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1ZMD
Biol. Unit 4
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
(14, 14)
Info
All Sites
01: CC5 (SOFTWARE)
02: CC6 (SOFTWARE)
03: CC7 (SOFTWARE)
04: CC8 (SOFTWARE)
05: CC9 (SOFTWARE)
06: DC1 (SOFTWARE)
07: DC2 (SOFTWARE)
08: DC3 (SOFTWARE)
09: DC4 (SOFTWARE)
10: EC7 (SOFTWARE)
11: EC8 (SOFTWARE)
12: EC9 (SOFTWARE)
13: FC1 (SOFTWARE)
14: FC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC5
SOFTWARE
ARG F:299 , ARG F:301 , LYS G:265
BINDING SITE FOR RESIDUE SO4 F 2022
02
CC6
SOFTWARE
HIS G:64 , GLY G:68 , THR G:69 , HOH G:2080
BINDING SITE FOR RESIDUE SO4 G 2023
03
CC7
SOFTWARE
THR G:284 , ASN G:286 , LEU G:287 , GLY G:288 , LEU G:289 , GLU G:290 , GLU G:291 , HOH G:2220
BINDING SITE FOR RESIDUE SO4 G 2024
04
CC8
SOFTWARE
ILE G:379 , GLU G:380 , GLN G:409
BINDING SITE FOR RESIDUE SO4 G 2025
05
CC9
SOFTWARE
LYS F:265 , ARG G:299
BINDING SITE FOR RESIDUE SO4 G 2026
06
DC1
SOFTWARE
HIS H:64 , GLY H:68 , THR H:69 , HOH H:2069 , HOH H:2190
BINDING SITE FOR RESIDUE SO4 H 2027
07
DC2
SOFTWARE
ASN H:286 , LEU H:287 , GLY H:288 , LEU H:289 , GLU H:290 , GLU H:291 , HOH H:2281
BINDING SITE FOR RESIDUE SO4 H 2028
08
DC3
SOFTWARE
LYS G:111 , ILE H:379 , GLU H:380 , GLN H:409 , HOH H:2071
BINDING SITE FOR RESIDUE SO4 H 2029
09
DC4
SOFTWARE
ARG H:299 , ARG H:301 , ALA H:323 , GLY H:324
BINDING SITE FOR RESIDUE SO4 H 2030
10
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
11
EC8
SOFTWARE
ILE G:12 , GLY G:13 , SER G:14 , GLY G:15 , PRO G:16 , GLY G:17 , GLU G:36 , LYS G:37 , ASN G:38 , GLY G:43 , THR G:44 , CYS G:45 , VAL G:48 , GLY G:49 , CYS G:50 , SER G:53 , LYS G:54 , GLY G:117 , TYR G:118 , GLY G:119 , ALA G:147 , THR G:148 , GLY G:149 , SER G:150 , SER G:168 , ARG G:280 , PHE G:283 , GLY G:319 , ASP G:320 , MET G:326 , LEU G:327 , ALA G:328 , HIS G:329 , TYR G:359 , NAI G:481 , HOH G:2027 , HOH G:2028 , HOH G:2055 , HOH G:2166 , HIS H:452
BINDING SITE FOR RESIDUE FAD G 480
12
EC9
SOFTWARE
PHE G:155 , GLY G:185 , GLY G:187 , VAL G:188 , ILE G:189 , GLU G:192 , VAL G:207 , GLU G:208 , PHE G:209 , LEU G:210 , THR G:241 , VAL G:243 , CYS G:277 , ILE G:278 , GLY G:279 , ARG G:280 , MET G:326 , LEU G:327 , VAL G:357 , TYR G:359 , FAD G:480 , HOH G:2089 , HOH G:2093 , HOH G:2162 , HOH G:2203 , HOH G:2336 , HOH G:2338 , HOH G:2341
BINDING SITE FOR RESIDUE NAI G 481
13
FC1
SOFTWARE
HIS G:452 , PRO G:453 , ILE H:12 , GLY H:13 , SER H:14 , GLY H:15 , PRO H:16 , GLY H:17 , GLU H:36 , LYS H:37 , ASN H:38 , GLY H:43 , THR H:44 , CYS H:45 , VAL H:48 , GLY H:49 , CYS H:50 , SER H:53 , LYS H:54 , GLY H:117 , TYR H:118 , GLY H:119 , ALA H:147 , THR H:148 , GLY H:149 , SER H:150 , SER H:168 , PHE H:283 , GLY H:319 , ASP H:320 , MET H:326 , LEU H:327 , ALA H:328 , HIS H:329 , TYR H:359 , NAI H:481 , HOH H:2031 , HOH H:2036 , HOH H:2095 , HOH H:2207
BINDING SITE FOR RESIDUE FAD H 480
14
FC2
SOFTWARE
GLY H:185 , GLY H:187 , VAL H:188 , ILE H:189 , GLU H:192 , GLU H:208 , PHE H:209 , LEU H:210 , CYS H:277 , ILE H:278 , GLY H:279 , MET H:326 , LEU H:327 , VAL H:357 , TYR H:359 , FAD H:480 , HOH H:2051 , HOH H:2067 , HOH H:2086 , HOH H:2096 , HOH H:2110 , HOH H:2127 , HOH H:2166
BINDING SITE FOR RESIDUE NAI H 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 G/H, )
2: VAR_031922 (T69T, chain G/H, )
3: VAR_015820 (G194C, chain G/H, )
4: VAR_014555 (L296V, chain G/H, )
5: VAR_006908 (P453L, chain G/H, )
6: VAR_015821 (R460G, chain G/H, )
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)
---
G/H
K
37
E
2
UniProt
VAR_031922
K
104
T
DLDH_HUMAN
Polymorphism
1130477
G/H
T
69
T
3
UniProt
VAR_015820
G
229
C
DLDH_HUMAN
Disease (DLDD)
---
G/H
G
194
C
4
UniProt
VAR_014555
L
331
V
DLDH_HUMAN
Polymorphism
17624
G/H
L
296
V
5
UniProt
VAR_006908
P
488
L
DLDH_HUMAN
Disease (DLDD)
---
G/H
P
453
L
6
UniProt
VAR_015821
R
495
G
DLDH_HUMAN
Disease (DLDD)
---
G/H
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 (G:42-52,H: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
-
-
-
-
-
-
G:42-52
H:42-52
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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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
[
close SCOP info
]
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:
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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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