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1ZY8
Biol. Unit 5
Info
Asym.Unit (1.5 MB)
Biol.Unit 1 (163 KB)
Biol.Unit 2 (164 KB)
Biol.Unit 3 (164 KB)
Biol.Unit 4 (164 KB)
Biol.Unit 5 (162 KB)
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Models
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Title
:
THE CRYSTAL STRUCTURE OF DIHYDROLIPOAMIDE DEHYDROGENASE AND DIHYDROLIPOAMIDE DEHYDROGENASE-BINDING PROTEIN (DIDOMAIN) SUBCOMPLEX OF HUMAN PYRUVATE DEHYDROGENASE COMPLEX.
Authors
:
E. M. Ciszak, A. Makal, Y. S. Hong, A. K. Vettaikkorumakankauv, L. G. Korotchkina, M. S. Patel
Date
:
09 Jun 05 (Deposition) - 15 Nov 05 (Release) - 26 Jan 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.59
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O (2 x)
Biol. Unit 1: A,B,K (1x)
Biol. Unit 2: C,D,L (1x)
Biol. Unit 3: E,F,M (1x)
Biol. Unit 4: G,H,N (1x)
Biol. Unit 5: I,J,O (1x)
Keywords
:
Human, Dihydrolipoamide Dehydrogenase, E3, Dihydrolipoyl Dehydrogenase, Dihydrolipoamide Dehydrogenase Binding Protein, E3-Binding Protein, Pyruvate Dehydrogenase Complex, Alpha-Keto Acid Complex, Flavin Adenine Dinucleotide Cofactor, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. M. Ciszak, A. Makal, Y. S. Hong, A. K. Vettaikkorumakankauv, L. G. Korotchkina, M. S. Patel
How Dihydrolipoamide Dehydrogenase-Binding Protein Binds Dihydrolipoamide Dehydrogenase In The Human Pyruvate Dehydrogenase Complex.
J. Biol. Chem. V. 281 648 2006
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
1c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
1d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
1e: FLAVIN-ADENINE DINUCLEOTIDE (FADe)
1f: FLAVIN-ADENINE DINUCLEOTIDE (FADf)
1g: FLAVIN-ADENINE DINUCLEOTIDE (FADg)
1h: FLAVIN-ADENINE DINUCLEOTIDE (FADh)
1i: FLAVIN-ADENINE DINUCLEOTIDE (FADi)
1j: FLAVIN-ADENINE DINUCLEOTIDE (FADj)
1k: FLAVIN-ADENINE DINUCLEOTIDE (FADk)
1l: FLAVIN-ADENINE DINUCLEOTIDE (FADl)
1m: FLAVIN-ADENINE DINUCLEOTIDE (FADm)
1n: FLAVIN-ADENINE DINUCLEOTIDE (FADn)
1o: FLAVIN-ADENINE DINUCLEOTIDE (FADo)
1p: FLAVIN-ADENINE DINUCLEOTIDE (FADp)
1q: FLAVIN-ADENINE DINUCLEOTIDE (FADq)
1r: FLAVIN-ADENINE DINUCLEOTIDE (FADr)
1s: FLAVIN-ADENINE DINUCLEOTIDE (FADs)
1t: FLAVIN-ADENINE DINUCLEOTIDE (FADt)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
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Sites
(2, 2)
Info
All Sites
1: AC9 (SOFTWARE)
2: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC9
SOFTWARE
GLY I:13 , GLY I:15 , PRO I:16 , GLU I:36 , LYS I:37 , GLY I:43 , THR I:44 , CYS I:45 , VAL I:48 , GLY I:49 , CYS I:50 , SER I:53 , LYS I:54 , TYR I:118 , GLY I:119 , ALA I:147 , THR I:148 , GLY I:149 , SER I:150 , SER I:168 , ILE I:189 , PHE I:283 , GLY I:319 , ASP I:320 , MET I:326 , LEU I:327 , ALA I:328 , HIS I:329 , ALA I:331 , TYR I:359 , HOH I:4759 , HOH I:4761 , HOH I:4765 , HIS J:452
BINDING SITE FOR RESIDUE FAD I 4758
2
BC1
SOFTWARE
HIS I:452 , ILE J:12 , GLY J:13 , PRO J:16 , GLU J:36 , LYS J:37 , ASN J:38 , GLY J:43 , THR J:44 , CYS J:45 , VAL J:48 , CYS J:50 , LYS J:54 , TYR J:118 , GLY J:119 , ALA J:147 , THR J:148 , GLY J:149 , SER J:150 , SER J:168 , ILE J:189 , PHE J:283 , GLY J:319 , ASP J:320 , MET J:326 , LEU J:327 , ALA J:328 , HIS J:329 , TYR J:359 , HOH J:4762 , HOH J:4785
BINDING SITE FOR RESIDUE FAD J 4759
[
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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 I/J, )
2: VAR_031922 (K69T, chain I/J, )
3: VAR_015820 (G194C, chain I/J, )
4: VAR_014555 (L296V, chain I/J, )
5: VAR_006908 (P453L, chain I/J, )
6: VAR_015821 (R460G, chain I/J, )
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)
---
I/J
K
37
E
2
UniProt
VAR_031922
K
104
T
DLDH_HUMAN
Polymorphism
1130477
I/J
K
69
T
3
UniProt
VAR_015820
G
229
C
DLDH_HUMAN
Disease (DLDD)
---
I/J
G
194
C
4
UniProt
VAR_014555
L
331
V
DLDH_HUMAN
Polymorphism
17624
I/J
L
296
V
5
UniProt
VAR_006908
P
488
L
DLDH_HUMAN
Disease (DLDD)
---
I/J
P
453
L
6
UniProt
VAR_015821
R
495
G
DLDH_HUMAN
Disease (DLDD)
---
I/J
R
460
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 3)
Info
All PROSITE Patterns/Profiles
1: PYRIDINE_REDOX_1 (I:42-52,J:42-52)
2: PSBD (O:130-167)
;
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
-
-
-
-
-
-
-
-
I:42-52
J:42-52
2
PSBD
PS51826
Peripheral subunit-binding (PSBD) domain profile.
ODPX_HUMAN
183-220
1
-
-
-
-
O:130-167
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
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CATH Domains
(3, 35)
Info
all CATH domains
1a: CATH_1zy8A03 (A:351-474)
1b: CATH_1zy8B03 (B:351-474)
1c: CATH_1zy8C03 (C:351-474)
1d: CATH_1zy8D03 (D:351-474)
1e: CATH_1zy8E03 (E:351-474)
1f: CATH_1zy8F03 (F:351-474)
1g: CATH_1zy8G03 (G:351-474)
1h: CATH_1zy8H03 (H:351-474)
1i: CATH_1zy8I03 (I:351-474)
1j: CATH_1zy8J03 (J:351-474)
2a: CATH_1zy8A01 (A:1-152,A:279-350)
2b: CATH_1zy8G01 (G:1-152,G:279-350)
2c: CATH_1zy8H01 (H:1-152,H:279-350)
2d: CATH_1zy8I01 (I:1-152,I:279-350)
2e: CATH_1zy8J01 (J:1-152,J:279-350)
2f: CATH_1zy8A02 (A:153-278)
2g: CATH_1zy8B02 (B:153-278)
2h: CATH_1zy8C02 (C:153-278)
2i: CATH_1zy8D02 (D:153-278)
2j: CATH_1zy8E02 (E:153-278)
2k: CATH_1zy8F02 (F:153-278)
2l: CATH_1zy8G02 (G:153-278)
2m: CATH_1zy8H02 (H:153-278)
2n: CATH_1zy8I02 (I:153-278)
2o: CATH_1zy8J02 (J:153-278)
2p: CATH_1zy8B01 (B:1-152,B:279-350)
2q: CATH_1zy8C01 (C:1-152,C:279-350)
2r: CATH_1zy8D01 (D:1-152,D:279-350)
2s: CATH_1zy8E01 (E:1-152,E:279-350)
2t: CATH_1zy8F01 (F:1-152,F:279-350)
3a: CATH_1zy8K00 (K:130-173)
3b: CATH_1zy8L00 (L:130-173)
3c: CATH_1zy8M00 (M:130-173)
3d: CATH_1zy8N00 (N:130-173)
3e: CATH_1zy8O00 (O:130-173)
View:
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Classes
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)
(
)
Architectures
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Enolase-like; domain 1
(252)
Homologous Superfamily
:
[code=3.30.390.30, no name defined]
(99)
Human (Homo sapiens)
(26)
1a
1zy8A03
A:351-474
1b
1zy8B03
B:351-474
1c
1zy8C03
C:351-474
1d
1zy8D03
D:351-474
1e
1zy8E03
E:351-474
1f
1zy8F03
F:351-474
1g
1zy8G03
G:351-474
1h
1zy8H03
H:351-474
1i
1zy8I03
I:351-474
1j
1zy8J03
J:351-474
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
FAD/NAD(P)-binding domain
(373)
Homologous Superfamily
:
[code=3.50.50.60, no name defined]
(373)
Human (Homo sapiens)
(57)
2a
1zy8A01
A:1-152,A:279-350
2b
1zy8G01
G:1-152,G:279-350
2c
1zy8H01
H:1-152,H:279-350
2d
1zy8I01
I:1-152,I:279-350
2e
1zy8J01
J:1-152,J:279-350
2f
1zy8A02
A:153-278
2g
1zy8B02
B:153-278
2h
1zy8C02
C:153-278
2i
1zy8D02
D:153-278
2j
1zy8E02
E:153-278
2k
1zy8F02
F:153-278
2l
1zy8G02
G:153-278
2m
1zy8H02
H:153-278
2n
1zy8I02
I:153-278
2o
1zy8J02
J:153-278
2p
1zy8B01
B:1-152,B:279-350
2q
1zy8C01
C:1-152,C:279-350
2r
1zy8D01
D:1-152,D:279-350
2s
1zy8E01
E:1-152,E:279-350
2t
1zy8F01
F:1-152,F:279-350
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Dihydrolipoamide Transferase
(20)
Homologous Superfamily
:
Dihydrolipoamide Transferase
(20)
Human (Homo sapiens)
(2)
3a
1zy8K00
K:130-173
3b
1zy8L00
L:130-173
3c
1zy8M00
M:130-173
3d
1zy8N00
N:130-173
3e
1zy8O00
O:130-173
[
close CATH info
]
Pfam Domains
(4, 35)
Info
all PFAM domains
1a: PFAM_Pyr_redox_1zy8J01 (J:180-264)
1b: PFAM_Pyr_redox_1zy8J02 (J:180-264)
1c: PFAM_Pyr_redox_1zy8J03 (J:180-264)
1d: PFAM_Pyr_redox_1zy8J04 (J:180-264)
1e: PFAM_Pyr_redox_1zy8J05 (J:180-264)
1f: PFAM_Pyr_redox_1zy8J06 (J:180-264)
1g: PFAM_Pyr_redox_1zy8J07 (J:180-264)
1h: PFAM_Pyr_redox_1zy8J08 (J:180-264)
1i: PFAM_Pyr_redox_1zy8J09 (J:180-264)
1j: PFAM_Pyr_redox_1zy8J10 (J:180-264)
2a: PFAM_Pyr_redox_2_1zy8J11 (J:8-326)
2b: PFAM_Pyr_redox_2_1zy8J12 (J:8-326)
2c: PFAM_Pyr_redox_2_1zy8J13 (J:8-326)
2d: PFAM_Pyr_redox_2_1zy8J14 (J:8-326)
2e: PFAM_Pyr_redox_2_1zy8J15 (J:8-326)
2f: PFAM_Pyr_redox_2_1zy8J16 (J:8-326)
2g: PFAM_Pyr_redox_2_1zy8J17 (J:8-326)
2h: PFAM_Pyr_redox_2_1zy8J18 (J:8-326)
2i: PFAM_Pyr_redox_2_1zy8J19 (J:8-326)
2j: PFAM_Pyr_redox_2_1zy8J20 (J:8-326)
3a: PFAM_E3_binding_1zy8O01 (O:130-165)
3b: PFAM_E3_binding_1zy8O02 (O:130-165)
3c: PFAM_E3_binding_1zy8O03 (O:130-165)
3d: PFAM_E3_binding_1zy8O04 (O:130-165)
3e: PFAM_E3_binding_1zy8O05 (O:130-165)
4a: PFAM_Pyr_redox_dim_1zy8J21 (J:354-463)
4b: PFAM_Pyr_redox_dim_1zy8J22 (J:354-463)
4c: PFAM_Pyr_redox_dim_1zy8J23 (J:354-463)
4d: PFAM_Pyr_redox_dim_1zy8J24 (J:354-463)
4e: PFAM_Pyr_redox_dim_1zy8J25 (J:354-463)
4f: PFAM_Pyr_redox_dim_1zy8J26 (J:354-463)
4g: PFAM_Pyr_redox_dim_1zy8J27 (J:354-463)
4h: PFAM_Pyr_redox_dim_1zy8J28 (J:354-463)
4i: PFAM_Pyr_redox_dim_1zy8J29 (J:354-463)
4j: PFAM_Pyr_redox_dim_1zy8J30 (J:354-463)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
Pyr_redox
(62)
Homo sapiens (Human)
(8)
1a
Pyr_redox-1zy8J01
J:180-264
1b
Pyr_redox-1zy8J02
J:180-264
1c
Pyr_redox-1zy8J03
J:180-264
1d
Pyr_redox-1zy8J04
J:180-264
1e
Pyr_redox-1zy8J05
J:180-264
1f
Pyr_redox-1zy8J06
J:180-264
1g
Pyr_redox-1zy8J07
J:180-264
1h
Pyr_redox-1zy8J08
J:180-264
1i
Pyr_redox-1zy8J09
J:180-264
1j
Pyr_redox-1zy8J10
J:180-264
Family
:
Pyr_redox_2
(69)
Homo sapiens (Human)
(8)
2a
Pyr_redox_2-1zy8J11
J:8-326
2b
Pyr_redox_2-1zy8J12
J:8-326
2c
Pyr_redox_2-1zy8J13
J:8-326
2d
Pyr_redox_2-1zy8J14
J:8-326
2e
Pyr_redox_2-1zy8J15
J:8-326
2f
Pyr_redox_2-1zy8J16
J:8-326
2g
Pyr_redox_2-1zy8J17
J:8-326
2h
Pyr_redox_2-1zy8J18
J:8-326
2i
Pyr_redox_2-1zy8J19
J:8-326
2j
Pyr_redox_2-1zy8J20
J:8-326
Clan
:
no clan defined [family: E3_binding]
(14)
Family
:
E3_binding
(14)
Homo sapiens (Human)
(3)
3a
E3_binding-1zy8O01
O:130-165
3b
E3_binding-1zy8O02
O:130-165
3c
E3_binding-1zy8O03
O:130-165
3d
E3_binding-1zy8O04
O:130-165
3e
E3_binding-1zy8O05
O:130-165
Clan
:
no clan defined [family: Pyr_redox_dim]
(44)
Family
:
Pyr_redox_dim
(44)
Homo sapiens (Human)
(7)
4a
Pyr_redox_dim-1zy8J21
J:354-463
4b
Pyr_redox_dim-1zy8J22
J:354-463
4c
Pyr_redox_dim-1zy8J23
J:354-463
4d
Pyr_redox_dim-1zy8J24
J:354-463
4e
Pyr_redox_dim-1zy8J25
J:354-463
4f
Pyr_redox_dim-1zy8J26
J:354-463
4g
Pyr_redox_dim-1zy8J27
J:354-463
4h
Pyr_redox_dim-1zy8J28
J:354-463
4i
Pyr_redox_dim-1zy8J29
J:354-463
4j
Pyr_redox_dim-1zy8J30
J:354-463
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Asym.Unit (1.5 MB)
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Biol.Unit 1 (163 KB)
Header - Biol.Unit 1
Biol.Unit 2 (164 KB)
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Biol.Unit 3 (164 KB)
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