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1YXM
Asym. Unit
Info
Asym.Unit (181 KB)
Biol.Unit 1 (174 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PEROXISOMAL TRANS 2-ENOYL COA REDUCTASE
Authors
:
A. Jansson, S. Ng, C. Arrowsmith, S. Sharma, A. M. Edwards, F. Von Delft, M. Sundstrom, U. Oppermann, Structural Genomics Consortium (Sgc)
Date
:
22 Feb 05 (Deposition) - 15 Mar 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Perioxisomes, Fatty Acid Synthesis, Enoyl Coa, Short-Chain Dehydrogenases/Reductases, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Jansson, S. Ng, C. Arrowsmith, S. Sharma, A. M. Edwards, F. Von Delft, M. Sundstrom, U. Oppermann
Crystal Structure Of Perixomal Trans 2-Enoyl Coa Reductase (Pecra)
To Be Published
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: ADENINE (ADEa)
2a: PHOSPHATE ION (PO4a)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADE
1
Ligand/Ion
ADENINE
2
PO4
1
Ligand/Ion
PHOSPHATE ION
3
SO4
4
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:17 , LYS A:70 , GLN A:71 , ALA A:72
BINDING SITE FOR RESIDUE SO4 A 304
2
AC2
SOFTWARE
THR D:28 , GLY D:29 , ILE D:30 , GLY D:31 , ASN D:107 , HOH D:2056 , HOH D:2086 , HOH D:2088
BINDING SITE FOR RESIDUE SO4 D 1001
3
AC3
SOFTWARE
GLY D:29 , SER D:206 , GLN D:207 , THR D:208
BINDING SITE FOR RESIDUE SO4 D 2001
4
AC4
SOFTWARE
SER B:49 , ARG B:50 , LYS B:51 , ADE B:4002
BINDING SITE FOR RESIDUE PO4 B 3001
5
AC5
SOFTWARE
GLN B:17 , LYS B:70 , GLN B:71 , ALA B:72 , SER B:219
BINDING SITE FOR RESIDUE SO4 B 4001
6
AC6
SOFTWARE
SER B:49 , ARG B:50 , CYS B:79 , ASN B:80 , ILE B:81 , GLY B:109 , THR B:130 , PO4 B:3001
BINDING SITE FOR RESIDUE ADE B 4002
[
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SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_021535 (E149K, chain A/B/C/D, )
2: VAR_021536 (F297L, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_021535
E
149
K
PECR_HUMAN
Polymorphism
1429148
A/B/C/D
E
149
K
2
UniProt
VAR_021536
F
297
L
PECR_HUMAN
Polymorphism
9288513
A/B/C/D
F
297
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
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Exons
(8, 32)
Info
All Exons
Exon 1.2a (A:7-42 | B:8-42 | C:5-42 | D:8-42)
Exon 1.3b (A:42-86 | B:42-86 | C:42-86 (gaps)...)
Exon 1.4b (A:87-142 | B:87-142 | C:87-142 (ga...)
Exon 1.6 (A:142-169 | B:142-169 | C:142-169 ...)
Exon 1.8a (A:169-201 | B:169-201 | C:169-201 ...)
Exon 1.10 (A:202-238 | B:202-238 (gaps) | C:2...)
Exon 1.11b (A:239-276 | B:239-276 | C:239-276 ...)
Exon 1.12c (A:276-303 | B:276-298 | C:276-299 ...)
View:
Select:
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All Exon Boundaries
1: Boundary -/1.2a
2: Boundary 1.2a/1.3b
3: Boundary 1.3b/1.4b
4: Boundary 1.4b/1.6
5: Boundary 1.6/1.8a
6: Boundary 1.8a/1.10
7: Boundary 1.10/1.11b
8: Boundary 1.11b/1.12c
9: Boundary 1.12c/-
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
ENST00000265322
2a
ENSE00001904119
chr2:
216946539-216946341
199
PECR_HUMAN
1-42
42
4
A:7-42
B:8-42
C:5-42
D:8-42
36
35
38
35
1.3b
ENST00000265322
3b
ENSE00001504586
chr2:
216931241-216931108
134
PECR_HUMAN
42-86
45
4
A:42-86
B:42-86
C:42-86 (gaps)
D:42-86 (gaps)
45
45
45
45
1.4b
ENST00000265322
4b
ENSE00001504585
chr2:
216930200-216930035
166
PECR_HUMAN
87-142
56
4
A:87-142
B:87-142
C:87-142 (gaps)
D:87-142
56
56
56
56
1.6
ENST00000265322
6
ENSE00001504583
chr2:
216923699-216923618
82
PECR_HUMAN
142-169
28
4
A:142-169
B:142-169
C:142-169 (gaps)
D:142-169
28
28
28
28
1.8a
ENST00000265322
8a
ENSE00001796093
chr2:
216916268-216916172
97
PECR_HUMAN
169-201
33
4
A:169-201
B:169-201
C:169-201
D:169-201
33
33
33
33
1.10
ENST00000265322
10
ENSE00001679013
chr2:
216914096-216913986
111
PECR_HUMAN
202-238
37
4
A:202-238
B:202-238 (gaps)
C:202-238 (gaps)
D:202-238
37
37
37
37
1.11b
ENST00000265322
11b
ENSE00001641430
chr2:
216908738-216908627
112
PECR_HUMAN
239-276
38
4
A:239-276
B:239-276
C:239-276
D:239-276
38
38
38
38
1.12c
ENST00000265322
12c
ENSE00001696405
chr2:
216904083-216903132
952
PECR_HUMAN
276-303
28
4
A:276-303
B:276-298
C:276-299
D:276-303
28
23
24
28
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1yxma1 (A:7-303)
1b: SCOP_d1yxmb_ (B:)
1c: SCOP_d1yxmc_ (C:)
1d: SCOP_d1yxmd_ (D:)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Tyrosine-dependent oxidoreductases
(503)
Protein domain
:
Peroxisomal trans 2-enoyl CoA reductase
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1yxma1
A:7-303
1b
d1yxmb_
B:
1c
d1yxmc_
C:
1d
d1yxmd_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1yxmC00 (C:5-299)
1b: CATH_1yxmB00 (B:8-298)
1c: CATH_1yxmD00 (D:8-303)
1d: CATH_1yxmA00 (A:7-303)
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(
)
Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
1a
1yxmC00
C:5-299
1b
1yxmB00
B:8-298
1c
1yxmD00
D:8-303
1d
1yxmA00
A:7-303
[
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]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_adh_short_C2_1yxmD01 (D:25-266)
1b: PFAM_adh_short_C2_1yxmD02 (D:25-266)
1c: PFAM_adh_short_C2_1yxmD03 (D:25-266)
1d: PFAM_adh_short_C2_1yxmD04 (D:25-266)
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Clan
:
NADP_Rossmann
(1239)
Family
:
adh_short_C2
(98)
Homo sapiens (Human)
(7)
1a
adh_short_C2-1yxmD01
D:25-266
1b
adh_short_C2-1yxmD02
D:25-266
1c
adh_short_C2-1yxmD03
D:25-266
1d
adh_short_C2-1yxmD04
D:25-266
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