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2F5Z
Biol. Unit 2
Info
Asym.Unit (825 KB)
Biol.Unit 1 (167 KB)
Biol.Unit 2 (175 KB)
Biol.Unit 3 (175 KB)
Biol.Unit 4 (178 KB)
Biol.Unit 5 (171 KB)
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Title
:
CRYSTAL STRUCTURE OF HUMAN DIHYDROLIPOAMIDE DEHYDROGENASE (E3) COMPLEXED TO THE E3-BINDING DOMAIN OF HUMAN E3-BINDING PROTEIN
Authors
:
C. A. Brautigam, J. L. Chuang, R. M. Wynn, D. R. Tomchick, M. Machius, D. T. Chuang
Date
:
28 Nov 05 (Deposition) - 17 Jan 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.18
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O
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
:
Protein-Protein Complex, Oxidoreductase/Protein Binding Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. A. Brautigam, R. M. Wynn, J. L. Chuang, M. Machius, D. R. Tomchick, D. T. Chuang
Structural Insight Into Interactions Between Dihydrolipoamide Dehydrogenase (E3) And E3 Binding Protein Of Human Pyruvate Dehydrogenase Complex.
Structure V. 14 611 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 10)
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)
2a: SULFATE ION (SO4a)
2aa: SULFATE ION (SO4aa)
2ab: SULFATE ION (SO4ab)
2ac: SULFATE ION (SO4ac)
2ad: SULFATE ION (SO4ad)
2ae: SULFATE ION (SO4ae)
2af: SULFATE ION (SO4af)
2ag: SULFATE ION (SO4ag)
2ah: SULFATE ION (SO4ah)
2ai: SULFATE ION (SO4ai)
2aj: SULFATE ION (SO4aj)
2ak: SULFATE ION (SO4ak)
2al: SULFATE ION (SO4al)
2am: SULFATE ION (SO4am)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
2s: SULFATE ION (SO4s)
2t: SULFATE ION (SO4t)
2u: SULFATE ION (SO4u)
2v: SULFATE ION (SO4v)
2w: SULFATE ION (SO4w)
2x: SULFATE ION (SO4x)
2y: SULFATE ION (SO4y)
2z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(10, 10)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC3 (SOFTWARE)
07: BC5 (SOFTWARE)
08: BC7 (SOFTWARE)
09: EC6 (SOFTWARE)
10: EC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
ARG C:299 , ARG C:301 , ALA C:323 , GLY C:324 , HOH C:2594 , HOH C:2601
BINDING SITE FOR RESIDUE SO4 C 2490
02
AC4
SOFTWARE
HIS C:64 , GLY C:68 , THR C:69 , ASP C:70 , HOH C:2543
BINDING SITE FOR RESIDUE SO4 C 2491
03
AC6
SOFTWARE
LEU C:210 , GLY C:211 , HIS C:212
BINDING SITE FOR RESIDUE SO4 C 2492
04
AC8
SOFTWARE
ASN C:286 , LEU C:287 , GLY C:288 , LEU C:289 , GLU C:290 , GLU C:291
BINDING SITE FOR RESIDUE SO4 C 2493
05
BC1
SOFTWARE
HOH A:2597 , ARG D:299 , ARG D:301 , ALA D:323 , GLY D:324 , HOH D:2571
BINDING SITE FOR RESIDUE SO4 D 2494
06
BC3
SOFTWARE
HIS D:64 , GLY D:68 , THR D:69
BINDING SITE FOR RESIDUE SO4 D 2495
07
BC5
SOFTWARE
LEU D:210 , GLY D:211 , HIS D:212
BINDING SITE FOR RESIDUE SO4 D 2496
08
BC7
SOFTWARE
THR D:284 , ASN D:286 , LEU D:287 , GLY D:288 , LEU D:289 , GLU D:290 , HOH D:2657
BINDING SITE FOR RESIDUE SO4 D 2497
09
EC6
SOFTWARE
GLY C:13 , SER C:14 , 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 , SER C:53 , LYS C:54 , GLY C:117 , TYR C:118 , GLY C:119 , ALA C:147 , THR C:148 , GLY C:149 , SER C:150 , 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 , TYR C:359 , HOH C:2496 , HOH C:2497 , HOH C:2502 , HOH C:2524 , HOH C:2602 , HIS D:452
BINDING SITE FOR RESIDUE FAD C 480
10
EC7
SOFTWARE
HIS C:452 , ILE D:12 , GLY D:13 , SER D:14 , 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 , SER D:53 , LYS D:54 , GLY D:117 , 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 , ALA D:331 , TYR D:359 , HOH D:2500 , HOH D:2503 , HOH D:2557 , HOH D:2574 , HOH D:2654
BINDING SITE FOR RESIDUE FAD D 480
[
close Site info
]
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 (T69T, 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
T
69
T
3
UniProt
VAR_015820
G
229
C
DLDH_HUMAN
Disease (DLDD)
---
C/D
G
194
C
4
UniProt
VAR_014555
L
331
V
DLDH_HUMAN
Polymorphism
17624
C/D
L
296
V
5
UniProt
VAR_006908
P
488
L
DLDH_HUMAN
Disease (DLDD)
---
C/D
P
453
L
6
UniProt
VAR_015821
R
495
G
DLDH_HUMAN
Disease (DLDD)
---
C/D
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 (C:42-52,D:42-52)
2: PSBD (L: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
-
-
C:42-52
D:42-52
-
-
-
-
-
-
2
PSBD
PS51826
Peripheral subunit-binding (PSBD) domain profile.
ODPX_HUMAN
183-220
1
-
L:130-167
-
-
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
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
(2, 30)
Info
all CATH domains
1a: CATH_2f5zA03 (A:351-474)
1b: CATH_2f5zB03 (B:351-474)
1c: CATH_2f5zC03 (C:351-474)
1d: CATH_2f5zD03 (D:351-474)
1e: CATH_2f5zE03 (E:351-474)
1f: CATH_2f5zF03 (F:351-474)
1g: CATH_2f5zG03 (G:351-474)
1h: CATH_2f5zH03 (H:351-474)
1i: CATH_2f5zI03 (I:351-474)
1j: CATH_2f5zJ03 (J:351-474)
2a: CATH_2f5zB01 (B:4-152,B:279-350)
2b: CATH_2f5zA02 (A:153-278)
2c: CATH_2f5zB02 (B:153-278)
2d: CATH_2f5zC02 (C:153-278)
2e: CATH_2f5zD02 (D:153-278)
2f: CATH_2f5zE02 (E:153-278)
2g: CATH_2f5zF02 (F:153-278)
2h: CATH_2f5zG02 (G:153-278)
2i: CATH_2f5zH02 (H:153-278)
2j: CATH_2f5zJ02 (J:153-278)
2k: CATH_2f5zI02 (I:153-278)
2l: CATH_2f5zD01 (D:4-152,D:279-350)
2m: CATH_2f5zF01 (F:4-152,F:279-350)
2n: CATH_2f5zA01 (A:3-152,A:279-350)
2o: CATH_2f5zC01 (C:3-152,C:279-350)
2p: CATH_2f5zE01 (E:3-152,E:279-350)
2q: CATH_2f5zG01 (G:3-152,G:279-350)
2r: CATH_2f5zH01 (H:3-152,H:279-350)
2s: CATH_2f5zI01 (I:3-152,I:279-350)
2t: CATH_2f5zJ01 (J:3-152,J:279-350)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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
2f5zA03
A:351-474
1b
2f5zB03
B:351-474
1c
2f5zC03
C:351-474
1d
2f5zD03
D:351-474
1e
2f5zE03
E:351-474
1f
2f5zF03
F:351-474
1g
2f5zG03
G:351-474
1h
2f5zH03
H:351-474
1i
2f5zI03
I:351-474
1j
2f5zJ03
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
2f5zB01
B:4-152,B:279-350
2b
2f5zA02
A:153-278
2c
2f5zB02
B:153-278
2d
2f5zC02
C:153-278
2e
2f5zD02
D:153-278
2f
2f5zE02
E:153-278
2g
2f5zF02
F:153-278
2h
2f5zG02
G:153-278
2i
2f5zH02
H:153-278
2j
2f5zJ02
J:153-278
2k
2f5zI02
I:153-278
2l
2f5zD01
D:4-152,D:279-350
2m
2f5zF01
F:4-152,F:279-350
2n
2f5zA01
A:3-152,A:279-350
2o
2f5zC01
C:3-152,C:279-350
2p
2f5zE01
E:3-152,E:279-350
2q
2f5zG01
G:3-152,G:279-350
2r
2f5zH01
H:3-152,H:279-350
2s
2f5zI01
I:3-152,I:279-350
2t
2f5zJ01
J:3-152,J:279-350
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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Asymmetric Unit 1
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Asym.Unit (825 KB)
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