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3MPJ
Biol. Unit 2
Info
Asym.Unit (397 KB)
Biol.Unit 1 (266 KB)
Biol.Unit 2 (256 KB)
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(1)
Title
:
STRUCTURE OF THE GLUTARYL-COENZYME A DEHYDROGENASE
Authors
:
S. Wischgoll, E. Warkentin, M. Boll, U. Ermler
Date
:
27 Apr 10 (Deposition) - 18 Aug 10 (Release) - 05 Sep 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,D,E,F,G,Y
Biol. Unit 1: A,B,Y (2x)
Biol. Unit 2: D,E,F,G (1x)
Keywords
:
Alpha-Beta Fold, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
S. Wischgoll, U. Demmer, E. Warkentin, R. Gunther, M. Boll, U. Ermler
Structural Basis For Promoting And Preventing Decarboxylation In Glutaryl-Coenzyme A Dehydrogenases.
Biochemistry V. 49 5350 2010
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
2d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
2e: FLAVIN-ADENINE DINUCLEOTIDE (FADe)
2f: FLAVIN-ADENINE DINUCLEOTIDE (FADf)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
FAD
4
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
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Sites
(8, 8)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC1 (SOFTWARE)
7: BC2 (SOFTWARE)
8: BC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
PHE D:126 , ILE D:128 , THR D:129 , GLY D:134 , SER D:135 , TRP D:159 , ILE D:160 , SER D:161 , MET D:365 , VAL D:366 , GLU D:367 , SER D:369 , ASN D:371 , MET D:375 , HOH D:7422 , HOH D:7424 , HOH D:7436 , HOH D:7481 , HOH D:7586 , HOH D:7689 , HOH D:7981 , ARG E:271 , GLN E:273 , PHE E:274 , PHE E:281 , ASN E:284 , ARG E:340 , ILE E:341 , GLY E:343 , ALA E:344 , TYR E:345 , GLN G:282
BINDING SITE FOR RESIDUE FAD D 400
2
AC6
SOFTWARE
LYS D:204 , HIS D:208
BINDING SITE FOR RESIDUE CL D 401
3
AC7
SOFTWARE
ARG D:271 , GLN D:273 , PHE D:274 , PHE D:281 , ASN D:284 , ARG D:340 , ILE D:341 , GLY D:343 , ALA D:344 , MET E:92 , PHE E:126 , ILE E:128 , THR E:129 , GLY E:134 , SER E:135 , TRP E:159 , SER E:161 , MET E:365 , VAL E:366 , GLU E:367 , SER E:369 , ASN E:371 , MET E:375 , HOH E:7692 , HOH E:7693 , HOH E:7849 , HOH E:7973 , GLN F:282
BINDING SITE FOR RESIDUE FAD E 400
4
AC8
SOFTWARE
ASN E:35 , LYS E:204 , HIS E:208
BINDING SITE FOR RESIDUE CL E 401
5
AC9
SOFTWARE
GLN E:282 , MET F:92 , PHE F:126 , ILE F:128 , THR F:129 , GLY F:134 , SER F:135 , TRP F:159 , SER F:161 , MET F:365 , VAL F:366 , GLU F:367 , SER F:369 , ASN F:371 , MET F:375 , HOH F:7403 , HOH F:7404 , HOH F:7421 , HOH F:7551 , HOH F:7705 , ARG G:271 , GLN G:273 , PHE G:274 , PHE G:281 , ASN G:284 , ARG G:340 , ILE G:341 , GLY G:343 , ALA G:344 , HOH G:7405
BINDING SITE FOR RESIDUE FAD F 400
6
BC1
SOFTWARE
ASN F:35 , LYS F:204 , HIS F:208 , HOH F:7527
BINDING SITE FOR RESIDUE CL F 401
7
BC2
SOFTWARE
GLN D:282 , ARG F:271 , GLN F:273 , PHE F:274 , PHE F:281 , ASN F:284 , ARG F:340 , ILE F:341 , GLY F:343 , ALA F:344 , HOH F:7433 , MET G:92 , PHE G:126 , ILE G:128 , THR G:129 , GLY G:134 , SER G:135 , TRP G:159 , SER G:161 , MET G:365 , VAL G:366 , GLU G:367 , SER G:369 , ASN G:371 , MET G:375 , HOH G:7406 , HOH G:7445 , HOH G:7533 , HOH G:7593 , HOH G:7604 , HOH G:7653 , HOH G:7976
BINDING SITE FOR RESIDUE FAD G 400
8
BC3
SOFTWARE
LYS G:204 , HIS G:208
BINDING SITE FOR RESIDUE CL G 401
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ACYL_COA_DH_1 (D:127-139,E:127-139,F:127-139,G:12...)
;
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.
ACD_DESML
127-139
4
-
-
D:127-139
E:127-139
F:127-139
G:127-139
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d3mpja2 (A:232-389)
1b: SCOP_d3mpjb2 (B:232-393)
1c: SCOP_d3mpjd2 (D:232-390)
1d: SCOP_d3mpje2 (E:232-391)
1e: SCOP_d3mpjf2 (F:232-390)
1f: SCOP_d3mpjg2 (G:232-389)
2a: SCOP_d3mpja1 (A:1-231)
2b: SCOP_d3mpjb1 (B:1-231)
2c: SCOP_d3mpjd1 (D:1-231)
2d: SCOP_d3mpje1 (E:1-231)
2e: SCOP_d3mpjf1 (F:1-231)
2f: SCOP_d3mpjg1 (G:1-231)
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Protein Domains
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Organisms
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Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
Acyl-CoA dehydrogenase C-terminal domain-like
(61)
Family
:
automated matches
(29)
Protein domain
:
automated matches
(29)
Desulfococcus multivorans [TaxId: 897]
(2)
1a
d3mpja2
A:232-389
1b
d3mpjb2
B:232-393
1c
d3mpjd2
D:232-390
1d
d3mpje2
E:232-391
1e
d3mpjf2
F:232-390
1f
d3mpjg2
G:232-389
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
:
automated matches
(26)
Protein domain
:
automated matches
(26)
Desulfococcus multivorans [TaxId: 897]
(2)
2a
d3mpja1
A:1-231
2b
d3mpjb1
B:1-231
2c
d3mpjd1
D:1-231
2d
d3mpje1
E:1-231
2e
d3mpjf1
F:1-231
2f
d3mpjg1
G:1-231
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(0, 0)
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Sorry, no Info available
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Chain F
Chain G
Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (397 KB)
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