
Asym. Unit
Info
Asym.Unit (263 KB)
Biol.Unit 1 (257 KB)
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Title
:
CRYSTALLOGRAPHIC AND KINETIC STUDIES OF HUMAN MITOCHONDRIAL ACETOACETYL-COA THIOLASE (T2): THE IMPORTANCE OF POTASSIUM AND CHLORIDE FOR ITS STRUCTURE AND FUNCTION
Authors
:
A. M. Haapalainen, R. K. Wierenga
Date
:
11 Sep 06 (Deposition) - 03 Apr 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Thiolase Fold, Potassium Ion, Chloride, Beta-Alpha-Beta-Alpha-Beta- Alpha-Beta-Beta Topology, Alpha-Beta-Alpha-Beta-Alpha Layered Structure, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. M. Haapalainen, G. Merilainen, P. L. Pirila, N. Kondo, T. Fukao, R. K. Wierenga
Crystallographic And Kinetic Studies Of Human Mitochondrial Acetoacetyl-Coa Thiolase: The Importance Of Potassium And Chloride Ions For Its Structure And Function
Biochemistry V. 46 4305 2007
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Hetero Components
(4, 17)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
3c: POTASSIUM ION (Kc)
3d: POTASSIUM ION (Kd)
4a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
4b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
4c: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESc)
4d: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
4
Ligand/Ion
CHLORIDE ION
2
GOL
5
Ligand/Ion
GLYCEROL
3
K
4
Ligand/Ion
POTASSIUM ION
4
MES
4
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
[
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Sites
(17, 17)
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)
17: BC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:414 , CYS B:119
BINDING SITE FOR RESIDUE CL B 2001
02
AC2
SOFTWARE
CYS A:119 , ASN B:414
BINDING SITE FOR RESIDUE CL A 2002
03
AC3
SOFTWARE
ASN C:414 , CYS D:119
BINDING SITE FOR RESIDUE CL D 2003
04
AC4
SOFTWARE
CYS C:119 , ASN D:414 , HOH D:3090
BINDING SITE FOR RESIDUE CL C 2004
05
AC5
SOFTWARE
TYR A:219 , ALA A:280 , ALA A:281 , ALA A:283 , VAL A:381 , HOH A:5100
BINDING SITE FOR RESIDUE K A 3001
06
AC6
SOFTWARE
TYR B:219 , ALA B:280 , ALA B:281 , ALA B:283 , VAL B:381 , HOH B:5069
BINDING SITE FOR RESIDUE K B 3002
07
AC7
SOFTWARE
TYR C:219 , ALA C:280 , ALA C:281 , ALA C:283 , VAL C:381 , HOH C:5016
BINDING SITE FOR RESIDUE K C 3003
08
AC8
SOFTWARE
TYR D:219 , ALA D:280 , ALA D:281 , ALA D:283 , VAL D:381 , HOH D:3061
BINDING SITE FOR RESIDUE K D 3004
09
AC9
SOFTWARE
PHE A:55 , LEU A:56 , LEU A:286 , HOH B:5042
BINDING SITE FOR RESIDUE MES A 5001
10
BC1
SOFTWARE
HOH A:5026 , PHE B:55 , LEU B:56 , LEU B:286 , HOH B:5296 , TYR D:170 , HOH D:3099
BINDING SITE FOR RESIDUE MES B 5002
11
BC2
SOFTWARE
TYR A:170 , PHE C:55 , LEU C:56
BINDING SITE FOR RESIDUE MES C 5003
12
BC3
SOFTWARE
PHE D:55 , LEU D:56
BINDING SITE FOR RESIDUE MES B 5004
13
BC4
SOFTWARE
LEU A:184 , SER A:284 , LEU A:286 , HOH A:5040 , HOH A:5217 , HOH A:5225
BINDING SITE FOR RESIDUE GOL A 4001
14
BC5
SOFTWARE
SER B:284 , THR B:285 , HOH B:5041 , HOH D:3135
BINDING SITE FOR RESIDUE GOL B 4002
15
BC6
SOFTWARE
ALA A:201 , ASN A:205 , THR A:277 , HOH A:5101 , HOH A:5142
BINDING SITE FOR RESIDUE GOL A 4003
16
BC7
SOFTWARE
HIS A:192 , VAL A:270 , PHE A:271
BINDING SITE FOR RESIDUE GOL A 4004
17
BC8
SOFTWARE
HIS C:192 , SER C:284 , HOH C:5018
BINDING SITE FOR RESIDUE GOL C 4005
[
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]
SAPs(SNPs)/Variants
(10, 40)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_007498 (N93S, chain A/B/C/D, )
02: VAR_007499 (G152A, chain A/B/C/D, )
03: VAR_007500 (N158D, chain A/B/C/D, )
04: VAR_007501 (G183R, chain A/B/C/D, )
05: VAR_007502 (T297M, chain A/B/C/D, )
06: VAR_007503 (A301P, chain A/B/C/D, )
07: VAR_007504 (I312T, chain A/B/C/D, )
08: VAR_007505 (A333P, chain A/B/C/D, )
09: VAR_007506 (G379V, chain A/B/C/D, )
10: VAR_007507 (A380T, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_007498
N
93
S
THIL_HUMAN
Disease (3KTD)
---
A/B/C/D
N
93
S
02
UniProt
VAR_007499
G
152
A
THIL_HUMAN
Disease (3KTD)
---
A/B/C/D
G
152
A
03
UniProt
VAR_007500
N
158
D
THIL_HUMAN
Disease (3KTD)
---
A/B/C/D
N
158
D
04
UniProt
VAR_007501
G
183
R
THIL_HUMAN
Disease (3KTD)
---
A/B/C/D
G
183
R
05
UniProt
VAR_007502
T
297
M
THIL_HUMAN
Disease (3KTD)
---
A/B/C/D
T
297
M
06
UniProt
VAR_007503
A
301
P
THIL_HUMAN
Disease (3KTD)
---
A/B/C/D
A
301
P
07
UniProt
VAR_007504
I
312
T
THIL_HUMAN
Disease (3KTD)
---
A/B/C/D
I
312
T
08
UniProt
VAR_007505
A
333
P
THIL_HUMAN
Disease (3KTD)
---
A/B/C/D
A
333
P
09
UniProt
VAR_007506
G
379
V
THIL_HUMAN
Disease (3KTD)
---
A/B/C/D
G
379
V
10
UniProt
VAR_007507
A
380
T
THIL_HUMAN
Disease (3KTD)
---
A/B/C/D
A
380
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 12)
Info
All PROSITE Patterns/Profiles
1: THIOLASE_1 (A:122-140,B:122-140,C:122-140,D:12...)
2: THIOLASE_2 (A:375-391,B:375-391,C:375-391,D:37...)
3: THIOLASE_3 (A:408-421,B:408-421,C:408-421,D:40...)
;
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_HUMAN
122-140
4
A:122-140
B:122-140
C:122-140
D:122-140
2
THIOLASE_2
PS00737
Thiolases signature 2.
THIL_HUMAN
375-391
4
A:375-391
B:375-391
C:375-391
D:375-391
3
THIOLASE_3
PS00099
Thiolases active site.
THIL_HUMAN
408-421
4
A:408-421
B:408-421
C:408-421
D:408-421
[
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]
Exons
(11, 44)
Info
All Exons
Exon 1.5 (A:37-40 | B:37-40 | C:36-40 | D:35...)
Exon 1.6a (A:41-80 | B:41-80 | C:41-80 | D:41...)
Exon 1.7b (A:80-112 | B:80-112 | C:80-112 | D...)
Exon 1.8b (A:112-145 | B:112-145 | C:112-145 ...)
Exon 1.10b (A:146-193 | B:146-193 | C:146-193 ...)
Exon 1.11c (A:194-244 | B:194-244 | C:194-244 ...)
Exon 1.12 (A:244-276 | B:244-276 | C:244-276 ...)
Exon 1.13a (A:276-314 | B:276-314 | C:276-314 ...)
Exon 1.14a (A:314-335 | B:314-335 | C:314-335 ...)
Exon 1.15b (A:336-388 | B:336-388 | C:336-388 ...)
Exon 1.16b (A:388-427 | B:388-427 | C:388-427 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.5
02: Boundary 1.5/1.6a
03: Boundary 1.6a/1.7b
04: Boundary 1.7b/1.8b
05: Boundary 1.8b/1.10b
06: Boundary 1.10b/1.11c
07: Boundary 1.11c/1.12
08: Boundary 1.12/1.13a
09: Boundary 1.13a/1.14a
10: Boundary 1.14a/1.15b
11: Boundary 1.15b/1.16b
12: Boundary 1.16b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000265838
1a
ENSE00001101645
chr11:
107992243-107992405
163
THIL_HUMAN
1-24
24
0
-
-
1.5
ENST00000265838
5
ENSE00001373389
chr11:
108002634-108002681
48
THIL_HUMAN
25-40
16
4
A:37-40
B:37-40
C:36-40
D:35-40
4
4
5
6
1.6a
ENST00000265838
6a
ENSE00001101659
chr11:
108004547-108004664
118
THIL_HUMAN
41-80
40
4
A:41-80
B:41-80
C:41-80
D:41-80
40
40
40
40
1.7b
ENST00000265838
7b
ENSE00001101630
chr11:
108004948-108005043
96
THIL_HUMAN
80-112
33
4
A:80-112
B:80-112
C:80-112
D:80-112
33
33
33
33
1.8b
ENST00000265838
8b
ENSE00001101665
chr11:
108005869-108005969
101
THIL_HUMAN
112-145
34
4
A:112-145
B:112-145
C:112-145
D:112-145
34
34
34
34
1.10b
ENST00000265838
10b
ENSE00000746482
chr11:
108009625-108009768
144
THIL_HUMAN
146-193
48
4
A:146-193
B:146-193
C:146-193
D:146-193
48
48
48
48
1.11c
ENST00000265838
11c
ENSE00001005122
chr11:
108010792-108010942
151
THIL_HUMAN
194-244
51
4
A:194-244
B:194-244
C:194-244
D:194-244
51
51
51
51
1.12
ENST00000265838
12
ENSE00001101670
chr11:
108012332-108012427
96
THIL_HUMAN
244-276
33
4
A:244-276
B:244-276
C:244-276
D:244-276
33
33
33
33
1.13a
ENST00000265838
13a
ENSE00001101653
chr11:
108013164-108013277
114
THIL_HUMAN
276-314
39
4
A:276-314
B:276-314
C:276-314
D:276-314
39
39
39
39
1.14a
ENST00000265838
14a
ENSE00001101638
chr11:
108014710-108014774
65
THIL_HUMAN
314-335
22
4
A:314-335
B:314-335
C:314-335
D:314-335
22
22
22
22
1.15b
ENST00000265838
15b
ENSE00001101628
chr11:
108016929-108017086
158
THIL_HUMAN
336-388
53
4
A:336-388
B:336-388
C:336-388
D:336-388
53
53
53
53
1.16b
ENST00000265838
16b
ENSE00001101634
chr11:
108017997-108018503
507
THIL_HUMAN
388-427
40
4
A:388-427
B:388-427
C:388-427
D:388-427
40
40
40
40
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_2ib8A01 (A:37-161,A:230-312)
1b: CATH_2ib8D01 (D:35-161,D:230-312)
1c: CATH_2ib8A02 (A:188-229,A:313-424)
1d: CATH_2ib8B02 (B:188-229,B:313-424)
1e: CATH_2ib8C02 (C:188-229,C:313-424)
1f: CATH_2ib8D02 (D:188-229,D:313-424)
1g: CATH_2ib8B01 (B:37-161,B:230-312)
1h: CATH_2ib8C01 (C:36-161,C:230-312)
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(
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Organisms
(
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(
)
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)
Human (Homo sapiens)
(12)
1a
2ib8A01
A:37-161,A:230-312
1b
2ib8D01
D:35-161,D:230-312
1c
2ib8A02
A:188-229,A:313-424
1d
2ib8B02
B:188-229,B:313-424
1e
2ib8C02
C:188-229,C:313-424
1f
2ib8D02
D:188-229,D:313-424
1g
2ib8B01
B:37-161,B:230-312
1h
2ib8C01
C:36-161,C:230-312
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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