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1ZMC
Biol. Unit 1
Info
Asym.Unit (624 KB)
Biol.Unit 1 (160 KB)
Biol.Unit 2 (161 KB)
Biol.Unit 3 (163 KB)
Biol.Unit 4 (163 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN DIHYDROLIPOAMIDE DEHYDROGENASE COMPLEXED TO NAD+
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
:
2.53
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
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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: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
2d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
2e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
2f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
2g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
2h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
3a: SULFATE ION (SO4a)
3aa: SULFATE ION (SO4aa)
3ab: SULFATE ION (SO4ab)
3ac: SULFATE ION (SO4ac)
3ad: SULFATE ION (SO4ad)
3ae: SULFATE ION (SO4ae)
3af: SULFATE ION (SO4af)
3ag: SULFATE ION (SO4ag)
3ah: SULFATE ION (SO4ah)
3ai: SULFATE ION (SO4ai)
3aj: SULFATE ION (SO4aj)
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
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: EC1 (SOFTWARE)
10: EC2 (SOFTWARE)
11: EC3 (SOFTWARE)
12: EC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:64 , THR A:69 , HOH A:2026
BINDING SITE FOR RESIDUE SO4 A 2000
02
AC2
SOFTWARE
THR A:284 , ASN A:286 , LEU A:287 , GLY A:288 , LEU A:289 , GLU A:290 , GLU A:291 , HOH A:2054
BINDING SITE FOR RESIDUE SO4 A 2001
03
AC3
SOFTWARE
ARG A:299 , ARG A:301 , GLY A:324
BINDING SITE FOR RESIDUE SO4 A 2002
04
AC4
SOFTWARE
LEU A:210 , GLY A:211 , HIS A:212
BINDING SITE FOR RESIDUE SO4 A 2003
05
AC5
SOFTWARE
HIS B:64 , GLY B:68 , THR B:69
BINDING SITE FOR RESIDUE SO4 B 2004
06
AC6
SOFTWARE
LYS A:111 , ILE B:379 , GLU B:380 , GLN B:409 , HOH B:2036
BINDING SITE FOR RESIDUE SO4 B 2005
07
AC7
SOFTWARE
ARG B:299 , ARG B:301 , ALA B:323 , GLY B:324
BINDING SITE FOR RESIDUE SO4 B 2006
08
AC8
SOFTWARE
LEU B:210 , GLY B:211 , HIS B:212
BINDING SITE FOR RESIDUE SO4 B 2007
09
EC1
SOFTWARE
ILE A:12 , GLY A:13 , GLY A:15 , PRO A:16 , GLY A:17 , GLU A:36 , LYS A:37 , ASN A:38 , GLY A:43 , THR A:44 , CYS A:45 , GLY A:49 , CYS A:50 , LYS A:54 , GLY A:117 , TYR A:118 , GLY A:119 , ALA A:147 , THR A:148 , GLY A:149 , SER A:150 , SER A:168 , ILE A:189 , ARG A:280 , PHE A:283 , GLY A:319 , ASP A:320 , MET A:326 , LEU A:327 , ALA A:328 , HIS A:329 , ALA A:331 , TYR A:359 , HOH A:2004 , HOH A:2005 , HOH A:2013 , HOH A:2017 , HIS B:452
BINDING SITE FOR RESIDUE FAD A 480
10
EC2
SOFTWARE
GLY A:185 , GLY A:187 , VAL A:188 , VAL A:207 , GLU A:208 , PHE A:209 , LEU A:210 , VAL A:216 , THR A:241 , LYS A:242 , VAL A:243 , CYS A:277 , ILE A:278 , GLY A:279 , ARG A:280 , ARG A:299 , HOH A:2161
BINDING SITE FOR RESIDUE NAD A 481
11
EC3
SOFTWARE
HIS A:452 , ILE B:12 , GLY B:13 , GLY B:15 , PRO B:16 , GLY B:17 , GLU B:36 , LYS B:37 , ASN B:38 , GLY B:43 , THR B:44 , CYS B:45 , GLY B:49 , CYS B:50 , LYS B:54 , GLY B:117 , TYR B:118 , GLY B:119 , ALA B:147 , THR B:148 , GLY B:149 , SER B:150 , SER B:168 , ILE B:189 , ARG B:280 , LEU B:287 , GLY B:319 , ASP B:320 , MET B:326 , LEU B:327 , ALA B:328 , HIS B:329 , TYR B:359 , HOH B:2023 , HOH B:2041 , HOH B:2099
BINDING SITE FOR RESIDUE FAD B 480
12
EC4
SOFTWARE
PHE B:155 , GLY B:185 , GLY B:187 , VAL B:207 , GLU B:208 , PHE B:209 , LEU B:210 , GLY B:215 , VAL B:216 , THR B:241 , VAL B:243 , CYS B:277 , ILE B:278 , GLY B:279 , HOH B:2057
BINDING SITE FOR RESIDUE NAD B 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 A/B, )
2: VAR_031922 (T69T, chain A/B, )
3: VAR_015820 (G194C, chain A/B, )
4: VAR_014555 (L296V, chain A/B, )
5: VAR_006908 (P453L, chain A/B, )
6: VAR_015821 (R460G, chain A/B, )
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)
---
A/B
K
37
E
2
UniProt
VAR_031922
K
104
T
DLDH_HUMAN
Polymorphism
1130477
A/B
T
69
T
3
UniProt
VAR_015820
G
229
C
DLDH_HUMAN
Disease (DLDD)
---
A/B
G
194
C
4
UniProt
VAR_014555
L
331
V
DLDH_HUMAN
Polymorphism
17624
A/B
L
296
V
5
UniProt
VAR_006908
P
488
L
DLDH_HUMAN
Disease (DLDD)
---
A/B
P
453
L
6
UniProt
VAR_015821
R
495
G
DLDH_HUMAN
Disease (DLDD)
---
A/B
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 (A:42-52,B: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
A:42-52
B:42-52
-
-
-
-
-
-
[
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, 24)
Info
all CATH domains
1a: CATH_1zmcA03 (A:351-474)
1b: CATH_1zmcB03 (B:351-474)
1c: CATH_1zmcC03 (C:351-474)
1d: CATH_1zmcD03 (D:351-474)
1e: CATH_1zmcE03 (E:351-474)
1f: CATH_1zmcF03 (F:351-474)
1g: CATH_1zmcG03 (G:351-474)
1h: CATH_1zmcH03 (H:351-474)
2a: CATH_1zmcB01 (B:4-152,B:279-350)
2b: CATH_1zmcA02 (A:153-278)
2c: CATH_1zmcB02 (B:153-278)
2d: CATH_1zmcC02 (C:153-278)
2e: CATH_1zmcD02 (D:153-278)
2f: CATH_1zmcE02 (E:153-278)
2g: CATH_1zmcF02 (F:153-278)
2h: CATH_1zmcG02 (G:153-278)
2i: CATH_1zmcH02 (H:153-278)
2j: CATH_1zmcC01 (C:4-152,C:279-350)
2k: CATH_1zmcF01 (F:4-152,F:279-350)
2l: CATH_1zmcH01 (H:4-152,H:279-350)
2m: CATH_1zmcA01 (A:3-152,A:279-350)
2n: CATH_1zmcE01 (E:3-152,E:279-350)
2o: CATH_1zmcG01 (G:3-152,G:279-350)
2p: CATH_1zmcD01 (D:1-152,D:279-350)
View:
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)
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)
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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
1zmcA03
A:351-474
1b
1zmcB03
B:351-474
1c
1zmcC03
C:351-474
1d
1zmcD03
D:351-474
1e
1zmcE03
E:351-474
1f
1zmcF03
F:351-474
1g
1zmcG03
G:351-474
1h
1zmcH03
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
1zmcB01
B:4-152,B:279-350
2b
1zmcA02
A:153-278
2c
1zmcB02
B:153-278
2d
1zmcC02
C:153-278
2e
1zmcD02
D:153-278
2f
1zmcE02
E:153-278
2g
1zmcF02
F:153-278
2h
1zmcG02
G:153-278
2i
1zmcH02
H:153-278
2j
1zmcC01
C:4-152,C:279-350
2k
1zmcF01
F:4-152,F:279-350
2l
1zmcH01
H:4-152,H:279-350
2m
1zmcA01
A:3-152,A:279-350
2n
1zmcE01
E:3-152,E:279-350
2o
1zmcG01
G:3-152,G:279-350
2p
1zmcD01
D:1-152,D:279-350
[
close CATH info
]
Pfam Domains
(3, 24)
Info
all PFAM domains
1a: PFAM_Pyr_redox_1zmcH01 (H:180-264)
1b: PFAM_Pyr_redox_1zmcH02 (H:180-264)
1c: PFAM_Pyr_redox_1zmcH03 (H:180-264)
1d: PFAM_Pyr_redox_1zmcH04 (H:180-264)
1e: PFAM_Pyr_redox_1zmcH05 (H:180-264)
1f: PFAM_Pyr_redox_1zmcH06 (H:180-264)
1g: PFAM_Pyr_redox_1zmcH07 (H:180-264)
1h: PFAM_Pyr_redox_1zmcH08 (H:180-264)
2a: PFAM_Pyr_redox_2_1zmcH09 (H:8-326)
2b: PFAM_Pyr_redox_2_1zmcH10 (H:8-326)
2c: PFAM_Pyr_redox_2_1zmcH11 (H:8-326)
2d: PFAM_Pyr_redox_2_1zmcH12 (H:8-326)
2e: PFAM_Pyr_redox_2_1zmcH13 (H:8-326)
2f: PFAM_Pyr_redox_2_1zmcH14 (H:8-326)
2g: PFAM_Pyr_redox_2_1zmcH15 (H:8-326)
2h: PFAM_Pyr_redox_2_1zmcH16 (H:8-326)
3a: PFAM_Pyr_redox_dim_1zmcH17 (H:354-463)
3b: PFAM_Pyr_redox_dim_1zmcH18 (H:354-463)
3c: PFAM_Pyr_redox_dim_1zmcH19 (H:354-463)
3d: PFAM_Pyr_redox_dim_1zmcH20 (H:354-463)
3e: PFAM_Pyr_redox_dim_1zmcH21 (H:354-463)
3f: PFAM_Pyr_redox_dim_1zmcH22 (H:354-463)
3g: PFAM_Pyr_redox_dim_1zmcH23 (H:354-463)
3h: PFAM_Pyr_redox_dim_1zmcH24 (H: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-1zmcH01
H:180-264
1b
Pyr_redox-1zmcH02
H:180-264
1c
Pyr_redox-1zmcH03
H:180-264
1d
Pyr_redox-1zmcH04
H:180-264
1e
Pyr_redox-1zmcH05
H:180-264
1f
Pyr_redox-1zmcH06
H:180-264
1g
Pyr_redox-1zmcH07
H:180-264
1h
Pyr_redox-1zmcH08
H:180-264
Family
:
Pyr_redox_2
(69)
Homo sapiens (Human)
(8)
2a
Pyr_redox_2-1zmcH09
H:8-326
2b
Pyr_redox_2-1zmcH10
H:8-326
2c
Pyr_redox_2-1zmcH11
H:8-326
2d
Pyr_redox_2-1zmcH12
H:8-326
2e
Pyr_redox_2-1zmcH13
H:8-326
2f
Pyr_redox_2-1zmcH14
H:8-326
2g
Pyr_redox_2-1zmcH15
H:8-326
2h
Pyr_redox_2-1zmcH16
H:8-326
Clan
:
no clan defined [family: Pyr_redox_dim]
(44)
Family
:
Pyr_redox_dim
(44)
Homo sapiens (Human)
(7)
3a
Pyr_redox_dim-1zmcH17
H:354-463
3b
Pyr_redox_dim-1zmcH18
H:354-463
3c
Pyr_redox_dim-1zmcH19
H:354-463
3d
Pyr_redox_dim-1zmcH20
H:354-463
3e
Pyr_redox_dim-1zmcH21
H:354-463
3f
Pyr_redox_dim-1zmcH22
H:354-463
3g
Pyr_redox_dim-1zmcH23
H:354-463
3h
Pyr_redox_dim-1zmcH24
H:354-463
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