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1QR6
Biol. Unit 1
Info
Asym.Unit (205 KB)
Biol.Unit 1 (386 KB)
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(1)
Title
:
HUMAN MITOCHONDRIAL NAD(P)-DEPENDENT MALIC ENZYME
Authors
:
Y. Xu, G. Bhargava, H. Wu, G. Loeber, L. Tong
Date
:
18 Jun 99 (Deposition) - 05 Jul 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Four Domains, Rossmann Fold, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Xu, G. Bhargava, H. Wu, G. Loeber, L. Tong
Crystal Structure Of Human Mitochondrial Nad(P)(+)-Dependen Malic Enzyme: A New Class Of Oxidative Decarboxylases.
Structure V. 7 877 1999
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Hetero Components
(2, 64)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1aa: SELENOMETHIONINE (MSEaa)
1ab: SELENOMETHIONINE (MSEab)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
1m: SELENOMETHIONINE (MSEm)
1n: SELENOMETHIONINE (MSEn)
1o: SELENOMETHIONINE (MSEo)
1p: SELENOMETHIONINE (MSEp)
1q: SELENOMETHIONINE (MSEq)
1r: SELENOMETHIONINE (MSEr)
1s: SELENOMETHIONINE (MSEs)
1t: SELENOMETHIONINE (MSEt)
1u: SELENOMETHIONINE (MSEu)
1v: SELENOMETHIONINE (MSEv)
1w: SELENOMETHIONINE (MSEw)
1x: SELENOMETHIONINE (MSEx)
1y: SELENOMETHIONINE (MSEy)
1z: SELENOMETHIONINE (MSEz)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
2d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
56
Mod. Amino Acid
SELENOMETHIONINE
2
NAD
8
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:165 , ASN A:259 , THR A:283 , LEU A:310 , GLY A:311 , ALA A:312 , GLY A:313 , GLU A:314 , ALA A:315 , PHE A:344 , ASP A:345 , LYS A:346 , VAL A:392 , ALA A:393 , GLY A:394 , LEU A:398 , LEU A:419 , SER A:420 , ASN A:421 , GLY A:446 , GLY A:465 , ASN A:467 , HOH A:2008 , HOH A:2048 , HOH A:2275 , HOH A:2398
BINDING SITE FOR RESIDUE NAD A 601
2
AC2
SOFTWARE
HIS A:154 , LYS A:156 , GLY A:192 , ILE A:193 , ARG A:194 , ARG A:197 , ILE A:479 , LEU A:480 , ASN A:482 , ARG A:542 , ARG A:556 , HOH A:2233 , HOH A:2301 , HOH A:2302 , HOH A:2324 , HOH A:2510 , HOH A:2542 , HOH A:2631 , THR B:1243 , ASP B:1244 , ARG B:1248 , ARG B:1484
BINDING SITE FOR RESIDUE NAD A 602
3
AC3
SOFTWARE
ARG B:1165 , ASN B:1259 , THR B:1283 , GLY B:1311 , ALA B:1312 , GLY B:1313 , GLU B:1314 , ALA B:1315 , ASP B:1345 , LYS B:1346 , VAL B:1392 , ALA B:1393 , GLY B:1394 , ALA B:1395 , LEU B:1419 , SER B:1420 , ASN B:1421 , GLY B:1446 , GLY B:1465 , ASN B:1467 , HOH B:2035 , HOH B:2046 , HOH B:2093 , HOH B:2173 , HOH B:2326 , HOH B:2673
BINDING SITE FOR RESIDUE NAD B 1601
4
AC4
SOFTWARE
THR A:243 , ASP A:244 , GLY A:247 , ARG A:248 , ARG A:484 , HIS B:1154 , LYS B:1156 , GLY B:1192 , ILE B:1193 , ARG B:1194 , ARG B:1197 , ILE B:1479 , LEU B:1480 , ASN B:1482 , ARG B:1542 , ARG B:1556 , HOH B:2017 , HOH B:2129 , HOH B:2352 , HOH B:2676 , HOH B:2721
BINDING SITE FOR RESIDUE NAD B 1602
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SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_034104 (P1114L, chain A/A/B, )
2: VAR_050017 (G1450E, chain A/A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_034104
P
114
L
MAOM_HUMAN
Polymorphism
16952692
A
A/B
P
114
1114
L
2
UniProt
VAR_050017
G
450
E
MAOM_HUMAN
Polymorphism
649224
A
A/B
G
450
1450
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: MALIC_ENZYMES (A:276-292,B:1276-1292)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MALIC_ENZYMES
PS00331
Malic enzymes signature.
MAOM_HUMAN
276-292
4
A:276-292
B:1276-1292
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1qr6a2 (A:23-279)
1b: SCOP_d1qr6b2 (B:1023-1279)
2a: SCOP_d1qr6a1 (A:280-573)
2b: SCOP_d1qr6b1 (B:1280-1573)
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)
Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Superfamily
:
Aminoacid dehydrogenase-like, N-terminal domain
(100)
Family
:
Malic enzyme N-domain
(14)
Protein domain
:
Mitochondrial NAD(P)-dependent malic enzyme
(13)
Human (Homo sapiens) [TaxId: 9606]
(10)
1a
d1qr6a2
A:23-279
1b
d1qr6b2
B:1023-1279
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Aminoacid dehydrogenase-like, C-terminal domain
(67)
Protein domain
:
Mitochondrial NAD(P)-dependent malic enzyme
(13)
Human (Homo sapiens) [TaxId: 9606]
(10)
2a
d1qr6a1
A:280-573
2b
d1qr6b1
B:1280-1573
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1qr6A01 (A:23-277)
1b: CATH_1qr6B01 (B:1023-1277)
2a: CATH_1qr6A02 (A:278-573)
2b: CATH_1qr6B02 (B:1278-1573)
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)
Topologies
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)
(
)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Aminoacid dehydrogenase-like, N-terminal domain. Chain A
(17)
Human (Homo sapiens)
(11)
1a
1qr6A01
A:23-277
1b
1qr6B01
B:1023-1277
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
2a
1qr6A02
A:278-573
2b
1qr6B02
B:1278-1573
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Malic_M_1qr6B01 (B:1280-1535)
1b: PFAM_Malic_M_1qr6B02 (B:1280-1535)
2a: PFAM_malic_1qr6B03 (B:1089-1270)
2b: PFAM_malic_1qr6B04 (B:1089-1270)
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Clans
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(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
Malic_M
(9)
Homo sapiens (Human)
(5)
1a
Malic_M-1qr6B01
B:1280-1535
1b
Malic_M-1qr6B02
B:1280-1535
Clan
:
no clan defined [family: malic]
(9)
Family
:
malic
(9)
Homo sapiens (Human)
(5)
2a
malic-1qr6B03
B:1089-1270
2b
malic-1qr6B04
B:1089-1270
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