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2VZE
Asym. Unit
Info
Asym.Unit (242 KB)
Biol.Unit 1 (82 KB)
Biol.Unit 2 (81 KB)
Biol.Unit 3 (80 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
Authors
:
W. W. Yue, G. T. Kochan, E. S. Pilka, C. Bhatia, F. Von Delft, C. H. Arrows A. M. Edwards, M. Wikstrom, C. Bountra, U. Oppermann
Date
:
31 Jul 08 (Deposition) - 14 Oct 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.45
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Ligase, Metal-Binding, Transit Peptide, Lipid Metabolism, Nucleotide-Binding, Atp-Binding, Adenylate-Forming Enzyme, Fatty Acid Metabolism, Fatty Acid-Coa Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Kochan, E. S. Pilka, F. V. 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
(2, 4)
Info
All Hetero Components
1a: ADENOSINE MONOPHOSPHATE (AMPa)
1b: ADENOSINE MONOPHOSPHATE (AMPb)
1c: ADENOSINE MONOPHOSPHATE (AMPc)
2a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AMP
3
Ligand/Ion
ADENOSINE MONOPHOSPHATE
2
MG
1
Ligand/Ion
MAGNESIUM ION
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
MET C:483 , HIS C:485 , VAL C:488
BINDING SITE FOR RESIDUE MG C1570
2
AC2
SOFTWARE
TRP A:265 , 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 , ASN A:467 , ARG A:472 , HOH A:2157 , HOH A:2212 , HOH A:2215 , HOH A:2256
BINDING SITE FOR RESIDUE AMP A1570
3
AC3
SOFTWARE
TRP C:265 , GLY C:338 , GLU C:339 , SER C:340 , GLU C:359 , SER C:360 , TYR C:361 , GLY C:362 , GLN C:363 , THR C:364 , ASP C:446 , PHE C:458 , ARG C:461 , ASN C:467 , ARG C:472 , HOH C:2093 , HOH C:2163 , HOH C:2164 , HOH C:2165
BINDING SITE FOR RESIDUE AMP C1571
4
AC4
SOFTWARE
TRP B:265 , GLY B:338 , GLU B:339 , SER B:340 , GLU B:359 , SER B:360 , TYR B:361 , GLY B:362 , GLN B:363 , THR B:364 , ASP B:446 , PHE B:458 , ARG B:461 , ARG B:472 , HOH B:2145 , HOH B:2233 , HOH B:2234
BINDING SITE FOR RESIDUE AMP B1570
[
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SAPs(SNPs)/Variants
(5, 15)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_058692 (V335L, chain A/B/C, )
2: VAR_058693 (T336A, chain A/B/C, )
3: VAR_058694 (V337G, chain A/B/C, )
4: VAR_035247 (S513L, chain A/B/C, )
5: VAR_035248 (A561T, chain A/B/C, )
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/B/C
V
335
L
2
UniProt
VAR_058693
T
336
A
ACS2A_HUMAN
Polymorphism
5002299
A/B/C
T
336
A
3
UniProt
VAR_058694
V
337
G
ACS2A_HUMAN
Polymorphism
4586421
A/B/C
V
337
G
4
UniProt
VAR_035247
S
513
L
ACS2A_HUMAN
Polymorphism
1133607
A/B/C
S
513
L
5
UniProt
VAR_035248
A
561
T
ACS2A_HUMAN
Polymorphism
1054977
A/B/C
A
561
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: AMP_BINDING (A:218-229,B:218-229,C: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
3
A:218-229
B:218-229
C:218-229
[
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Exons
(13, 39)
Info
All Exons
Exon 1.2a (A:37-59 | B:37-59 | C:34-59)
Exon 1.3 (A:60-130 | B:60-130 | C:60-130)
Exon 1.4 (A:130-199 | B:130-199 | C:130-199)
Exon 1.6b (A:199-247 | B:199-247 | C:199-247)
Exon 1.7 (A:247-298 | B:247-298 | C:247-298)
Exon 1.8 (A:299-325 | B:299-325 | C:299-325)
Exon 1.9 (A:325-366 | B:325-366 | C:325-366)
Exon 1.10 (A:367-393 | B:367-393 | C:367-393)
Exon 1.11 (A:394-427 | B:394-427 | C:394-427)
Exon 1.12 (A:428-470 | B:428-470 | C:428-470)
Exon 1.13 (A:470-503 | B:470-503 | C:470-503)
Exon 1.14 (A:504-543 | B:504-543 | C:504-543)
Exon 1.15b (A:544-569 | B:544-569 | C: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
3
A:37-59
B:37-59
C:34-59
23
23
26
1.3
ENST00000396104
3
ENSE00001682005
chr16:
20476839-20477049
211
ACS2A_HUMAN
60-130
71
3
A:60-130
B:60-130
C:60-130
71
71
71
1.4
ENST00000396104
4
ENSE00001771411
chr16:
20480834-20481041
208
ACS2A_HUMAN
130-199
70
3
A:130-199
B:130-199
C:130-199
70
70
70
1.6b
ENST00000396104
6b
ENSE00001731165
chr16:
20482395-20482538
144
ACS2A_HUMAN
199-247
49
3
A:199-247
B:199-247
C:199-247
49
49
49
1.7
ENST00000396104
7
ENSE00001594810
chr16:
20482858-20483011
154
ACS2A_HUMAN
247-298
52
3
A:247-298
B:247-298
C:247-298
52
52
52
1.8
ENST00000396104
8
ENSE00001697128
chr16:
20486684-20486763
80
ACS2A_HUMAN
299-325
27
3
A:299-325
B:299-325
C:299-325
27
27
27
1.9
ENST00000396104
9
ENSE00001626853
chr16:
20486972-20487095
124
ACS2A_HUMAN
325-366
42
3
A:325-366
B:325-366
C:325-366
42
42
42
1.10
ENST00000396104
10
ENSE00001780247
chr16:
20488691-20488771
81
ACS2A_HUMAN
367-393
27
3
A:367-393
B:367-393
C:367-393
27
27
27
1.11
ENST00000396104
11
ENSE00000516753
chr16:
20489898-20489999
102
ACS2A_HUMAN
394-427
34
3
A:394-427
B:394-427
C:394-427
34
34
34
1.12
ENST00000396104
12
ENSE00001611767
chr16:
20491895-20492022
128
ACS2A_HUMAN
428-470
43
3
A:428-470
B:428-470
C:428-470
43
43
43
1.13
ENST00000396104
13
ENSE00001600227
chr16:
20492144-20492243
100
ACS2A_HUMAN
470-503
34
3
A:470-503
B:470-503
C:470-503
34
34
34
1.14
ENST00000396104
14
ENSE00001682277
chr16:
20494380-20494499
120
ACS2A_HUMAN
504-543
40
3
A:504-543
B:504-543
C:504-543
40
40
40
1.15b
ENST00000396104
15b
ENSE00001523880
chr16:
20497896-20498989
1094
ACS2A_HUMAN
544-577
34
3
A:544-569
B:544-569
C:544-569
26
26
26
[
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]
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d2vzea_ (A:)
1b: SCOP_d2vzeb_ (B:)
1c: SCOP_d2vzec_ (C:)
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(
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(
)
(
)
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(
)
(
)
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
d2vzea_
A:
1b
d2vzeb_
B:
1c
d2vzec_
C:
[
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_2vzeA02 (A:463-569)
1b: CATH_2vzeB02 (B:463-569)
1c: CATH_2vzeC02 (C:463-569)
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(
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(
)
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(
)
(
)
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)
Human (Homo sapiens)
(5)
1a
2vzeA02
A:463-569
1b
2vzeB02
B:463-569
1c
2vzeC02
C:463-569
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_AMP_binding_2vzeC01 (C:82-493)
1b: PFAM_AMP_binding_2vzeC02 (C:82-493)
1c: PFAM_AMP_binding_2vzeC03 (C:82-493)
2a: PFAM_DUF4009_2vzeC04 (C:538-569)
2b: PFAM_DUF4009_2vzeC05 (C:538-569)
2c: PFAM_DUF4009_2vzeC06 (C:538-569)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
ANL
(32)
Family
:
AMP-binding
(32)
Homo sapiens (Human)
(2)
1a
AMP-binding-2vzeC01
C:82-493
1b
AMP-binding-2vzeC02
C:82-493
1c
AMP-binding-2vzeC03
C:82-493
Clan
:
no clan defined [family: DUF4009]
(14)
Family
:
DUF4009
(14)
Homo sapiens (Human)
(2)
2a
DUF4009-2vzeC04
C:538-569
2b
DUF4009-2vzeC05
C:538-569
2c
DUF4009-2vzeC06
C:538-569
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Asym.Unit (242 KB)
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