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3MDE
Asym. Unit
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Asym.Unit (133 KB)
Biol.Unit 1 (252 KB)
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(1)
Title
:
CRYSTAL STRUCTURES OF MEDIUM CHAIN ACYL-COA DEHYDROGENASE FROM PIG LIVER MITOCHONDRIA WITH AND WITHOUT SUBSTRATE
Authors
:
J. -J. P. Kim, M. Wang, R. Paschke
Date
:
13 Jul 94 (Deposition) - 30 Sep 94 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Oxidoreductase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
J. J. Kim, M. Wang, R. Paschke
Crystal Structures Of Medium-Chain Acyl-Coa Dehydrogenase From Pig Liver Mitochondria With And Without Substrate.
Proc. Natl. Acad. Sci. Usa V. 90 7523 1993
(for further references see the
PDB file header
)
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: OCTANOYL-COENZYME A (CO8a)
1b: OCTANOYL-COENZYME A (CO8b)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
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No.
Name
Count
Type
Full Name
1
CO8
2
Ligand/Ion
OCTANOYL-COENZYME A
2
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:96 , GLU A:99 , LEU A:103 , GLY A:141 , SER A:142 , VAL A:144 , ALA A:145 , SER A:191 , PHE A:245 , MET A:249 , PHE A:252 , ASP A:253 , ARG A:256 , ARG A:324 , THR A:326 , TYR A:375 , GLU A:376 , GLY A:377 , ILE A:381 , FAD A:399 , HOH A:803 , HOH A:845 , HOH A:860 , HOH A:868 , HOH A:888 , HOH A:986
BINDING SITE FOR RESIDUE CO8 A 400
2
AC2
SOFTWARE
THR B:96 , GLU B:99 , LEU B:103 , GLY B:141 , SER B:142 , VAL B:144 , SER B:191 , PHE B:245 , MET B:249 , PHE B:252 , THR B:326 , TYR B:375 , GLU B:376 , GLY B:377 , FAD B:399 , HOH B:946 , HOH B:960
BINDING SITE FOR RESIDUE CO8 B 400
3
AC3
SOFTWARE
TYR A:133 , VAL A:135 , THR A:136 , GLY A:141 , SER A:142 , TRP A:166 , ILE A:167 , THR A:168 , ILE A:371 , ILE A:374 , THR A:378 , GLN A:380 , CO8 A:400 , HOH A:802 , HOH A:804 , HOH A:805 , HOH A:846 , HOH A:850 , ARG B:281 , THR B:283 , PHE B:284 , LEU B:288 , GLN B:292 , ILE B:294 , GLN B:349 , VAL B:350 , GLY B:353 , HOH B:806
BINDING SITE FOR RESIDUE FAD A 399
4
AC4
SOFTWARE
ARG A:281 , THR A:283 , PHE A:284 , LEU A:288 , HIS A:291 , GLN A:292 , GLN A:349 , VAL A:350 , GLY A:353 , TYR B:133 , VAL B:135 , THR B:136 , GLY B:141 , SER B:142 , TRP B:166 , THR B:168 , ILE B:371 , ILE B:374 , TYR B:375 , THR B:378 , GLN B:380 , CO8 B:400 , HOH B:901 , HOH B:903 , HOH B:904 , HOH B:925 , HOH B:926
BINDING SITE FOR RESIDUE FAD B 399
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: ACYL_COA_DH_1 (A:134-146,B:134-146)
2: ACYL_COA_DH_2 (A:349-368,B:349-368)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ACYL_COA_DH_1
PS00072
Acyl-CoA dehydrogenases signature 1.
ACADM_PIG
159-171
2
A:134-146
B:134-146
2
ACYL_COA_DH_2
PS00073
Acyl-CoA dehydrogenases signature 2.
ACADM_PIG
374-393
2
A:349-368
B:349-368
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3mdea1 (A:242-395)
1b: SCOP_d3mdeb1 (B:242-395)
2a: SCOP_d3mdea2 (A:11-241)
2b: SCOP_d3mdeb2 (B:11-241)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
Acyl-CoA dehydrogenase C-terminal domain-like
(61)
Family
:
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain
(29)
Protein domain
:
Medium chain acyl-CoA dehydrogenase, C-domain
(8)
Pig (Sus scrofa) [TaxId: 9823]
(3)
1a
d3mdea1
A:242-395
1b
d3mdeb1
B:242-395
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Superfamily
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Family
:
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains
(32)
Protein domain
:
Medium chain acyl-CoA dehydrogenase, NM domains
(8)
Pig (Sus scrofa) [TaxId: 9823]
(3)
2a
d3mdea2
A:11-241
2b
d3mdeb2
B:11-241
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_3mdeA01 (A:11-130)
1b: CATH_3mdeB01 (B:11-130)
2a: CATH_3mdeA03 (A:252-395)
2b: CATH_3mdeB03 (B:252-395)
3a: CATH_3mdeA02 (A:131-251)
3b: CATH_3mdeB02 (B:131-251)
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)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Butyryl-Coa Dehydrogenase, subunit A; domain 1
(28)
Homologous Superfamily
:
Butyryl-Coa Dehydrogenase, subunit A, domain 1
(28)
Pig (Sus scrofa)
(3)
1a
3mdeA01
A:11-130
1b
3mdeB01
B:11-130
Architecture
:
Up-down Bundle
(3216)
Topology
:
Butyryl-CoA Dehydrogenase, subunit A; domain 3
(76)
Homologous Superfamily
:
Butyryl-CoA Dehydrogenase, subunit A, domain 3
(37)
Pig (Sus scrofa)
(3)
2a
3mdeA03
A:252-395
2b
3mdeB03
B:252-395
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Butyryl-CoA Dehydrogenase, subunit A; domain 2
(35)
Homologous Superfamily
:
Butyryl-CoA Dehydrogenase, subunit A, domain 2
(35)
Pig (Sus scrofa)
(3)
3a
3mdeA02
A:131-251
3b
3mdeB02
B:131-251
[
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]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Acyl_CoA_dh_1_3mdeB01 (B:242-391)
1b: PFAM_Acyl_CoA_dh_1_3mdeB02 (B:242-391)
2a: PFAM_Acyl_CoA_dh_M_3mdeB03 (B:132-183)
2b: PFAM_Acyl_CoA_dh_M_3mdeB04 (B:132-183)
3a: PFAM_Acyl_CoA_dh_N_3mdeB05 (B:17-128)
3b: PFAM_Acyl_CoA_dh_N_3mdeB06 (B:17-128)
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Clans
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Families
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(
)
Organisms
(
)
(
)
Clan
:
Acyl-CoA_dh
(32)
Family
:
Acyl-CoA_dh_1
(24)
Sus scrofa (Pig)
(3)
1a
Acyl-CoA_dh_1-3mdeB01
B:242-391
1b
Acyl-CoA_dh_1-3mdeB02
B:242-391
Clan
:
no clan defined [family: Acyl-CoA_dh_M]
(24)
Family
:
Acyl-CoA_dh_M
(24)
Sus scrofa (Pig)
(3)
2a
Acyl-CoA_dh_M-3mdeB03
B:132-183
2b
Acyl-CoA_dh_M-3mdeB04
B:132-183
Clan
:
no clan defined [family: Acyl-CoA_dh_N]
(23)
Family
:
Acyl-CoA_dh_N
(23)
Sus scrofa (Pig)
(3)
3a
Acyl-CoA_dh_N-3mdeB05
B:17-128
3b
Acyl-CoA_dh_N-3mdeB06
B:17-128
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