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3DAY
Asym. Unit
Info
Asym.Unit (110 KB)
Biol.Unit 1 (104 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY MEMBER 2A (L64P MUTATION) IN COMPLEX WITH AMP-CPP
Authors
:
E. S. Pilka, G. T. Kochan, W. W. Yue, C. Bhatia, F. Von Delft, C. H. Arrows A. M. Edwards, M. Wikstrom, C. Bountra, U. Oppermann, Structural Gen Consortium (Sgc)
Date
:
30 May 08 (Deposition) - 15 Jul 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Middle-Chain Acyl-Coa Synthetase, Xenobiotic/Medium-Chain Fatty Acid- Coa Ligase, Structural Genomics Consortium, Sgc, Atp-Binding, Fatty Acid Metabolism, Lipid Metabolism, Magnesium, Metal-Binding, Mitochondrion, Nucleotide-Binding Polymorphism, Transit Peptide, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Kochan, E. S. Pilka, F. Von Delft, U. Oppermann, W. W. Yue
Structural Snapshots For The Conformation-Dependent Catalysis By Human Medium-Chain Acyl-Coenzyme A Synthetase Acsm2A.
J. Mol. Biol. V. 388 997 2009
[
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Hetero Components
(6, 19)
Info
All Hetero Components
1a: DIPHOSPHOMETHYLPHOSPHONIC ACID ADE... (APCa)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
3a: GLYCEROL (GOLa)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
6a: UNKNOWN ATOM OR ION (UNXa)
6b: UNKNOWN ATOM OR ION (UNXb)
6c: UNKNOWN ATOM OR ION (UNXc)
6d: UNKNOWN ATOM OR ION (UNXd)
6e: UNKNOWN ATOM OR ION (UNXe)
6f: UNKNOWN ATOM OR ION (UNXf)
6g: UNKNOWN ATOM OR ION (UNXg)
6h: UNKNOWN ATOM OR ION (UNXh)
6i: UNKNOWN ATOM OR ION (UNXi)
6j: UNKNOWN ATOM OR ION (UNXj)
6k: UNKNOWN ATOM OR ION (UNXk)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
APC
1
Ligand/Ion
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2
CL
3
Ligand/Ion
CHLORIDE ION
3
GOL
1
Ligand/Ion
GLYCEROL
4
MG
2
Ligand/Ion
MAGNESIUM ION
5
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
6
UNX
11
Ligand/Ion
UNKNOWN ATOM OR ION
[
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]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
MET A:483 , HIS A:485 , HOH A:924 , HOH A:936 , HOH A:939
BINDING SITE FOR RESIDUE MG A 601
2
AC2
SOFTWARE
HOH A:791 , HOH A:1361 , HOH A:1362 , HOH A:1411
BINDING SITE FOR RESIDUE MG A 602
3
AC3
SOFTWARE
ARG A:316 , LEU A:342 , THR A:345
BINDING SITE FOR RESIDUE CL A 603
4
AC4
SOFTWARE
LEU A:288 , PRO A:289 , LYS A:290 , PHE A:291 , ASP A:292 , HOH A:694
BINDING SITE FOR RESIDUE CL A 604
5
AC5
SOFTWARE
ASP A:49 , HIS A:53
BINDING SITE FOR RESIDUE CL A 605
6
AC6
SOFTWARE
THR A:221 , SER A:222 , GLY A:223 , THR A:224 , SER A:225 , LYS A:229 , GLY A:338 , GLU A:339 , SER A:340 , GLU A:359 , SER A:360 , TYR A:361 , GLY A:362 , GLN A:363 , THR A:364 , ASP A:446 , PHE A:458 , ARG A:461 , LYS A:557 , HOH A:734 , HOH A:761 , HOH A:776 , HOH A:791 , HOH A:874 , HOH A:1211 , HOH A:1361 , HOH A:1362 , HOH A:1402 , HOH A:1411
BINDING SITE FOR RESIDUE APC A 606
7
AC7
SOFTWARE
MET A:80 , TRP A:81 , GLU A:85 , HOH A:910
BINDING SITE FOR RESIDUE TRS A 607
8
AC8
SOFTWARE
TRP A:71 , LYS A:77 , LEU A:79 , PRO A:117 , GLU A:118 , LYS A:195 , HOH A:832 , HOH A:883
BINDING SITE FOR RESIDUE GOL A 608
[
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SAPs(SNPs)/Variants
(5, 5)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_058692 (V335L, chain A, )
2: VAR_058693 (T336A, chain A, )
3: VAR_058694 (V337G, chain A, )
4: VAR_035247 (S513L, chain A, )
5: VAR_035248 (A561T, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_058692
V
335
L
ACS2A_HUMAN
Polymorphism
4643305
A
V
335
L
2
UniProt
VAR_058693
T
336
A
ACS2A_HUMAN
Polymorphism
5002299
A
T
336
A
3
UniProt
VAR_058694
V
337
G
ACS2A_HUMAN
Polymorphism
4586421
A
V
337
G
4
UniProt
VAR_035247
S
513
L
ACS2A_HUMAN
Polymorphism
1133607
A
S
513
L
5
UniProt
VAR_035248
A
561
T
ACS2A_HUMAN
Polymorphism
1054977
A
A
561
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: AMP_BINDING (A:218-229)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AMP_BINDING
PS00455
Putative AMP-binding domain signature.
ACS2A_HUMAN
218-229
1
A:218-229
[
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]
Exons
(13, 13)
Info
All Exons
Exon 1.2a (A:33-59)
Exon 1.3 (A:60-130)
Exon 1.4 (A:130-199)
Exon 1.6b (A:199-247)
Exon 1.7 (A:247-298)
Exon 1.8 (A:299-325)
Exon 1.9 (A:325-366)
Exon 1.10 (A:367-393)
Exon 1.11 (A:394-427)
Exon 1.12 (A:428-470)
Exon 1.13 (A:470-503 (gaps))
Exon 1.14 (A:504-543)
Exon 1.15b (A:544-569)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.2a
02: Boundary 1.2a/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.6b
05: Boundary 1.6b/1.7
06: Boundary 1.7/1.8
07: Boundary 1.8/1.9
08: Boundary 1.9/1.10
09: Boundary 1.10/1.11
10: Boundary 1.11/1.12
11: Boundary 1.12/1.13
12: Boundary 1.13/1.14
13: Boundary 1.14/1.15b
14: Boundary 1.15b/-
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
1.2a
ENST00000396104
2a
ENSE00001773140
chr16:
20471426-20471613
188
ACS2A_HUMAN
1-59
59
1
A:33-59
27
1.3
ENST00000396104
3
ENSE00001682005
chr16:
20476839-20477049
211
ACS2A_HUMAN
60-130
71
1
A:60-130
71
1.4
ENST00000396104
4
ENSE00001771411
chr16:
20480834-20481041
208
ACS2A_HUMAN
130-199
70
1
A:130-199
70
1.6b
ENST00000396104
6b
ENSE00001731165
chr16:
20482395-20482538
144
ACS2A_HUMAN
199-247
49
1
A:199-247
49
1.7
ENST00000396104
7
ENSE00001594810
chr16:
20482858-20483011
154
ACS2A_HUMAN
247-298
52
1
A:247-298
52
1.8
ENST00000396104
8
ENSE00001697128
chr16:
20486684-20486763
80
ACS2A_HUMAN
299-325
27
1
A:299-325
27
1.9
ENST00000396104
9
ENSE00001626853
chr16:
20486972-20487095
124
ACS2A_HUMAN
325-366
42
1
A:325-366
42
1.10
ENST00000396104
10
ENSE00001780247
chr16:
20488691-20488771
81
ACS2A_HUMAN
367-393
27
1
A:367-393
27
1.11
ENST00000396104
11
ENSE00000516753
chr16:
20489898-20489999
102
ACS2A_HUMAN
394-427
34
1
A:394-427
34
1.12
ENST00000396104
12
ENSE00001611767
chr16:
20491895-20492022
128
ACS2A_HUMAN
428-470
43
1
A:428-470
43
1.13
ENST00000396104
13
ENSE00001600227
chr16:
20492144-20492243
100
ACS2A_HUMAN
470-503
34
1
A:470-503 (gaps)
34
1.14
ENST00000396104
14
ENSE00001682277
chr16:
20494380-20494499
120
ACS2A_HUMAN
504-543
40
1
A:504-543
40
1.15b
ENST00000396104
15b
ENSE00001523880
chr16:
20497896-20498989
1094
ACS2A_HUMAN
544-577
34
1
A:544-569
26
[
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]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3daya_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Acetyl-CoA synthetase-like
(64)
Superfamily
:
Acetyl-CoA synthetase-like
(64)
Family
:
automated matches
(26)
Protein domain
:
automated matches
(26)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d3daya_
A:
[
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_3dayA02 (A:466-569)
View:
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Classes
(
)
(
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Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
GMP Synthetase; Chain A, domain 3
(192)
Homologous Superfamily
:
[code=3.30.300.30, no name defined]
(30)
Homo sapiens. Organism_taxid: 9606.
(1)
1a
3dayA02
A:466-569
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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