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1ZMD
Biol. Unit 3
Info
Asym.Unit (637 KB)
Biol.Unit 1 (163 KB)
Biol.Unit 2 (163 KB)
Biol.Unit 3 (167 KB)
Biol.Unit 4 (168 KB)
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Title
:
CRYSTAL STRUCTURE OF HUMAN DIHYDROLIPOAMIDE DEHYDROGENASE COMPLEXED TO NADH
Authors
:
C. A. Brautigam, J. L. Chuang, D. R. Tomchick, M. Machius, D. T. Chuang
Date
:
10 May 05 (Deposition) - 28 Jun 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.08
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Keywords
:
E3, Lipoamide Dehydrogenase, Pyruvate Dehydrogenase, Alpha- Ketoglutarate Dehydrogenase, Branched-Chain Alpha-Ketoacid Dehydrogenase, Glycine Decarboxylase, Glycine Cleavage, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. A. Brautigam, J. L. Chuang, D. R. Tomchick, M. Machius, D. T. Chuang
Crystal Structure Of Human Dihydrolipoamide Dehydrogenase: Nad+/Nadh Binding And The Structural Basis Of Disease-Causing Mutations
J. Mol. Biol. V. 350 543 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 12)
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)
2a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
2b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
2c: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIc)
2d: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAId)
2e: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIe)
2f: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIf)
2g: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIg)
2h: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIh)
3a: SULFATE ION (SO4a)
3aa: SULFATE ION (SO4aa)
3ab: SULFATE ION (SO4ab)
3ac: SULFATE ION (SO4ac)
3ad: SULFATE ION (SO4ad)
3ae: SULFATE ION (SO4ae)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
3s: SULFATE ION (SO4s)
3t: SULFATE ION (SO4t)
3u: SULFATE ION (SO4u)
3v: SULFATE ION (SO4v)
3w: SULFATE ION (SO4w)
3x: SULFATE ION (SO4x)
3y: SULFATE ION (SO4y)
3z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
NAI
2
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(13, 13)
Info
All Sites
01: BC7 (SOFTWARE)
02: BC8 (SOFTWARE)
03: BC9 (SOFTWARE)
04: CC1 (SOFTWARE)
05: CC2 (SOFTWARE)
06: CC3 (SOFTWARE)
07: CC4 (SOFTWARE)
08: CC5 (SOFTWARE)
09: CC9 (SOFTWARE)
10: EC4 (SOFTWARE)
11: EC5 (SOFTWARE)
12: EC6 (SOFTWARE)
13: EC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC7
SOFTWARE
HIS E:64 , GLY E:68 , THR E:69 , HOH E:2052
BINDING SITE FOR RESIDUE SO4 E 2015
02
BC8
SOFTWARE
THR E:284 , ASN E:286 , LEU E:287 , GLY E:288 , LEU E:289 , GLU E:290
BINDING SITE FOR RESIDUE SO4 E 2016
03
BC9
SOFTWARE
GLY E:378 , ILE E:379 , GLU E:380 , GLN E:409 , HOH E:2057 , HOH E:2121 , HOH E:2122 , LYS F:111
BINDING SITE FOR RESIDUE SO4 E 2017
04
CC1
SOFTWARE
ARG E:299 , ARG E:301 , ALA E:323 , GLY E:324 , HOH E:2063
BINDING SITE FOR RESIDUE SO4 E 2018
05
CC2
SOFTWARE
HIS F:64 , GLY F:68 , THR F:69 , HOH F:2079
BINDING SITE FOR RESIDUE SO4 F 2019
06
CC3
SOFTWARE
THR F:284 , LEU F:287 , GLY F:288 , LEU F:289 , GLU F:290 , GLU F:291 , HOH F:2291 , HOH F:2304
BINDING SITE FOR RESIDUE SO4 F 2020
07
CC4
SOFTWARE
GLY F:378 , ILE F:379 , GLU F:380 , GLN F:409
BINDING SITE FOR RESIDUE SO4 F 2021
08
CC5
SOFTWARE
ARG F:299 , ARG F:301 , LYS G:265
BINDING SITE FOR RESIDUE SO4 F 2022
09
CC9
SOFTWARE
LYS F:265 , ARG G:299
BINDING SITE FOR RESIDUE SO4 G 2026
10
EC4
SOFTWARE
ILE E:12 , GLY E:13 , SER E:14 , GLY E:15 , PRO E:16 , GLY E:17 , GLU E:36 , LYS E:37 , ASN E:38 , GLY E:43 , THR E:44 , CYS E:45 , VAL E:48 , GLY E:49 , CYS E:50 , SER E:53 , LYS E:54 , TYR E:118 , GLY E:119 , ALA E:147 , THR E:148 , GLY E:149 , SER E:150 , SER E:168 , ILE E:189 , PHE E:283 , GLY E:319 , ASP E:320 , MET E:326 , LEU E:327 , ALA E:328 , HIS E:329 , TYR E:359 , NAI E:481 , HOH E:2021 , HOH E:2024 , HOH E:2243 , HOH E:2248 , HIS F:452 , PRO F:453
BINDING SITE FOR RESIDUE FAD E 480
11
EC5
SOFTWARE
GLY E:185 , GLY E:187 , VAL E:188 , ILE E:189 , GLU E:192 , GLU E:208 , PHE E:209 , LEU E:210 , CYS E:277 , ILE E:278 , GLY E:279 , ARG E:280 , MET E:326 , LEU E:327 , VAL E:357 , TYR E:359 , FAD E:480 , HOH E:2043 , HOH E:2048 , HOH E:2071 , HOH E:2075 , HOH E:2091 , HOH E:2129 , HOH E:2140 , HOH E:2241 , HOH E:2242
BINDING SITE FOR RESIDUE NAI E 481
12
EC6
SOFTWARE
HIS E:452 , PRO E:453 , ILE F:12 , GLY F:13 , SER F:14 , GLY F:15 , PRO F:16 , GLY F:17 , GLU F:36 , LYS F:37 , ASN F:38 , GLY F:43 , THR F:44 , CYS F:45 , VAL F:48 , GLY F:49 , CYS F:50 , SER F:53 , LYS F:54 , GLY F:117 , TYR F:118 , GLY F:119 , ALA F:147 , THR F:148 , GLY F:149 , SER F:150 , SER F:168 , ARG F:280 , PHE F:283 , GLY F:319 , ASP F:320 , MET F:326 , LEU F:327 , ALA F:328 , HIS F:329 , ALA F:331 , TYR F:359 , NAI F:481 , HOH F:2023 , HOH F:2024 , HOH F:2035 , HOH F:2218
BINDING SITE FOR RESIDUE FAD F 480
13
EC7
SOFTWARE
PHE F:155 , ILE F:184 , GLY F:185 , GLY F:187 , VAL F:188 , ILE F:189 , GLU F:192 , GLU F:208 , PHE F:209 , CYS F:277 , ILE F:278 , GLY F:279 , ARG F:280 , MET F:326 , LEU F:327 , VAL F:357 , TYR F:359 , FAD F:480 , HOH F:2095 , HOH F:2098 , HOH F:2147 , HOH F:2170 , HOH F:2172 , HOH F:2194 , HOH F:2196 , HOH F:2307 , SER G:262
BINDING SITE FOR RESIDUE NAI F 481
[
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 E/F, )
2: VAR_031922 (T69T, chain E/F, )
3: VAR_015820 (G194C, chain E/F, )
4: VAR_014555 (L296V, chain E/F, )
5: VAR_006908 (P453L, chain E/F, )
6: VAR_015821 (R460G, chain E/F, )
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)
---
E/F
K
37
E
2
UniProt
VAR_031922
K
104
T
DLDH_HUMAN
Polymorphism
1130477
E/F
T
69
T
3
UniProt
VAR_015820
G
229
C
DLDH_HUMAN
Disease (DLDD)
---
E/F
G
194
C
4
UniProt
VAR_014555
L
331
V
DLDH_HUMAN
Polymorphism
17624
E/F
L
296
V
5
UniProt
VAR_006908
P
488
L
DLDH_HUMAN
Disease (DLDD)
---
E/F
P
453
L
6
UniProt
VAR_015821
R
495
G
DLDH_HUMAN
Disease (DLDD)
---
E/F
R
460
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PYRIDINE_REDOX_1 (E:42-52,F:42-52)
;
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
-
-
-
-
E:42-52
F:42-52
-
-
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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, 24)
Info
all CATH domains
1a: CATH_1zmdA03 (A:351-474)
1b: CATH_1zmdB03 (B:351-474)
1c: CATH_1zmdC03 (C:351-474)
1d: CATH_1zmdD03 (D:351-474)
1e: CATH_1zmdE03 (E:351-474)
1f: CATH_1zmdF03 (F:351-474)
1g: CATH_1zmdG03 (G:351-474)
1h: CATH_1zmdH03 (H:351-474)
2a: CATH_1zmdB01 (B:4-152,B:279-350)
2b: CATH_1zmdA02 (A:153-278)
2c: CATH_1zmdB02 (B:153-278)
2d: CATH_1zmdC02 (C:153-278)
2e: CATH_1zmdD02 (D:153-278)
2f: CATH_1zmdE02 (E:153-278)
2g: CATH_1zmdF02 (F:153-278)
2h: CATH_1zmdG02 (G:153-278)
2i: CATH_1zmdH02 (H:153-278)
2j: CATH_1zmdC01 (C:4-152,C:279-350)
2k: CATH_1zmdF01 (F:4-152,F:279-350)
2l: CATH_1zmdH01 (H:4-152,H:279-350)
2m: CATH_1zmdA01 (A:3-152,A:279-350)
2n: CATH_1zmdD01 (D:3-152,D:279-350)
2o: CATH_1zmdG01 (G:3-152,G:279-350)
2p: CATH_1zmdE01 (E:2-152,E: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
1zmdA03
A:351-474
1b
1zmdB03
B:351-474
1c
1zmdC03
C:351-474
1d
1zmdD03
D:351-474
1e
1zmdE03
E:351-474
1f
1zmdF03
F:351-474
1g
1zmdG03
G:351-474
1h
1zmdH03
H: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
1zmdB01
B:4-152,B:279-350
2b
1zmdA02
A:153-278
2c
1zmdB02
B:153-278
2d
1zmdC02
C:153-278
2e
1zmdD02
D:153-278
2f
1zmdE02
E:153-278
2g
1zmdF02
F:153-278
2h
1zmdG02
G:153-278
2i
1zmdH02
H:153-278
2j
1zmdC01
C:4-152,C:279-350
2k
1zmdF01
F:4-152,F:279-350
2l
1zmdH01
H:4-152,H:279-350
2m
1zmdA01
A:3-152,A:279-350
2n
1zmdD01
D:3-152,D:279-350
2o
1zmdG01
G:3-152,G:279-350
2p
1zmdE01
E:2-152,E:279-350
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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