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3RNM
Biol. Unit 2
Info
Asym.Unit (635 KB)
Biol.Unit 1 (318 KB)
Biol.Unit 2 (315 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF THE SUBUNIT BINDING OF HUMAN DIHYDROLIPOAMIDE TRANSACYLASE (E2B) BOUND TO HUMAN DIHYDROLIPOAMIDE DEHYDROGENASE (E3)
Authors
:
C. A. Brautigam, R. M. Wynn, J. C. Chuang, B. B. Young, D. T. Chuang
Date
:
22 Apr 11 (Deposition) - 04 May 11 (Release) - 20 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,E (1x)
Biol. Unit 2: C,D,F (1x)
Keywords
:
Protein-Protein Interaction, Redox Protein, Mitochondrion, Oxidoreductase-Protein Binding Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
C. A. Brautigam, R. M. Wynn, J. L. Chuang, M. T. Naik, B. B. Young, T. H. Huang, D. T. Chuang
Structural And Thermodynamic Basis For Weak Interactions Between Dihydrolipoamide Dehydrogenase And Subunit-Binding Domain Of The Branched-Chain {Alpha}-Ketoacid Dehydrogenase Complex.
J. Biol. Chem. V. 286 23476 2011
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: BETA-MERCAPTOETHANOL (BMEa)
1b: BETA-MERCAPTOETHANOL (BMEb)
1c: BETA-MERCAPTOETHANOL (BMEc)
1d: BETA-MERCAPTOETHANOL (BMEd)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
2d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
3a: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFON... (NHEa)
3b: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFON... (NHEb)
3c: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFON... (NHEc)
3d: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFON... (NHEd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BME
2
Ligand/Ion
BETA-MERCAPTOETHANOL
2
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
3
NHE
2
Ligand/Ion
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
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Sites
(6, 6)
Info
All Sites
1: AC7 (SOFTWARE)
2: AC8 (SOFTWARE)
3: AC9 (SOFTWARE)
4: BC1 (SOFTWARE)
5: BC2 (SOFTWARE)
6: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC7
SOFTWARE
ILE C:189 , CYS C:277 , GLY C:279 , HOH C:503 , HOH C:527 , HIS E:160
BINDING SITE FOR RESIDUE BME C 500
2
AC8
SOFTWARE
ILE C:12 , GLY C:13 , GLY C:15 , PRO C:16 , GLY C:17 , GLU C:36 , LYS C:37 , ASN C:38 , GLY C:43 , THR C:44 , CYS C:45 , VAL C:48 , GLY C:49 , CYS C:50 , LYS C:54 , GLY C:117 , TYR C:118 , GLY C:119 , ALA C:147 , THR C:148 , GLY C:149 , SER C:150 , SER C:168 , ILE C:189 , ARG C:280 , PHE C:283 , GLY C:319 , ASP C:320 , MET C:326 , LEU C:327 , ALA C:328 , HIS C:329 , ALA C:331 , TYR C:359 , HOH C:476 , HOH C:491 , HOH C:496 , HOH C:504 , HIS D:452
BINDING SITE FOR RESIDUE FAD C 480
3
AC9
SOFTWARE
ASN C:225 , GLY C:402 , PHE C:474
BINDING SITE FOR RESIDUE NHE C 475
4
BC1
SOFTWARE
SER D:168 , ILE D:189 , CYS D:277 , ARG D:280 , FAD D:480
BINDING SITE FOR RESIDUE BME D 500
5
BC2
SOFTWARE
HIS C:452 , ILE D:12 , GLY D:13 , GLY D:15 , PRO D:16 , GLY D:17 , GLU D:36 , LYS D:37 , ASN D:38 , GLY D:43 , THR D:44 , CYS D:45 , VAL D:48 , GLY D:49 , CYS D:50 , LYS D:54 , TYR D:118 , GLY D:119 , ALA D:147 , THR D:148 , GLY D:149 , SER D:150 , SER D:168 , ILE D:189 , ARG D:280 , PHE D:283 , GLY D:319 , ASP D:320 , MET D:326 , LEU D:327 , ALA D:328 , HIS D:329 , TYR D:359 , HOH D:476 , HOH D:486 , HOH D:489 , HOH D:490 , BME D:500
BINDING SITE FOR RESIDUE FAD D 480
6
BC3
SOFTWARE
ASN D:225 , PRO D:387 , GLY D:402 , HOH D:548
BINDING SITE FOR RESIDUE NHE D 475
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SAPs(SNPs)/Variants
(6, 12)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_006907 (K37E, chain C/D, )
2: VAR_031922 (K69T, chain C/D, )
3: VAR_015820 (G194C, chain C/D, )
4: VAR_014555 (L296V, chain C/D, )
5: VAR_006908 (P453L, chain C/D, )
6: VAR_015821 (R460G, chain C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_006907
K
72
E
DLDH_HUMAN
Disease (DLDD)
---
C/D
K
37
E
2
UniProt
VAR_031922
K
104
T
DLDH_HUMAN
Polymorphism
1130477
C/D
K
69
T
4
UniProt
VAR_015820
G
229
C
DLDH_HUMAN
Disease (DLDD)
---
C/D
G
194
C
5
UniProt
VAR_014555
L
331
V
DLDH_HUMAN
Polymorphism
17624
C/D
L
296
V
6
UniProt
VAR_006908
P
488
L
DLDH_HUMAN
Disease (DLDD)
---
C/D
P
453
L
7
UniProt
VAR_015821
R
495
G
DLDH_HUMAN
Disease (DLDD)
---
C/D
R
460
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(2, 3)
Info
All PROSITE Patterns/Profiles
1: PYRIDINE_REDOX_1 (C:42-52,D:42-52)
2: PSBD (F:111-148)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PYRIDINE_REDOX_1
PS00076
Pyridine nucleotide-disulphide oxidoreductases class-I active site.
DLDH_HUMAN
77-87
2
-
-
C:42-52
D:42-52
2
PSBD
PS51826
Peripheral subunit-binding (PSBD) domain profile.
ODB2_HUMAN
172-209
1
-
F:111-148
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Exons
(0, 0)
Info
All Exons
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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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3rnme_ (E:)
1b: SCOP_d3rnmf_ (F:)
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Class
:
All alpha proteins
(14657)
Fold
:
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
(21)
Superfamily
:
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
(21)
Family
:
automated matches
(5)
Protein domain
:
automated matches
(5)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d3rnme_
E:
1b
d3rnmf_
F:
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(4, 14)
Info
all PFAM domains
1a: PFAM_Pyr_redox_3rnmD01 (D:180-264)
1b: PFAM_Pyr_redox_3rnmD02 (D:180-264)
1c: PFAM_Pyr_redox_3rnmD03 (D:180-264)
1d: PFAM_Pyr_redox_3rnmD04 (D:180-264)
2a: PFAM_Pyr_redox_2_3rnmD05 (D:8-326)
2b: PFAM_Pyr_redox_2_3rnmD06 (D:8-326)
2c: PFAM_Pyr_redox_2_3rnmD07 (D:8-326)
2d: PFAM_Pyr_redox_2_3rnmD08 (D:8-326)
3a: PFAM_E3_binding_3rnmF01 (F:111-146)
3b: PFAM_E3_binding_3rnmF02 (F:111-146)
4a: PFAM_Pyr_redox_dim_3rnmD09 (D:354-463)
4b: PFAM_Pyr_redox_dim_3rnmD10 (D:354-463)
4c: PFAM_Pyr_redox_dim_3rnmD11 (D:354-463)
4d: PFAM_Pyr_redox_dim_3rnmD12 (D:354-463)
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Clans
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(
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Families
(
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(
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Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
Pyr_redox
(62)
Homo sapiens (Human)
(8)
1a
Pyr_redox-3rnmD01
D:180-264
1b
Pyr_redox-3rnmD02
D:180-264
1c
Pyr_redox-3rnmD03
D:180-264
1d
Pyr_redox-3rnmD04
D:180-264
Family
:
Pyr_redox_2
(69)
Homo sapiens (Human)
(8)
2a
Pyr_redox_2-3rnmD05
D:8-326
2b
Pyr_redox_2-3rnmD06
D:8-326
2c
Pyr_redox_2-3rnmD07
D:8-326
2d
Pyr_redox_2-3rnmD08
D:8-326
Clan
:
no clan defined [family: E3_binding]
(14)
Family
:
E3_binding
(14)
Homo sapiens (Human)
(3)
3a
E3_binding-3rnmF01
F:111-146
3b
E3_binding-3rnmF02
F:111-146
Clan
:
no clan defined [family: Pyr_redox_dim]
(44)
Family
:
Pyr_redox_dim
(44)
Homo sapiens (Human)
(7)
4a
Pyr_redox_dim-3rnmD09
D:354-463
4b
Pyr_redox_dim-3rnmD10
D:354-463
4c
Pyr_redox_dim-3rnmD11
D:354-463
4d
Pyr_redox_dim-3rnmD12
D:354-463
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