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2DFD
Asym. Unit
Info
Asym.Unit (215 KB)
Biol.Unit 1 (104 KB)
Biol.Unit 2 (107 KB)
Biol.Unit 3 (206 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN MALATE DEHYDROGENASE TYPE 2
Authors
:
E. Ugochukwu, N. Shafqat, A. Rojkova, M. Sundstrom, C. Arrowsmith, J. W A. Edwards, F. Von Delft, U. Oppermann, Structural Genomics Conso (Sgc)
Date
:
28 Feb 06 (Deposition) - 28 Mar 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Dehydrogenase, Citric Acid Cycle, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Ugochukwu, N. Shafqat, A. Rojkova, M. Sundstrom, C. Arrowsmith, J. Weigelt, A. Edwards, F. Von Delft, U. Oppermann
Crystal Structure Of Human Malate Dehydrogenase Type 2
To Be Published
[
close entry info
]
Hetero Components
(5, 19)
Info
All Hetero Components
1a: ALANINE (ALAa)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
3a: HISTIDINE (HISa)
3b: HISTIDINE (HISb)
3c: HISTIDINE (HISc)
4a: MALATE ION (MLTa)
4b: MALATE ION (MLTb)
4c: MALATE ION (MLTc)
4d: MALATE ION (MLTd)
5a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
5b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
5c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
5d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ALA
1
Mod. Amino Acid
ALANINE
2
CL
7
Ligand/Ion
CHLORIDE ION
3
HIS
3
Mod. Amino Acid
HISTIDINE
4
MLT
4
Ligand/Ion
MALATE ION
5
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(19, 19)
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: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG D:86 , ARG D:92 , ASN D:124 , ARG D:158 , HIS D:182 , GLY D:216 , NAD D:3004 , HOH D:3399 , HOH D:3400
BINDING SITE FOR RESIDUE MLT D 3101
02
AC2
SOFTWARE
ARG B:86 , ARG B:92 , ASN B:124 , ARG B:158 , HIS B:182 , GLY B:216 , NAD B:3001 , HOH B:3405 , HOH B:3528
BINDING SITE FOR RESIDUE MLT B 3102
03
AC3
SOFTWARE
ARG C:86 , ARG C:92 , ASN C:124 , ARG C:158 , HIS C:182 , GLY C:216 , ALA C:229 , NAD C:3002 , HOH C:3509 , HOH C:3729
BINDING SITE FOR RESIDUE MLT C 3103
04
AC4
SOFTWARE
ARG A:86 , ARG A:92 , ASN A:124 , ARG A:158 , HIS A:182 , GLY A:216 , ALA A:229 , NAD A:3003 , HOH A:3337 , HOH A:3341
BINDING SITE FOR RESIDUE MLT A 3104
05
AC5
SOFTWARE
ARG C:92 , HOH C:3553
BINDING SITE FOR RESIDUE CL C 3201
06
AC6
SOFTWARE
ARG D:92 , HOH D:3318
BINDING SITE FOR RESIDUE CL D 3202
07
AC7
SOFTWARE
ARG A:92
BINDING SITE FOR RESIDUE CL A 3203
08
AC8
SOFTWARE
GLN C:263 , HOH C:3597
BINDING SITE FOR RESIDUE CL C 3204
09
AC9
SOFTWARE
ASN A:146
BINDING SITE FOR RESIDUE CL A 3205
10
BC1
SOFTWARE
VAL B:198 , PHE B:200 , HOH B:3533
BINDING SITE FOR RESIDUE CL B 3206
11
BC2
SOFTWARE
VAL D:198 , HOH D:3416
BINDING SITE FOR RESIDUE CL D 3207
12
BC3
SOFTWARE
SER B:15 , GLY B:16 , GLY B:17 , ILE B:18 , TYR B:38 , ASP B:39 , ILE B:40 , PRO B:81 , ALA B:82 , GLY B:83 , VAL B:84 , PRO B:85 , ASN B:99 , ILE B:102 , ILE B:122 , ASN B:124 , VAL B:151 , HIS B:182 , ALA B:229 , THR B:230 , MET B:233 , MLT B:3102 , HOH B:3404 , HOH B:3405 , HOH B:3415 , HOH B:3420 , HOH B:3429 , HOH B:3452 , HOH B:3476 , HOH B:3497 , HOH B:3501 , HOH B:3519 , HOH B:3527
BINDING SITE FOR RESIDUE NAD B 3001
13
BC4
SOFTWARE
GLY C:13 , SER C:15 , GLY C:16 , GLY C:17 , ILE C:18 , TYR C:38 , ASP C:39 , ILE C:40 , PRO C:81 , ALA C:82 , GLY C:83 , VAL C:84 , PRO C:85 , LEU C:95 , ASN C:99 , ILE C:102 , ILE C:122 , ASN C:124 , VAL C:126 , VAL C:151 , HIS C:182 , ALA C:229 , THR C:230 , MET C:233 , MLT C:3103 , HOH C:3509 , HOH C:3520 , HOH C:3526 , HOH C:3540 , HOH C:3557 , HOH C:3626 , HOH C:3636 , HOH C:3646 , HOH C:3691 , HOH C:3730
BINDING SITE FOR RESIDUE NAD C 3002
14
BC5
SOFTWARE
SER A:15 , GLY A:16 , GLY A:17 , ILE A:18 , TYR A:38 , ASP A:39 , ILE A:40 , PRO A:81 , ALA A:82 , GLY A:83 , VAL A:84 , PRO A:85 , ASN A:99 , ILE A:102 , ILE A:122 , ASN A:124 , VAL A:126 , VAL A:151 , HIS A:182 , ALA A:229 , THR A:230 , MET A:233 , MLT A:3104 , HOH A:3304 , HOH A:3305 , HOH A:3337 , HOH A:3344 , HOH A:3347 , HOH A:3379 , HOH A:3389 , HOH A:3427 , HOH A:3476 , HOH A:3478
BINDING SITE FOR RESIDUE NAD A 3003
15
BC6
SOFTWARE
SER D:15 , GLY D:16 , GLY D:17 , ILE D:18 , TYR D:38 , ASP D:39 , ILE D:40 , PRO D:81 , ALA D:82 , GLY D:83 , VAL D:84 , PRO D:85 , LEU D:95 , ASN D:99 , ILE D:102 , ILE D:122 , ASN D:124 , VAL D:126 , VAL D:151 , HIS D:182 , ALA D:229 , THR D:230 , MET D:233 , MLT D:3101 , HOH D:3220 , HOH D:3224 , HOH D:3236 , HOH D:3237 , HOH D:3251 , HOH D:3313 , HOH D:3335 , HOH D:3341 , HOH D:3361 , HOH D:3393 , HOH D:3399
BINDING SITE FOR RESIDUE NAD D 3004
16
BC7
SOFTWARE
ASN A:160 , PRO A:171 , ALA A:172 , VAL A:174 , ASN A:175 , ARG A:239 , ALA A:3302 , GLU B:54 , HOH B:3434
BINDING SITE FOR RESIDUE HIS A 3301
17
BC8
SOFTWARE
ARG A:239 , SER A:243 , HIS A:3301 , HOH A:3359
BINDING SITE FOR RESIDUE ALA A 3302
18
BC9
SOFTWARE
GLU A:54 , ASN B:160 , PRO B:171 , ALA B:172 , VAL B:174 , ASN B:175 , ARG B:239
BINDING SITE FOR RESIDUE HIS B 3401
19
CC1
SOFTWARE
ASN C:160 , PRO C:171 , ALA C:172 , VAL C:174 , ASN C:175 , ARG C:239 , GLU D:54
BINDING SITE FOR RESIDUE HIS C 3501
[
close Site info
]
SAPs(SNPs)/Variants
(3, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_078001 (G19R, chain A/B/C/D, )
2: VAR_078002 (P115L, chain A/B/C/D, )
3: VAR_078003 (P189L, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_078001
G
37
R
MDHM_HUMAN
Disease (EIEE51)
782308462
A/B/C/D
G
19
R
2
UniProt
VAR_078002
P
133
L
MDHM_HUMAN
Disease (EIEE51)
375002796
A/B/C/D
P
115
L
3
UniProt
VAR_078003
P
207
L
MDHM_HUMAN
Disease (EIEE51)
1057519566
A/B/C/D
P
189
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: MDH (A:151-163,B:151-163,C:151-163,D:15...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MDH
PS00068
Malate dehydrogenase active site signature.
MDHM_HUMAN
169-181
4
A:151-163
B:151-163
C:151-163
D:151-163
[
close PROSITE info
]
Exons
(8, 32)
Info
All Exons
Exon 1.3b (A:6-61 | B:6-61 | C:6-61 | D:6-61)
Exon 1.4c (A:61-89 | B:61-89 | C:61-89 | D:61...)
Exon 1.5a (A:89-125 | B:89-125 | C:89-125 | D...)
Exon 1.6b (A:126-167 | B:126-167 | C:126-167 ...)
Exon 1.7 (A:168-193 | B:168-193 | C:168-193 ...)
Exon 1.8 (A:194-227 | B:194-227 | C:194-227 ...)
Exon 1.9a (A:227-277 | B:227-277 | C:227-277 ...)
Exon 1.10c (A:278-319 | B:278-319 | C:278-319 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1b/1.3b
2: Boundary 1.3b/1.4c
3: Boundary 1.4c/1.5a
4: Boundary 1.5a/1.6b
5: Boundary 1.6b/1.7
6: Boundary 1.7/1.8
7: Boundary 1.8/1.9a
8: Boundary 1.9a/1.10c
9: Boundary 1.10c/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1b
ENST00000315758
1b
ENSE00001905498
chr7:
75677385-75677544
160
MDHM_HUMAN
1-22
22
0
-
-
1.3b
ENST00000315758
3b
ENSE00000976862
chr7:
75684148-75684316
169
MDHM_HUMAN
23-79
57
4
A:6-61
B:6-61
C:6-61
D:6-61
56
56
56
56
1.4c
ENST00000315758
4c
ENSE00001772678
chr7:
75686728-75686811
84
MDHM_HUMAN
79-107
29
4
A:61-89
B:61-89
C:61-89
D:61-89
29
29
29
29
1.5a
ENST00000315758
5a
ENSE00001804254
chr7:
75687287-75687396
110
MDHM_HUMAN
107-143
37
4
A:89-125
B:89-125
C:89-125
D:89-125
37
37
37
37
1.6b
ENST00000315758
6b
ENSE00001803022
chr7:
75689691-75689816
126
MDHM_HUMAN
144-185
42
4
A:126-167
B:126-167
C:126-167
D:126-167
42
42
42
42
1.7
ENST00000315758
7
ENSE00001619723
chr7:
75692833-75692910
78
MDHM_HUMAN
186-211
26
4
A:168-193
B:168-193
C:168-193
D:168-193
26
26
26
26
1.8
ENST00000315758
8
ENSE00001717303
chr7:
75693657-75693756
100
MDHM_HUMAN
212-245
34
4
A:194-227
B:194-227
C:194-227
D:194-227
34
34
34
34
1.9a
ENST00000315758
9a
ENSE00001703408
chr7:
75694120-75694271
152
MDHM_HUMAN
245-295
51
4
A:227-277
B:227-277
C:227-277
D:227-277
51
51
51
51
1.10c
ENST00000315758
10c
ENSE00001663150
chr7:
75695597-75696826
1230
MDHM_HUMAN
296-338
43
4
A:278-319
B:278-319
C:278-319
D:278-319
42
42
42
42
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2dfda2 (A:151-319)
1b: SCOP_d2dfdb2 (B:151-319)
1c: SCOP_d2dfdc2 (C:151-319)
1d: SCOP_d2dfdd2 (D:151-319)
2a: SCOP_d2dfda1 (A:6-150)
2b: SCOP_d2dfdb1 (B:6-150)
2c: SCOP_d2dfdc1 (C:6-150)
2d: SCOP_d2dfdd1 (D:6-150)
View:
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)
(
)
Folds
(
)
(
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(
)
(
)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
LDH C-terminal domain-like
(172)
Superfamily
:
LDH C-terminal domain-like
(172)
Family
:
Lactate & malate dehydrogenases, C-terminal domain
(125)
Protein domain
:
automated matches
(30)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2dfda2
A:151-319
1b
d2dfdb2
B:151-319
1c
d2dfdc2
C:151-319
1d
d2dfdd2
D:151-319
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
LDH N-terminal domain-like
(117)
Protein domain
:
automated matches
(15)
Human (Homo sapiens) [TaxId: 9606]
(1)
2a
d2dfda1
A:6-150
2b
d2dfdb1
B:6-150
2c
d2dfdc1
C:6-150
2d
d2dfdd1
D:6-150
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2dfdA01 (A:6-151)
1b: CATH_2dfdB01 (B:6-151)
1c: CATH_2dfdC01 (C:6-151)
1d: CATH_2dfdD01 (D:6-151)
2a: CATH_2dfdA02 (A:152-318)
2b: CATH_2dfdB02 (B:152-318)
2c: CATH_2dfdC02 (C:152-318)
2d: CATH_2dfdD02 (D:152-318)
View:
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Architectures
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Topologies
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Homologous Superfamilies
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
1a
2dfdA01
A:6-151
1b
2dfdB01
B:6-151
1c
2dfdC01
C:6-151
1d
2dfdD01
D:6-151
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
(116)
Homologous Superfamily
:
L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2
(116)
Human (Homo sapiens)
(4)
2a
2dfdA02
A:152-318
2b
2dfdB02
B:152-318
2c
2dfdC02
C:152-318
2d
2dfdD02
D:152-318
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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